diff --git a/R/hurdle.R b/R/hurdle.R index 4b9dd2c..84121e5 100644 --- a/R/hurdle.R +++ b/R/hurdle.R @@ -600,8 +600,8 @@ hurdle <- function(data, model.eff, model.cost, model.se = se ~ 1, model.sc = sc if(exists("gamma.prior.c", where = prior)) {gamma.prior.c = prior$gamma.prior.c} else {gamma.prior.c = NULL } if(exists("gamma0.prior.e", where = prior)) {gamma0.prior.e = prior$gamma0.prior.e} else {gamma0.prior.e = NULL } if(exists("gamma0.prior.c", where = prior)) {gamma0.prior.c = prior$gamma0.prior.c} else {gamma0.prior.c = NULL } - if(exists("se.prior", where = prior)) {se.prior = prior$se.prior} else {se.prior = 0.0000001 } - if(exists("sc.prior", where = prior)) {sc.prior = prior$sc.prior} else {sc.prior = 0.0000001 } + if(exists("se.prior", where = prior)) {se.prior = prior$se.prior} else {se.prior = 0.001 } + if(exists("sc.prior", where = prior)) {sc.prior = prior$sc.prior} else {sc.prior = 0.001 } if(exists("beta_f.prior", where = prior)) {beta_f.prior = prior$beta_f.prior} else {beta_f.prior = NULL } if(exists("mu.a0.prior", where = prior)) {mu.a0.prior = prior$mu.a0.prior} else {mu.a0.prior = NULL } if(exists("s.a0.prior", where = prior)) {s.a0.prior = prior$s.a0.prior} else {s.a0.prior = NULL } @@ -684,4 +684,4 @@ hurdle <- function(data, model.eff, model.cost, model.se = se ~ 1, model.sc = sc res <- list(data_set = data_set, model_output = model_output, cea = cea, type = type, data_format = format) class(res) <- "missingHE" return(res) -} \ No newline at end of file +} diff --git a/R/prior_hurdle.R b/R/prior_hurdle.R index 053cf3e..f035363 100644 --- a/R/prior_hurdle.R +++ b/R/prior_hurdle.R @@ -139,24 +139,24 @@ prior_hurdle <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, zc if(length(alpha0.prior) != 2) {stop("provide correct hyper prior values") } prior_mue <- alpha0.prior prior_mue_str <- paste("alpha1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags, fixed = TRUE) prior_mue_str <- paste("alpha2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags, fixed = TRUE) } } else if(pe_fixed > 1){ if(is.null(alpha0.prior) == FALSE & grepl("alpha1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("alpha2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(alpha0.prior) != 2) {stop("provide correct hyper prior values") } prior_mue <- alpha0.prior prior_mue_str <- paste("alpha1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags, fixed = TRUE) prior_mue_str <- paste("alpha2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags, fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("alpha2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(alpha.prior) != 2) {stop("provide correct hyper prior values") } prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha2[j, 1] ~ dnorm(", prior_alphae[1],",", prior_alphae[2]) - model_string_jags <- gsub("alpha2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } if(length(model_e_random) != 0 & pe_random == 1) { if(is.null(mu.a0.prior) == FALSE & grepl("mu_a_hat[t] ~ ", model_string_jags, fixed = TRUE) == TRUE) { @@ -186,31 +186,31 @@ prior_hurdle <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, zc if(length(beta0.prior) != 2) {stop("provide correct hyper prior values") } prior_muc <- beta0.prior prior_muc_str <- paste("beta1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) prior_muc_str <- paste("beta2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) } } else if(pc_fixed > 1) { if(is.null(beta.prior) == FALSE & grepl("beta1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("beta2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(beta.prior) != 2) {stop("provide correct hyper prior values") } prior_muc <- beta.prior prior_muc_str <- paste("beta1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) prior_muc_str <- paste("beta2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("beta2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(beta0.prior) != 2) {stop("provide correct hyper prior values") } prior_muc <- beta0.prior prior_muc_str <- paste("beta1[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta1[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) prior_muc_str <- paste("beta2[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta2[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta2[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("beta2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(beta.prior) != 2){stop("provide correct hyper prior values") } prior_betac <- beta.prior prior_betac_str <- paste("beta1[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta1[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta2[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta2[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta2[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } if(length(model_c_random) != 0 & pc_random == 1) { if(is.null(mu.b0.prior) == FALSE & grepl("mu_b_hat[t] ~ ", model_string_jags, fixed = TRUE) == TRUE) { @@ -390,15 +390,15 @@ prior_hurdle <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, zc if(is.null(se) == FALSE & is.null(sc) == TRUE) { prior_beta_f <- beta_f.prior prior_beta_f_str <- paste("beta_f[1] ~ dnorm(", prior_beta_f[1], ",", prior_beta_f[2]) - model_string_jags <- gsub("beta_f[1] ~ dnorm(0, 0.0000001", prior_beta_f_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f[1] ~ dnorm(0, 0.001", prior_beta_f_str, model_string_jags, fixed = TRUE) prior_beta_f_str <- paste("beta_f[2] ~ dnorm(", prior_beta_f[1], ",", prior_beta_f[2]) - model_string_jags <- gsub("beta_f[2] ~ dnorm(0, 0.0000001", prior_beta_f_str, model_string_jags, fixed = TRUE)} + model_string_jags <- gsub("beta_f[2] ~ dnorm(0, 0.001", prior_beta_f_str, model_string_jags, fixed = TRUE)} if(is.null(sc) == FALSE) { prior_beta_f <- beta_f.prior prior_beta_f_str <- paste("beta_f1[1] ~ dnorm(", prior_beta_f[1], ",", prior_beta_f[2]) - model_string_jags <- gsub("beta_f1[1] ~ dnorm(0, 0.0000001", prior_beta_f_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f1[1] ~ dnorm(0, 0.001", prior_beta_f_str, model_string_jags, fixed = TRUE) prior_beta_f_str <- paste("beta_f2[1] ~ dnorm(", prior_beta_f[1], ",",prior_beta_f[2]) - model_string_jags <- gsub("beta_f2[1] ~ dnorm(0, 0.0000001", prior_beta_f_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_f2[1] ~ dnorm(0, 0.001", prior_beta_f_str, model_string_jags, fixed = TRUE) } } } if(exists("mu.b_f.prior") == TRUE) { @@ -419,4 +419,4 @@ prior_hurdle <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, zc } model_string_prior <- model_string_jags return(model_string_prior) -})) \ No newline at end of file +})) diff --git a/R/prior_long_miss.R b/R/prior_long_miss.R index b1383b9..cb0d0bd 100644 --- a/R/prior_long_miss.R +++ b/R/prior_long_miss.R @@ -165,22 +165,22 @@ prior_long_miss <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(alpha0.prior) != 2) {stop("provide correct hyper prior values") } prior_mue <- alpha0.prior prior_mue_str <- paste("alpha[1, time] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha[1, time] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) + model_string_jags <- gsub("alpha[1, time] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) prior_mue_str <- paste("alpha[2, time] ~ dnorm(", prior_mue[1],",", prior_mue[2]) - model_string_jags <- gsub("alpha[2, time] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha[2, time] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags, fixed = TRUE) } } else if(pe_fixed > 1){ if(is.null(alpha0.prior) == FALSE & grepl("alpha[1, 1, time] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("alpha[1, 2, time] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(alpha0.prior) != 2) {stop("provide correct hyper prior values") } prior_mue <- alpha0.prior prior_mue_str <- paste("alpha[1, 1, time] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha[1, 1, time] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) + model_string_jags <- gsub("alpha[1, 1, time] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) prior_mue_str <- paste("alpha[1, 2, time] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha[1, 2, time] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha[1, 2, time] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags, fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha[j, t, time] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(alpha.prior) != 2) {stop("provide correct hyper prior values") } prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha[j, t, time] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha[j, t, time] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha[j, t, time] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } if(length(model_e_random) != 0 & pe_random == 1) { if(is.null(mu.a0.prior) == FALSE & grepl("mu_a_hat[t, time] ~ ", model_string_jags, fixed = TRUE) == TRUE) { @@ -210,22 +210,22 @@ prior_long_miss <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(beta0.prior) != 2) {stop("provide correct hyper prior values") } prior_muc <- beta0.prior prior_muc_str <- paste("beta[1, time] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta[1, time] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, time] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) prior_muc_str <- paste("beta[2, time] ~ dnorm(",prior_muc[1],",", prior_muc[2]) - model_string_jags <- gsub("beta[2, time] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta[2, time] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) } } else if(pc_fixed > 1) { if(is.null(beta0.prior) == FALSE & grepl("beta[1, 1, time] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("beta[1, 2, time] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(beta0.prior) != 2) {stop("provide correct hyper prior values") } prior_muc <- beta0.prior prior_muc_str <- paste("beta[1, 1, time] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta[1, 1, time] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, 1, time] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) prior_muc_str <- paste("beta[1, 2, time] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta[1, 2, time] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta[1, 2, time] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta[j, t, time] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(beta.prior) != 2){stop("provide correct hyper prior values") } prior_betac <- beta.prior prior_betac_str <- paste("beta[j, t, time] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta[j, t, time] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta[j, t, time] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } if(length(model_c_random) != 0 & pc_random == 1) { if(is.null(mu.b0.prior) == FALSE & grepl("mu_b_hat[t, time] ~ ", model_string_jags, fixed = TRUE) == TRUE) { @@ -308,7 +308,7 @@ prior_long_miss <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(beta_f.prior) != 2) {stop("provide correct hyper prior values") } prior_beta_f <- beta_f.prior prior_beta_f_str <- paste("beta_f[t, time] ~ dnorm(", prior_beta_f[1], ",", prior_beta_f[2]) - model_string_jags <- gsub("beta_f[t, time] ~ dnorm(0, 0.0000001", prior_beta_f_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f[t, time] ~ dnorm(0, 0.001", prior_beta_f_str, model_string_jags, fixed = TRUE) } } if(exists("mu.b_f.prior") == TRUE) { @@ -332,7 +332,7 @@ prior_long_miss <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(beta_te.prior) != 2) {stop("provide correct hyper prior values") } prior_beta_te <- beta_te.prior prior_beta_te_str <- paste("beta_te[t, time] ~ dnorm(", prior_beta_te[1], ",", prior_beta_te[2]) - model_string_jags <- gsub("beta_te[t, time] ~ dnorm(0, 0.0000001", prior_beta_te_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_te[t, time] ~ dnorm(0, 0.001", prior_beta_te_str, model_string_jags, fixed = TRUE) } } if(exists("beta_tc.prior") == TRUE) { @@ -340,7 +340,7 @@ prior_long_miss <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(beta_tc.prior) != 2) {stop("provide correct hyper prior values") } prior_beta_tc <- beta_tc.prior prior_beta_tc_str <- paste("beta_tc[t, time] ~ dnorm(", prior_beta_tc[1], ",", prior_beta_tc[2]) - model_string_jags <- gsub("beta_tc[t, time] ~ dnorm(0, 0.0000001", prior_beta_tc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_tc[t, time] ~ dnorm(0, 0.001", prior_beta_tc_str, model_string_jags, fixed = TRUE) } } if(exists("mu.b_te.prior") == TRUE) { @@ -380,7 +380,7 @@ prior_long_miss <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(alpha_te.prior) != 2) {stop("provide correct hyper prior values") } prior_alpha_te <- alpha_te.prior prior_alpha_te_str <- paste("alpha_te[t, time] ~ dnorm(", prior_alpha_te[1], ",", prior_alpha_te[2]) - model_string_jags <- gsub("alpha_te[t, time] ~ dnorm(0, 0.0000001", prior_alpha_te_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_te[t, time] ~ dnorm(0, 0.001", prior_alpha_te_str, model_string_jags, fixed = TRUE) } } if(exists("alpha_tc.prior") == TRUE) { @@ -388,7 +388,7 @@ prior_long_miss <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(alpha_tc.prior) != 2) {stop("provide correct hyper prior values") } prior_alpha_tc <- alpha_tc.prior prior_alpha_tc_str <- paste("alpha_tc[t, time] ~ dnorm(", prior_alpha_tc[1], ",", prior_alpha_tc[2]) - model_string_jags <- gsub("alpha_tc[t, time] ~ dnorm(0, 0.0000001", prior_alpha_tc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_tc[t, time] ~ dnorm(0, 0.001", prior_alpha_tc_str, model_string_jags, fixed = TRUE) } } if(exists("mu.a_te.prior") == TRUE) { @@ -425,4 +425,4 @@ prior_long_miss <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, } model_string_prior <- model_string_jags return(model_string_prior) -})) \ No newline at end of file +})) diff --git a/R/prior_pattern.R b/R/prior_pattern.R index 0e76a25..88392a9 100644 --- a/R/prior_pattern.R +++ b/R/prior_pattern.R @@ -33,100 +33,100 @@ prior_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, model_e_rand if(d_list$n_patterns[1] == 4) { if(grepl("alpha_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(grepl("alpha_p1[3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_c_obs == FALSE & restriction == "CC") { if(grepl("alpha_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(grepl("alpha_p1[3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_ec_obs == FALSE & restriction == "AC") { if(grepl("alpha_p1[3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_e_obs == FALSE & restriction == "CC") { if(grepl("alpha_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_ec_mis == FALSE) { if(grepl("alpha_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(grepl("alpha_p1[3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_c_obs == FALSE & d_list$d1$d1_e_obs == FALSE & restriction == "CC") { if(grepl("alpha_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_c_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "CC") { if(grepl("alpha_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(grepl("alpha_p1[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[2] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[2] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[2] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_e_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "CC") { if(grepl("alpha_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_ec_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "AC") { if(grepl("alpha_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p1[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } if(d_list$n_patterns[2] == 4) { if(grepl("alpha_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(grepl("alpha_p2[3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_c_obs == FALSE & restriction == "CC") { if(grepl("alpha_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(grepl("alpha_p2[3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_ec_obs == FALSE & restriction == "AC") { if(grepl("alpha_p2[3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_e_obs == FALSE & restriction == "CC") { if(grepl("alpha_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_ec_mis == FALSE) { if(grepl("alpha_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(grepl("alpha_p2[3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_c_obs == FALSE & d_list$d2$d2_e_obs == FALSE & restriction == "CC") { if(grepl("alpha_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_c_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "CC") { if(grepl("alpha_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(grepl("alpha_p2[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[2] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[2] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[2] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_e_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "CC") { if(grepl("alpha_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_ec_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "AC") { if(grepl("alpha_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue_str <- paste("alpha_p2[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } } } } else if(pe_fixed > 1){ @@ -141,79 +141,79 @@ prior_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, model_e_rand if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha_p1[j, 3] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_c_obs == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha_p1[j, 3] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_ec_obs == FALSE & restriction == "AC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 3] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_e_obs == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_ec_mis == FALSE) { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha_p1[j, 3] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_c_obs == FALSE & d_list$d1$d1_e_obs == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_c_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 2] <- ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 2] ~ dnorm(", prior_mue[1], ",", prior_mue[2], ")") @@ -221,105 +221,105 @@ prior_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, model_e_rand if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha_p1[j, 2] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 2] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 2] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_e_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_ec_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "AC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p1[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p1[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } if(d_list$n_patterns[2] == 4) { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha_p2[j, 3] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_c_obs == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha_p2[j, 3] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_ec_obs == FALSE & restriction == "AC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 3] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_e_obs == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_ec_mis == FALSE) { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 3] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 3] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha_p2[j, 3] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_c_obs == FALSE & d_list$d2$d2_e_obs == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_c_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 2] <- ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 2] ~ dnorm(", prior_mue[1], ",", prior_mue[2], ")") @@ -327,27 +327,27 @@ prior_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, model_e_rand if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) prior_alphae_str <- paste("alpha_p2[j, 2] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 2] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 2] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_e_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "CC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_ec_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "AC") { if(is.null(alpha0.prior) == FALSE & grepl("alpha_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_mue <- alpha0.prior prior_mue_str <- paste("alpha_p2[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha_p2[j, 1] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } } } @@ -358,100 +358,100 @@ prior_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, model_e_rand if(d_list$n_patterns[1] == 4) { if(grepl("beta_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(grepl("beta_p1[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_c_obs == FALSE & restriction == "CC") { if(grepl("beta_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_ec_obs == FALSE & restriction == "AC") { if(grepl("beta_p1[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_e_obs == FALSE & restriction == "CC") { if(grepl("beta_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(grepl("beta_p1[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_ec_mis == FALSE) { if(grepl("beta_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(grepl("beta_p1[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_c_obs == FALSE & d_list$d1$d1_e_obs == FALSE & restriction == "CC") { if(grepl("beta_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_c_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "CC") { if(grepl("beta_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_e_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "CC") { if(grepl("beta_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(grepl("beta_p1[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_ec_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "AC") { if(grepl("beta_p1[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p1[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } if(d_list$n_patterns[2] == 4) { if(grepl("beta_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(grepl("beta_p2[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_c_obs == FALSE & restriction == "CC") { if(grepl("beta_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_ec_obs == FALSE & restriction == "AC") { if(grepl("beta_p2[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_e_obs == FALSE & restriction == "CC") { if(grepl("beta_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(grepl("beta_p2[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_ec_mis == FALSE) { if(grepl("beta_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(grepl("beta_p2[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_c_obs == FALSE & d_list$d2$d2_e_obs == FALSE & restriction == "CC") { if(grepl("beta_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_c_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "CC") { if(grepl("beta_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_e_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "CC") { if(grepl("beta_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(grepl("beta_p2[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_ec_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "AC") { if(grepl("beta_p2[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc_str <- paste("beta_p2[2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } } } } else if(pc_fixed > 1){ @@ -466,213 +466,213 @@ prior_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, model_e_rand if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta_p1[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_c_obs == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_ec_obs == FALSE & restriction == "AC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_e_obs == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta_p1[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 3 & d_list$d1$d1_ec_mis == FALSE) { if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta_p1[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_c_obs == FALSE & d_list$d1$d1_e_obs == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_c_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_e_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta_p1[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[1] == 2 & d_list$d1$d1_ec_obs == FALSE & d_list$d1$d1_ec_mis == FALSE & restriction == "AC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p1[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p1[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p1[j, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p1[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } if(d_list$n_patterns[2] == 4) { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta_p2[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_c_obs == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_ec_obs == FALSE & restriction == "AC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_e_obs == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta_p2[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 3 & d_list$d2$d2_ec_mis == FALSE) { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta_p2[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_c_obs == FALSE & d_list$d2$d2_e_obs == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_c_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_e_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "CC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 1] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) prior_betac_str <- paste("beta_p2[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } else if(d_list$n_patterns[2] == 2 & d_list$d2$d2_ec_obs == FALSE & d_list$d2$d2_ec_mis == FALSE & restriction == "AC") { if(is.null(beta0.prior) == FALSE & grepl("beta_p2[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_muc <- beta0.prior prior_muc_str <- paste("beta_p2[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags,fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta_p2[j, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_betac <- beta.prior prior_betac_str <- paste("beta_p2[j, 2] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } } } @@ -1511,10 +1511,10 @@ prior_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, model_e_rand prior_beta_f <- beta_f.prior if(grepl("beta_f_p1[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_beta_f_str <- paste("beta_f_p1[1] ~ dnorm(", prior_beta_f[1], ",", prior_beta_f[2]) - model_string_jags <- gsub("beta_f_p1[1] ~ dnorm(0, 0.0000001", prior_beta_f_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_f_p1[1] ~ dnorm(0, 0.001", prior_beta_f_str, model_string_jags,fixed = TRUE) } if(grepl("beta_f_p2[1] ~ ", model_string_jags, fixed = TRUE) == TRUE) { prior_beta_f_str <- paste("beta_f_p2[1] ~ dnorm(", prior_beta_f[1], ",", prior_beta_f[2]) - model_string_jags <- gsub("beta_f_p2[1] ~ dnorm(0, 0.0000001", prior_beta_f_str, model_string_jags,fixed = TRUE) } + model_string_jags <- gsub("beta_f_p2[1] ~ dnorm(0, 0.001", prior_beta_f_str, model_string_jags,fixed = TRUE) } } } if(length(model_e_random) != 0 & pe_random == 1) { @@ -1581,4 +1581,4 @@ prior_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, model_e_rand } model_string_prior <- model_string_jags return(model_string_prior) -})) \ No newline at end of file +})) diff --git a/R/prior_selection.R b/R/prior_selection.R index f44271f..59bb2e3 100644 --- a/R/prior_selection.R +++ b/R/prior_selection.R @@ -157,22 +157,22 @@ prior_selection <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(alpha0.prior) != 2) {stop("provide correct hyper prior values") } prior_mue <- alpha0.prior prior_mue_str <- paste("alpha[1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha[1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) + model_string_jags <- gsub("alpha[1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) prior_mue_str <- paste("alpha[2] ~ dnorm(", prior_mue[1],",", prior_mue[2]) - model_string_jags <- gsub("alpha[2] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha[2] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags, fixed = TRUE) } } else if(pe_fixed > 1){ if(is.null(alpha0.prior) == FALSE & grepl("alpha[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("alpha[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(alpha0.prior) != 2) {stop("provide correct hyper prior values") } prior_mue <- alpha0.prior prior_mue_str <- paste("alpha[1, 1] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha[1, 1] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags,fixed = TRUE) + model_string_jags <- gsub("alpha[1, 1] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags,fixed = TRUE) prior_mue_str <- paste("alpha[1, 2] ~ dnorm(", prior_mue[1], ",", prior_mue[2]) - model_string_jags <- gsub("alpha[1, 2] ~ dnorm(0, 0.0000001", prior_mue_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha[1, 2] ~ dnorm(0, 0.001", prior_mue_str, model_string_jags, fixed = TRUE) } if(is.null(alpha.prior) == FALSE & grepl("alpha[j, t] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(alpha.prior) != 2) {stop("provide correct hyper prior values") } prior_alphae <- alpha.prior prior_alphae_str <- paste("alpha[j, t] ~ dnorm(", prior_alphae[1], ",", prior_alphae[2]) - model_string_jags <- gsub("alpha[j, t] ~ dnorm(0, 0.0000001", prior_alphae_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("alpha[j, t] ~ dnorm(0, 0.001", prior_alphae_str, model_string_jags, fixed = TRUE) } } if(length(model_e_random) != 0 & pe_random == 1) { if(is.null(mu.a0.prior) == FALSE & grepl("mu_a_hat[t] ~ ", model_string_jags, fixed = TRUE) == TRUE) { @@ -202,29 +202,29 @@ prior_selection <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(beta0.prior) != 2) {stop("provide correct hyper prior values") } prior_muc <- beta0.prior prior_muc_str <- paste("beta[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) prior_muc_str <- paste("beta[2] ~ dnorm(",prior_muc[1],",", prior_muc[2]) - model_string_jags <- gsub("beta[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) } } else if(pc_fixed > 1) { if(is.null(beta.prior) == FALSE & grepl("beta[1] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("beta[2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(beta.prior) != 2) {stop("provide correct hyper prior values") } prior_muc <- beta.prior prior_muc_str <- paste("beta[1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta[1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) prior_muc_str <- paste("beta[2] ~ dnorm(",prior_muc[1],",", prior_muc[2]) - model_string_jags <- gsub("beta[2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta[2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) } if(is.null(beta0.prior) == FALSE & grepl("beta[1, 1] ~ ", model_string_jags, fixed = TRUE) == TRUE & grepl("beta[1, 2] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(beta0.prior) != 2) {stop("provide correct hyper prior values") } prior_muc <- beta0.prior prior_muc_str <- paste("beta[1, 1] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta[1, 1] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, 1] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) prior_muc_str <- paste("beta[1, 2] ~ dnorm(", prior_muc[1], ",", prior_muc[2]) - model_string_jags <- gsub("beta[1, 2] ~ dnorm(0, 0.0000001", prior_muc_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta[1, 2] ~ dnorm(0, 0.001", prior_muc_str, model_string_jags, fixed = TRUE) } if(is.null(beta.prior) == FALSE & grepl("beta[j, t] ~ ", model_string_jags, fixed = TRUE) == TRUE) { if(length(beta.prior) != 2){stop("provide correct hyper prior values") } prior_betac <- beta.prior prior_betac_str <- paste("beta[j, t] ~ dnorm(", prior_betac[1], ",", prior_betac[2]) - model_string_jags <- gsub("beta[j, t] ~ dnorm(0, 0.0000001", prior_betac_str, model_string_jags, fixed = TRUE) } + model_string_jags <- gsub("beta[j, t] ~ dnorm(0, 0.001", prior_betac_str, model_string_jags, fixed = TRUE) } } if(length(model_c_random) != 0 & pc_random == 1) { if(is.null(mu.b0.prior) == FALSE & grepl("mu_b_hat[t] ~ ", model_string_jags, fixed = TRUE) == TRUE) { @@ -307,7 +307,7 @@ prior_selection <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, if(length(beta_f.prior) != 2) {stop("provide correct hyper prior values") } prior_beta_f <- beta_f.prior prior_beta_f_str <- paste("beta_f[t] ~ dnorm(", prior_beta_f[1], ",", prior_beta_f[2]) - model_string_jags <- gsub("beta_f[t] ~ dnorm(0, 0.0000001", prior_beta_f_str, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f[t] ~ dnorm(0, 0.001", prior_beta_f_str, model_string_jags, fixed = TRUE) } } if(exists("mu.b_f.prior") == TRUE) { @@ -328,4 +328,4 @@ prior_selection <- function(type, dist_e, dist_c, pe_fixed, pc_fixed , ze_fixed, } model_string_prior <- model_string_jags return(model_string_prior) -})) \ No newline at end of file +})) diff --git a/R/write_hurdle.R b/R/write_hurdle.R index 10e2aa1..af32781 100644 --- a/R/write_hurdle.R +++ b/R/write_hurdle.R @@ -160,24 +160,24 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc #priors for mean regression coefficients for (j in 2:pe_fixed) {#begin alpha priors effects - alpha1[j, 1] ~ dnorm(0, 0.0000001) - alpha2[j, 1] ~ dnorm(0, 0.0000001) + alpha1[j, 1] ~ dnorm(0, 0.001) + alpha2[j, 1] ~ dnorm(0, 0.001) alpha1[j, 2] <- 0 alpha2[j, 2] <- 0 }#end alpha priors effects - alpha1[1, 1] ~ dnorm(0, 0.0000001) - alpha2[1, 1] ~ dnorm(0, 0.0000001) + alpha1[1, 1] ~ dnorm(0, 0.001) + alpha2[1, 1] ~ dnorm(0, 0.001) alpha1[1, 2] <- se alpha2[1, 2] <- se for (j in 2:pc_fixed) {#begin beta priors costs - beta1[j, 1] ~ dnorm(0, 0.0000001) - beta2[j, 1] ~ dnorm(0, 0.0000001) + beta1[j, 1] ~ dnorm(0, 0.001) + beta2[j, 1] ~ dnorm(0, 0.001) beta1[j, 2] <- 0 beta2[j, 2] <- 0 }#end beta priors costs - beta1[1, 1] ~ dnorm(0, 0.0000001) - beta2[1, 1] ~ dnorm(0, 0.0000001) + beta1[1, 1] ~ dnorm(0, 0.001) + beta2[1, 1] ~ dnorm(0, 0.001) beta1[1, 2] <- sc beta2[1, 2] <- sc @@ -207,8 +207,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc ls_e2[2] <- sde #correlation - beta_f1[1] ~ dnorm(0, 0.0000001) - beta_f2[1] ~ dnorm(0, 0.0000001) + beta_f1[1] ~ dnorm(0, 0.001) + beta_f2[1] ~ dnorm(0, 0.001) beta_f1[2] <- 0 beta_f2[2] <- 0 @@ -697,8 +697,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc beta_nons_e1 <- "alpha[1] <- alpha1[1]" beta_nons_e2 <- "alpha[2] <- alpha2[1]" begin_prior_beta <- "#begin alpha priors effects" - prior_beta_e1 <- "alpha1[1] ~ dnorm(0, 0.0000001)" - prior_beta_e2 <- "alpha2[1] ~ dnorm(0, 0.0000001)" + prior_beta_e1 <- "alpha1[1] ~ dnorm(0, 0.001)" + prior_beta_e2 <- "alpha2[1] ~ dnorm(0, 0.001)" prior_beta_e1s <- "alpha1[2] <- se" prior_beta_e2s <- "alpha2[2] <- se" end_prior_beta <- "#end alpha priors effects" @@ -710,12 +710,12 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("alpha[j, 1] <- alpha1[j, 1]", beta_nons_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha[j, 2] <- alpha2[j, 1] }", beta_nons_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pe_fixed) {#begin alpha priors effects", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha1[j, 1] ~ dnorm(0, 0.0000001)", prior_beta_e1j, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha2[j, 1] ~ dnorm(0, 0.0000001)", prior_beta_e2j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[j, 1] ~ dnorm(0, 0.001)", prior_beta_e1j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha2[j, 1] ~ dnorm(0, 0.001)", prior_beta_e2j, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha1[j, 2] <- 0", prior_beta_e10, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha2[j, 2] <- 0", prior_beta_e20, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha1[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_e1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha2[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_e2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[1, 1] ~ dnorm(0, 0.001)", prior_beta_e1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha2[1, 1] ~ dnorm(0, 0.001)", prior_beta_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha1[1, 2] <- se", prior_beta_e1s, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha2[1, 2] <- se", prior_beta_e2s, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end alpha priors effects", end_prior_beta, model_string_jags, fixed = TRUE) @@ -745,8 +745,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc beta_nons_c1 <- "beta[1] <- beta1[1]" beta_nons_c2 <- "beta[2] <- beta2[1]" begin_prior_beta <- "#begin beta priors costs" - prior_beta_c1 <- "beta1[1] ~ dnorm(0, 0.0000001)" - prior_beta_c2 <- "beta2[1] ~ dnorm(0, 0.0000001)" + prior_beta_c1 <- "beta1[1] ~ dnorm(0, 0.001)" + prior_beta_c2 <- "beta2[1] ~ dnorm(0, 0.001)" prior_beta_c1s <- "beta1[2] <- sc" prior_beta_c2s <- "beta2[2] <- sc" end_prior_beta <- "#end beta priors costs" @@ -758,12 +758,12 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("beta[j, 1] <- beta1[j, 1]", beta_nons_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta[j, 2] <- beta2[j, 1] }", beta_nons_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pc_fixed) {#begin beta priors costs", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta1[j, 1] ~ dnorm(0, 0.0000001)", prior_beta_c1j, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta2[j, 1] ~ dnorm(0, 0.0000001)", prior_beta_c2j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[j, 1] ~ dnorm(0, 0.001)", prior_beta_c1j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta2[j, 1] ~ dnorm(0, 0.001)", prior_beta_c2j, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta1[j, 2] <- 0", prior_beta_c10, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta2[j, 2] <- 0", prior_beta_c20, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta1[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_c1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta2[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_c2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[1, 1] ~ dnorm(0, 0.001)", prior_beta_c1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta2[1, 1] ~ dnorm(0, 0.001)", prior_beta_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta1[1, 2] <- sc", prior_beta_c1s, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta2[1, 2] <- sc", prior_beta_c2s, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end beta priors costs", end_prior_beta, model_string_jags, fixed = TRUE) @@ -886,12 +886,12 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("p_e[2] <- ilogit(inprod(mean_z_e2_fixed[], gamma_e[, 2]) + inprod(mean_z_e2_random[], mu_g_e_hat[, 2]))", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("gamma_e[1, 1] ~ dlogis(0, 1)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("gamma_e[1, 2] ~ dlogis(0, 1)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha1[j, 1] ~ dnorm(0, 0.0000001)", "alpha1[j] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha2[j, 1] ~ dnorm(0, 0.0000001)", "alpha2[j] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[j, 1] ~ dnorm(0, 0.001)", "alpha1[j] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha2[j, 1] ~ dnorm(0, 0.001)", "alpha2[j] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha1[j, 2] <- 0", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha2[j, 2] <- 0", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha1[1, 1] ~ dnorm(0, 0.0000001)", "alpha1[1] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha2[1, 1] ~ dnorm(0, 0.0000001)", "alpha2[1] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[1, 1] ~ dnorm(0, 0.001)", "alpha1[1] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha2[1, 1] ~ dnorm(0, 0.001)", "alpha2[1] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha1[1, 2] <- se", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha2[1, 2] <- se", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("ls_e1[1] ~ dunif(-5, 10)", "ls_e1 ~ dunif(-5, 10)", model_string_jags, fixed = TRUE) @@ -1301,8 +1301,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc beta_nons_e1 <- "alpha[1] <- alpha1[1]" beta_nons_e2 <- "alpha[2] <- alpha2[1]" begin_prior_beta <- "#begin alpha priors effects" - prior_beta_e1 <- "alpha1[1] ~ dnorm(0, 0.0000001)" - prior_beta_e2 <- "alpha2[1] ~ dnorm(0, 0.0000001)" + prior_beta_e1 <- "alpha1[1] ~ dnorm(0, 0.001)" + prior_beta_e2 <- "alpha2[1] ~ dnorm(0, 0.001)" end_prior_beta <- "#end beta priors effects" model_string_jags <- gsub("inprod(X1_e_fixed[i, ], alpha1[])", inprod_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X2_e_fixed[i, ], alpha2[])", inprod_e2, model_string_jags, fixed = TRUE) @@ -1312,12 +1312,12 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("alpha[j, 1] <- alpha1[j]", beta_nons_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha[j, 2] <- alpha2[j] }", beta_nons_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pe_fixed) {#begin alpha priors effects", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha1[j] ~ dnorm(0, 0.0000001)", prior_beta_e1j, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha2[j] ~ dnorm(0, 0.0000001)", prior_beta_e2j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[j] ~ dnorm(0, 0.001)", prior_beta_e1j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha2[j] ~ dnorm(0, 0.001)", prior_beta_e2j, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha1[j] <- 0", prior_beta_e10, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha2[j] <- 0", prior_beta_e20, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha1[1] ~ dnorm(0, 0.0000001)", prior_beta_e1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha2[1] ~ dnorm(0, 0.0000001)", prior_beta_e2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[1] ~ dnorm(0, 0.001)", prior_beta_e1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha2[1] ~ dnorm(0, 0.001)", prior_beta_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end alpha priors effects", end_prior_beta, model_string_jags, fixed = TRUE) } if(length(model_e_random) != 0 & pe_random == 1) { @@ -1345,8 +1345,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc beta_nons_c1 <- "beta[1] <- beta1[1]" beta_nons_c2 <- "beta[2] <- beta2[1]" begin_prior_beta <- "#begin beta priors costs" - prior_beta_c1 <- "beta1[1] ~ dnorm(0, 0.0000001)" - prior_beta_c2 <- "beta2[1] ~ dnorm(0, 0.0000001)" + prior_beta_c1 <- "beta1[1] ~ dnorm(0, 0.001)" + prior_beta_c2 <- "beta2[1] ~ dnorm(0, 0.001)" prior_beta_c1s <- "beta1[2] <- sc" prior_beta_c2s <- "beta2[2] <- sc" end_prior_beta <- "#end beta priors costs" @@ -1358,12 +1358,12 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("beta[j, 1] <- beta1[j, 1]", beta_nons_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta[j, 2] <- beta2[j, 1] }", beta_nons_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pc_fixed) {#begin beta priors costs", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta1[j, 1] ~ dnorm(0, 0.0000001)", prior_beta_c1j, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta2[j, 1] ~ dnorm(0, 0.0000001)", prior_beta_c2j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[j, 1] ~ dnorm(0, 0.001)", prior_beta_c1j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta2[j, 1] ~ dnorm(0, 0.001)", prior_beta_c2j, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta1[j, 2] <- 0", prior_beta_c10, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta2[j, 2] <- 0", prior_beta_c20, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta1[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_c1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta2[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_c2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[1, 1] ~ dnorm(0, 0.001)", prior_beta_c1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta2[1, 1] ~ dnorm(0, 0.001)", prior_beta_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta1[1, 2] <- sc", prior_beta_c1s, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta2[1, 2] <- sc", prior_beta_c2s, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end beta priors costs", end_prior_beta, model_string_jags, fixed = TRUE) @@ -1450,12 +1450,12 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("p_c[2] <- ilogit(inprod(mean_z_c2_fixed[], gamma_c[, 2]) + inprod(mean_z_c2_random[], mu_g_c_hat[, 2]))", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("gamma_c[1, 1] ~ dlogis(0, 1)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("gamma_c[1, 2] ~ dlogis(0, 1)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta1[j, 1] ~ dnorm(0, 0.0000001)", "beta1[j] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta2[j, 1] ~ dnorm(0, 0.0000001)", "beta2[j] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[j, 1] ~ dnorm(0, 0.001)", "beta1[j] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta2[j, 1] ~ dnorm(0, 0.001)", "beta2[j] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta1[j, 2] <- 0", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta2[j, 2] <- 0", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta1[1, 1] ~ dnorm(0, 0.0000001)", "beta1[1] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta2[1, 1] ~ dnorm(0, 0.0000001)", "beta2[1] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[1, 1] ~ dnorm(0, 0.001)", "beta1[1] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta2[1, 1] ~ dnorm(0, 0.001)", "beta2[1] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta1[1, 2] <- sc", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta2[1, 2] <- sc", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("ls_c1[1] ~ dunif(-5, 10)", "ls_c1 ~ dunif(-5, 10)", model_string_jags, fixed = TRUE) @@ -1465,8 +1465,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("for (j in 2:zc_fixed) {#begin gamma priors costs", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("for(t in 1:2) {gamma_c[j, t] ~ dnorm(0, 0.01) }", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end gamma priors costs", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f1[1] ~ dnorm(0, 0.0000001)", "beta_f[1] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f2[1] ~ dnorm(0, 0.0000001)", "beta_f[2] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f1[1] ~ dnorm(0, 0.001)", "beta_f[1] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f2[1] ~ dnorm(0, 0.001)", "beta_f[2] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f1[2] <- 0", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f2[2] <- 0", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f[1] <- beta_f1[1]", "", model_string_jags, fixed = TRUE) @@ -1897,8 +1897,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc beta_nons_e1 <- "alpha[1] <- alpha1[1]" beta_nons_e2 <- "alpha[2] <- alpha2[1]" begin_prior_beta <- "#begin alpha priors effects" - prior_beta_e1 <- "alpha1[1] ~ dnorm(0, 0.0000001)" - prior_beta_e2 <- "alpha2[1] ~ dnorm(0, 0.0000001)" + prior_beta_e1 <- "alpha1[1] ~ dnorm(0, 0.001)" + prior_beta_e2 <- "alpha2[1] ~ dnorm(0, 0.001)" prior_beta_e1s <- "alpha1[2] <- se" prior_beta_e2s <- "alpha2[2] <- se" end_prior_beta <- "#end alpha priors effects" @@ -1910,12 +1910,12 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("alpha[j, 1] <- alpha1[j, 1]", beta_nons_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha[j, 2] <- alpha2[j, 1] }", beta_nons_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pe_fixed) {#begin alpha priors effects", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha1[j, 1] ~ dnorm(0, 0.0000001)", prior_beta_e1j, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha2[j, 1] ~ dnorm(0, 0.0000001)", prior_beta_e2j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[j, 1] ~ dnorm(0, 0.001)", prior_beta_e1j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha2[j, 1] ~ dnorm(0, 0.001)", prior_beta_e2j, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha1[j, 2] <- 0", prior_beta_e10, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha2[j, 2] <- 0", prior_beta_e20, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha1[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_e1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha2[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_e2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha1[1, 1] ~ dnorm(0, 0.001)", prior_beta_e1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha2[1, 1] ~ dnorm(0, 0.001)", prior_beta_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha1[1, 2] <- se", prior_beta_e1s, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha2[1, 2] <- se", prior_beta_e2s, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end alpha priors effects", end_prior_beta, model_string_jags, fixed = TRUE) @@ -1945,8 +1945,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc beta_nons_c1 <- "beta[1] <- beta1[1]" beta_nons_c2 <- "beta[2] <- beta2[1]" begin_prior_beta <- "#begin beta priors costs" - prior_beta_c1 <- "beta1[1] ~ dnorm(0, 0.0000001)" - prior_beta_c2 <- "beta2[1] ~ dnorm(0, 0.0000001)" + prior_beta_c1 <- "beta1[1] ~ dnorm(0, 0.001)" + prior_beta_c2 <- "beta2[1] ~ dnorm(0, 0.001)" end_prior_beta <- "#end beta priors costs" model_string_jags <- gsub("inprod(X1_c_fixed[i, ], beta1[])", inprod_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X2_c_fixed[i, ], beta2[])", inprod_c2, model_string_jags, fixed = TRUE) @@ -1956,12 +1956,12 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc model_string_jags <- gsub("beta[j, 1] <- beta1[j]", beta_nons_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta[j, 2] <- beta2[j] }", beta_nons_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pc_fixed) {#begin beta priors costs", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta1[j] ~ dnorm(0, 0.0000001)", prior_beta_c1j, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta2[j] ~ dnorm(0, 0.0000001)", prior_beta_c2j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[j] ~ dnorm(0, 0.001)", prior_beta_c1j, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta2[j] ~ dnorm(0, 0.001)", prior_beta_c2j, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta1[j] <- 0", prior_beta_c10, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta2[j] <- 0", prior_beta_c20, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta1[1] ~ dnorm(0, 0.0000001)", prior_beta_c1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta2[1] ~ dnorm(0, 0.0000001)", prior_beta_c2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta1[1] ~ dnorm(0, 0.001)", prior_beta_c1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta2[1] ~ dnorm(0, 0.001)", prior_beta_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end beta priors costs", end_prior_beta, model_string_jags, fixed = TRUE) } if(length(model_c_random) != 0 & pc_random == 1) { @@ -2021,8 +2021,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc if(is.null(sc) == FALSE) { model_string_jags <- gsub(" + beta_f1[d_cost1[i] + 1] * (eff1[i] - mu_e[1])", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub(" + beta_f2[d_cost2[i] + 1] * (eff2[i] - mu_e[2])", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f1[1] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f2[1] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f1[1] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f2[1] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f1[2] <- 0", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f2[2] <- 0", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f[1] <- beta_f1[1]", "", model_string_jags, fixed = TRUE) @@ -2031,8 +2031,8 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc } else if(is.null(sc) == TRUE) { model_string_jags <- gsub(" + beta_f[1] * (eff1[i] - mu_e[1])", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub(" + beta_f[2] * (eff2[i] - mu_e[2])", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f[1] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f[2] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f[1] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f[2] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("#correlation", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f[1] <- beta_f1[1]", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f[2] <- beta_f2[1]", "", model_string_jags, fixed = TRUE) @@ -2044,4 +2044,4 @@ write_hurdle <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, zc writeLines(model_string_jags, "hurdle.txt") model_string <- "hurdle.txt" return(model_string) -})) \ No newline at end of file +})) diff --git a/R/write_long_miss.R b/R/write_long_miss.R index ee31746..f70929a 100644 --- a/R/write_long_miss.R +++ b/R/write_long_miss.R @@ -223,18 +223,18 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, #priors for mean regression coefficients for(time in 1:max_time) {# loop through time alpha for (j in 2:pe_fixed) {#begin alpha priors effects - for(t in 1:2) {alpha[j, t, time] ~ dnorm(0, 0.0000001) } + for(t in 1:2) {alpha[j, t, time] ~ dnorm(0, 0.001) } }#end alpha priors effects - alpha[1, 1, time] ~ dnorm(0, 0.0000001) - alpha[1, 2, time] ~ dnorm(0, 0.0000001) + alpha[1, 1, time] ~ dnorm(0, 0.001) + alpha[1, 2, time] ~ dnorm(0, 0.001) }#end alpha loop time for(time in 1:max_time) {# loop through time beta for (j in 2:pc_fixed) {#begin beta priors costs - for(t in 1:2) {beta[j, t, time] ~ dnorm(0, 0.0000001) } + for(t in 1:2) {beta[j, t, time] ~ dnorm(0, 0.001) } }#end beta priors costs - beta[1, 1, time] ~ dnorm(0, 0.0000001) - beta[1, 2, time] ~ dnorm(0, 0.0000001) + beta[1, 1, time] ~ dnorm(0, 0.001) + beta[1, 2, time] ~ dnorm(0, 0.001) }#end beta loop time #priors for mean regression random coefficients @@ -267,13 +267,13 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, ls_e[t, time] ~ dunif(-5, 10) #correlation - beta_f[t, time] ~ dnorm(0, 0.0000001) + beta_f[t, time] ~ dnorm(0, 0.001) #time dependence - beta_te[t, time] ~ dnorm(0, 0.0000001) - beta_tc[t, time] ~ dnorm(0, 0.0000001) - alpha_te[t, time] ~ dnorm(0, 0.0000001) - alpha_tc[t, time] ~ dnorm(0, 0.0000001) + beta_te[t, time] ~ dnorm(0, 0.001) + beta_tc[t, time] ~ dnorm(0, 0.001) + alpha_te[t, time] ~ dnorm(0, 0.001) + alpha_tc[t, time] ~ dnorm(0, 0.001) # mean and sd mean regression random coefficients priors for(j in 1:pc_random) {mu_b_hat[j, t, time] ~ dnorm(0, 0.001) @@ -1009,7 +1009,7 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, model_string_jags <- gsub("+ beta_f[2, 1] * (eff2[i, 1] - mu_e[2, 1])", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("+ beta_f[1, time] * (eff1[i, time] - mu_e[1, time])", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("+ beta_f[2, time] * (eff2[i, time] - mu_e[2, time])", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f[t, time] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f[t, time] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("#correlation", "", model_string_jags, fixed = TRUE) } if(ind_time_fixed == TRUE | time_dep == "none") { @@ -1017,10 +1017,10 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, model_string_jags <- gsub("+ alpha_te[1, time] * (eff1[i, time - 1] - mu_e[1, time - 1]) + alpha_tc[1, time] * (cost1[i, time - 1] - mu_c[1, time - 1])", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("+ beta_te[2, time] * (eff2[i, time - 1] - mu_e[2, time - 1]) + beta_tc[2, time] * (cost2[i, time - 1] - mu_c[2, time - 1])", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("+ alpha_te[2, time] * (eff2[i, time - 1] - mu_e[2, time - 1]) + alpha_tc[2, time] * (cost2[i, time - 1] - mu_c[2, time - 1])", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_te[t, time] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_tc[t, time] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_te[t, time] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_tc[t, time] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_te[t, time] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_tc[t, time] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_te[t, time] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_tc[t, time] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("#time dependence", "", model_string_jags, fixed = TRUE) } if(dist_c == "norm") { @@ -1270,8 +1270,8 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, begin_prior_beta <- "#begin alpha priors effects" prior_beta <- "#" end_prior_beta <- "#end alpha priors effects" - prior_beta_e1 <- "alpha[1, time] ~ dnorm(0, 0.0000001)" - prior_beta_e2 <- "alpha[2, time] ~ dnorm(0, 0.0000001)" + prior_beta_e1 <- "alpha[1, time] ~ dnorm(0, 0.001)" + prior_beta_e2 <- "alpha[2, time] ~ dnorm(0, 0.001)" model_string_jags <- gsub("inprod(X1_e_fixed[i, ], alpha[, 1, 1])", inprod_e1_base, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X1_e_fixed[i, ], alpha[, 1, time])", inprod_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X2_e_fixed[i, ], alpha[, 2, 1])", inprod_e2_base, model_string_jags, fixed = TRUE) @@ -1279,10 +1279,10 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, model_string_jags <- gsub("inprod(mean_cov_e1_fixed[], alpha[, 1, time])", inprod_mean_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_e2_fixed[], alpha[, 2, time])", inprod_mean_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pe_fixed) {#begin alpha priors effects", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("for(t in 1:2) {alpha[j, t, time] ~ dnorm(0, 0.0000001) }", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("for(t in 1:2) {alpha[j, t, time] ~ dnorm(0, 0.001) }", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end alpha priors effects", end_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha[1, 1, time] ~ dnorm(0, 0.0000001)", prior_beta_e1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha[1, 2, time] ~ dnorm(0, 0.0000001)", prior_beta_e2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha[1, 1, time] ~ dnorm(0, 0.001)", prior_beta_e1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha[1, 2, time] ~ dnorm(0, 0.001)", prior_beta_e2, model_string_jags, fixed = TRUE) } if(length(model_e_random) != 0 & pe_random == 1) { model_string_jags <- gsub("inprod(X1_e_random[i, ], a1[, clus1_e[i], 1])", "X1_e_random[i] * a1[clus1_e[i], 1]", model_string_jags, fixed = TRUE) @@ -1312,8 +1312,8 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, begin_prior_beta <- "#begin beta priors costs" prior_beta <- "#" end_prior_beta <- "#end beta priors costs" - prior_beta_c1 <- "beta[1, time] ~ dnorm(0, 0.0000001)" - prior_beta_c2 <- "beta[2, time] ~ dnorm(0, 0.0000001)" + prior_beta_c1 <- "beta[1, time] ~ dnorm(0, 0.001)" + prior_beta_c2 <- "beta[2, time] ~ dnorm(0, 0.001)" model_string_jags <- gsub("inprod(X1_c_fixed[i, ], beta[, 1, 1])", inprod_c1_base, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X1_c_fixed[i, ], beta[, 1, time])", inprod_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X2_c_fixed[i, ], beta[, 2, 1])", inprod_c2_base, model_string_jags, fixed = TRUE) @@ -1321,10 +1321,10 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, model_string_jags <- gsub("inprod(mean_cov_c1_fixed[], beta[, 1, time])", inprod_mean_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_c2_fixed[], beta[, 2, time])", inprod_mean_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pc_fixed) {#begin beta priors costs", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("for(t in 1:2) {beta[j, t, time] ~ dnorm(0, 0.0000001) }", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("for(t in 1:2) {beta[j, t, time] ~ dnorm(0, 0.001) }", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end beta priors costs", end_prior_beta,model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta[1, 1, time] ~ dnorm(0, 0.0000001)", prior_beta_c1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta[1, 2, time] ~ dnorm(0, 0.0000001)", prior_beta_c2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, 1, time] ~ dnorm(0, 0.001)", prior_beta_c1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, 2, time] ~ dnorm(0, 0.001)", prior_beta_c2, model_string_jags, fixed = TRUE) } if(pc_fixed == 0 & ind_fixed == FALSE) { prior_beta <- "#" @@ -1346,10 +1346,10 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, model_string_jags <- gsub("inprod(mean_cov_c2_fixed[], beta[, 2, time])", "beta_f[2, time] * (mean(eff2[, time]) - mu_e[2, time])", model_string_jags, fixed = TRUE) } model_string_jags <- gsub("for (j in 2:pc_fixed) {#begin beta priors costs", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("for(t in 1:2) {beta[j, t, time] ~ dnorm(0, 0.0000001) }", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("for(t in 1:2) {beta[j, t, time] ~ dnorm(0, 0.001) }", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end beta priors costs", end_prior_beta,model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta[1, 1, time] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta[1, 2, time] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, 1, time] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, 2, time] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("for(time in 1:max_time) {# loop through time beta", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("#end beta priors costs", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end beta loop time", "", model_string_jags, fixed = TRUE) @@ -1504,4 +1504,4 @@ write_long_miss <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, writeLines(model_string_jags, "long_miss.txt") model_string <- "long_miss.txt" return(model_string) - })) \ No newline at end of file + })) diff --git a/R/write_pattern.R b/R/write_pattern.R index 594f859..fc1bd00 100644 --- a/R/write_pattern.R +++ b/R/write_pattern.R @@ -147,42 +147,42 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p #priors for mean regression coefficients for (j in 2:pe_fixed) {#begin alpha priors effects in each pattern - alpha_p1[j, 1] ~ dnorm(0, 0.0000001) + alpha_p1[j, 1] ~ dnorm(0, 0.001) alpha_p1[j, 2] <- alpha_p1[j, 1] - alpha_p1[j, 3] ~ dnorm(0, 0.0000001) + alpha_p1[j, 3] ~ dnorm(0, 0.001) alpha_p1[j, 4] <- alpha_p1[j, 1] - alpha_p2[j, 1] ~ dnorm(0, 0.0000001) + alpha_p2[j, 1] ~ dnorm(0, 0.001) alpha_p2[j, 2] <- alpha_p2[j, 1] - alpha_p2[j, 3] ~ dnorm(0, 0.0000001) + alpha_p2[j, 3] ~ dnorm(0, 0.001) alpha_p2[j, 4] <- alpha_p2[j, 1] }#end alpha priors effects - alpha_p1[1, 1] ~ dnorm(0, 0.0000001) + alpha_p1[1, 1] ~ dnorm(0, 0.001) alpha_p1[1, 2] <- alpha_p1[1, 1] - alpha_p1[1, 3] ~ dnorm(0, 0.0000001) + alpha_p1[1, 3] ~ dnorm(0, 0.001) alpha_p1[1, 4] <- alpha_p1[1, 1] - alpha_p2[1, 1] ~ dnorm(0, 0.0000001) + alpha_p2[1, 1] ~ dnorm(0, 0.001) alpha_p2[1, 2] <- alpha_p2[1, 1] - alpha_p2[1, 3] ~ dnorm(0, 0.0000001) + alpha_p2[1, 3] ~ dnorm(0, 0.001) alpha_p2[1, 4] <- alpha_p2[1, 1] for (j in 2:pc_fixed) {#begin beta priors costs - beta_p1[j, 1] ~ dnorm(0, 0.0000001) - beta_p1[j, 2] ~ dnorm(0, 0.0000001) + beta_p1[j, 1] ~ dnorm(0, 0.001) + beta_p1[j, 2] ~ dnorm(0, 0.001) beta_p1[j, 3] <- beta_p1[j, 1] beta_p1[j, 4] <- beta_p1[j, 1] - beta_p2[j, 1] ~ dnorm(0, 0.0000001) - beta_p2[j, 2] ~ dnorm(0, 0.0000001) + beta_p2[j, 1] ~ dnorm(0, 0.001) + beta_p2[j, 2] ~ dnorm(0, 0.001) beta_p2[j, 3] <- beta_p2[j, 1] beta_p2[j, 4] <- beta_p2[j, 1] }#end beta priors costs - beta_p1[1, 1] ~ dnorm(0, 0.0000001) - beta_p1[1, 2] ~ dnorm(0, 0.0000001) + beta_p1[1, 1] ~ dnorm(0, 0.001) + beta_p1[1, 2] ~ dnorm(0, 0.001) beta_p1[1, 3] <- beta_p1[1, 1] beta_p1[1, 4] <- beta_p1[1, 1] - beta_p2[1, 1] ~ dnorm(0, 0.0000001) - beta_p2[1, 2] ~ dnorm(0, 0.0000001) + beta_p2[1, 1] ~ dnorm(0, 0.001) + beta_p2[1, 2] ~ dnorm(0, 0.001) beta_p2[1, 3] <- beta_p2[1, 1] beta_p2[1, 4] <- beta_p2[1, 1] @@ -223,12 +223,12 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p ls_e_p2[4] <- ls_e_p2[1] #correlation - beta_f_p1[1] ~ dnorm(0, 0.0000001) + beta_f_p1[1] ~ dnorm(0, 0.001) beta_f_p1[2] <- beta_f_p1[1] beta_f_p1[3] <- beta_f_p1[1] beta_f_p1[4] <- beta_f_p1[1] - beta_f_p2[1] ~ dnorm(0, 0.0000001) + beta_f_p2[1] ~ dnorm(0, 0.001) beta_f_p2[2] <- beta_f_p2[1] beta_f_p2[3] <- beta_f_p2[1] beta_f_p2[4] <- beta_f_p2[1] @@ -383,11 +383,11 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(ind_fixed == TRUE) { model_string_jags <- gsub(" + beta_f_p1[d1[i]] * (eff1[i] - meane_p1[d1[i]])", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub(" + beta_f_p2[d2[i]] * (eff2[i] - meane_p2[d2[i]])", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f_p1[1] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f_p1[1] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f_p1[2] <- beta_f_p1[1]", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f_p1[3] <- beta_f_p1[1]", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f_p1[4] <- beta_f_p1[1]", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f_p2[1] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f_p2[1] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f_p2[2] <- beta_f_p2[1]", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f_p2[3] <- beta_f_p2[1]", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_f_p2[4] <- beta_f_p2[1]", "", model_string_jags, fixed = TRUE) @@ -762,30 +762,30 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p begin_prior_beta <- "#begin alpha priors effects" prior_beta <- "#" end_prior_beta <- "#end alpha priors effects" - prior_beta_e1_1 <- "alpha_p1[1] ~ dnorm(0, 0.0000001)" - prior_beta_e1_3 <- "alpha_p1[3] ~ dnorm(0, 0.0000001)" - prior_beta_e2_1 <- "alpha_p2[1] ~ dnorm(0, 0.0000001)" - prior_beta_e2_3 <- "alpha_p2[3] ~ dnorm(0, 0.0000001)" + prior_beta_e1_1 <- "alpha_p1[1] ~ dnorm(0, 0.001)" + prior_beta_e1_3 <- "alpha_p1[3] ~ dnorm(0, 0.001)" + prior_beta_e2_1 <- "alpha_p2[1] ~ dnorm(0, 0.001)" + prior_beta_e2_3 <- "alpha_p2[3] ~ dnorm(0, 0.001)" model_string_jags <- gsub("inprod(X1_e_fixed[i, ], alpha_p1[, d1[i]])", inprod_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X2_e_fixed[i, ], alpha_p2[, d2[i]])", inprod_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_e1_fixed[], alpha_p1[, d])", inprod_mean_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_e2_fixed[], alpha_p2[, d])", inprod_mean_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pe_fixed) {#begin alpha priors effects", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001)", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001)", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p1[j, 2] <- alpha_p1[j, 1]", prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.0000001)", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.001)", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p1[j, 4] <- alpha_p1[j, 1]", prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001)", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001)", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p2[j, 2] <- alpha_p2[j, 1]", prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.0000001)", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.001)", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p2[j, 4] <- alpha_p2[j, 1]", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end alpha priors effects", end_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_e1_1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.0000001)", prior_beta_e1_3, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001)", prior_beta_e1_1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.001)", prior_beta_e1_3, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p1[1, 2] <- alpha_p1[1, 1]", "alpha_p1[2] <- alpha_p1[1]", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p1[1, 4] <- alpha_p1[1, 1]", "alpha_p1[4] <- alpha_p1[1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_e2_1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.0000001)", prior_beta_e2_3, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001)", prior_beta_e2_1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.001)", prior_beta_e2_3, model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p2[1, 2] <- alpha_p2[1, 1]", "alpha_p2[2] <- alpha_p2[1]", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p2[1, 4] <- alpha_p2[1, 1]", "alpha_p2[4] <- alpha_p2[1]", model_string_jags, fixed = TRUE) if(restriction == "AC"){ @@ -823,30 +823,30 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p begin_prior_beta <- "#begin beta priors costs" prior_beta <- "#" end_prior_beta <- "#end beta priors costs" - prior_beta_c1_1 <- "beta_p1[1] ~ dnorm(0, 0.0000001)" - prior_beta_c1_2 <- "beta_p1[2] ~ dnorm(0, 0.0000001)" - prior_beta_c2_1 <- "beta_p2[1] ~ dnorm(0, 0.0000001)" - prior_beta_c2_2 <- "beta_p2[2] ~ dnorm(0, 0.0000001)" + prior_beta_c1_1 <- "beta_p1[1] ~ dnorm(0, 0.001)" + prior_beta_c1_2 <- "beta_p1[2] ~ dnorm(0, 0.001)" + prior_beta_c2_1 <- "beta_p2[1] ~ dnorm(0, 0.001)" + prior_beta_c2_2 <- "beta_p2[2] ~ dnorm(0, 0.001)" model_string_jags <- gsub("inprod(X1_c_fixed[i, ], beta_p1[, d1[i]])", inprod_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X2_c_fixed[i, ], beta_p2[, d2[i]])", inprod_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_c1_fixed[], beta_p1[, d])", inprod_mean_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_c2_fixed[], beta_p2[, d])", inprod_mean_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pc_fixed) {#begin beta priors costs", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001)", prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001)", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001)", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001)", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p1[j, 3] <- beta_p1[j, 1]", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p1[j, 4] <- beta_p1[j, 1]", prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001)", prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001)", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001)", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001)", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p2[j, 3] <- beta_p2[j, 1]", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p2[j, 4] <- beta_p2[j, 1]", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end beta priors costs", end_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_c1_1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001)", prior_beta_c1_2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001)", prior_beta_c1_1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001)", prior_beta_c1_2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p1[1, 3] <- beta_p1[1, 1]", "beta_p1[3] <- beta_p1[1]", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p1[1, 4] <- beta_p1[1, 1]", "beta_p1[4] <- beta_p1[1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_c2_1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001)", prior_beta_c2_2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001)", prior_beta_c2_1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001)", prior_beta_c2_2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p2[1, 3] <- beta_p2[1, 1]", "beta_p2[3] <- beta_p2[1]", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p2[1, 4] <- beta_p2[1, 1]", "beta_p2[4] <- beta_p2[1]", model_string_jags, fixed = TRUE) if(restriction == "AC"){ @@ -904,10 +904,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d1 <- ifelse(d1 == 4, 3, d1) if(type == "MNAR" | type == "MNAR_eff") {model_string_jags <- gsub("mu_e_p1[3] <- meane_p1[3]", "mu_e_p1[3] <- meane_p1[3] + Delta_e[1]", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.0000001)", "alpha_p1[1, 3] <- alpha_p1[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.0000001)", "alpha_p1[j, 3] <- alpha_p1[j, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.001)", "alpha_p1[1, 3] <- alpha_p1[1, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.001)", "alpha_p1[j, 3] <- alpha_p1[j, 1]", model_string_jags, fixed = TRUE) } - if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.0000001)", "alpha_p1[3] <- alpha_p1[1]", model_string_jags, fixed = TRUE) } + if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.001)", "alpha_p1[3] <- alpha_p1[1]", model_string_jags, fixed = TRUE) } if(dist_e == "norm") {model_string_jags <- gsub("ls_e_p1[3] ~ dunif(-5, 10)", "ls_e_p1[3] <- ls_e_p1[1]", model_string_jags, fixed = TRUE) } if(dist_e == "beta") {model_string_jags <- gsub("s_e_p1[3] ~ dunif(0, sqrt(meane_p1[3] * (1 - meane_p1[3])))", "s_e_p1[3] <- s_e_p1[1]", model_string_jags, fixed = TRUE) } if(dist_e %in% c("gamma", "logis")) {model_string_jags <- gsub("s_e_p1[3] ~ dunif(0, 10000)", "s_e_p1[3] <- s_e_p1[1]", model_string_jags, fixed = TRUE) } @@ -920,10 +920,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d1 <- ifelse(d1 == 4, 2, d1) if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p1[2] <- meanc_p1[2]", "mu_c_p1[2] <- meanc_p1[2] + Delta_c[1]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001)", "beta_p1[1, 2] <- beta_p1[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001)", "beta_p1[j, 2] <- beta_p1[j, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001)", "beta_p1[1, 2] <- beta_p1[1, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001)", "beta_p1[j, 2] <- beta_p1[j, 1]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001)", "beta_p1[2] <- beta_p1[1]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001)", "beta_p1[2] <- beta_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p1[2] ~ dunif(-5, 10)", "ls_c_p1[2] <- ls_c_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p1[2] ~ dunif(0, 100)", "ls_c_p1[2] <- ls_c_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p1[2] ~ dunif(0, 10000)", "s_c_p1[2] <- s_c_p1[1]", model_string_jags, fixed = TRUE) } @@ -935,10 +935,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p1[3] <- meanc_p1[3] + Delta_c[1]", "", model_string_jags, fixed = TRUE) } if(type == "MNAR" | type == "MNAR_eff") {model_string_jags <- gsub("mu_e_p1[3] <- meane_p1[3]", "", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) } - if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) } + if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { model_string_jags <- gsub("beta_p1[1, 3] <- beta_p1[1, 1]", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p1[j, 3] <- beta_p1[j, 1]", "", model_string_jags, fixed = TRUE) @@ -959,18 +959,18 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d1 <- ifelse(d1 == 3, 2, d1) if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p1[2] <- meanc_p1[2]", "mu_c_p1[2] <- meanc_p1[2] + Delta_c[1]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001)", "beta_p1[1, 2] <- beta_p1[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001)", "beta_p1[j, 2] <- beta_p1[j, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001)", "beta_p1[1, 2] <- beta_p1[1, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001)", "beta_p1[j, 2] <- beta_p1[j, 1]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001)", "beta_p1[2] <- beta_p1[1]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001)", "beta_p1[2] <- beta_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p1[2] ~ dunif(-5, 10)", "ls_c_p1[2] <- ls_c_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p1[2] ~ dunif(0, 100)", "ls_c_p1[2] <- ls_c_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p1[2] ~ dunif(0, 10000)", "s_c_p1[2] <- s_c_p1[1]", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p1[1, 2] <- alpha_p1[1, 1]", "alpha_p1[1, 2] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[j, 2] <- alpha_p1[j, 1]", "alpha_p1[j, 2] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[1, 2] <- alpha_p1[1, 1]", "alpha_p1[1, 2] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 2] <- alpha_p1[j, 1]", "alpha_p1[j, 2] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) } - if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p1[2] <- alpha_p1[1]", "alpha_p1[2] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) } + if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p1[2] <- alpha_p1[1]", "alpha_p1[2] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) } if(dist_e == "norm") {model_string_jags <- gsub("ls_e_p1[2] <- ls_e_p1[1]", "ls_e_p1[2] ~ dunif(-5, 10)", model_string_jags, fixed = TRUE) } if(dist_e == "beta") {model_string_jags <- gsub("s_e_p1[2] <- s_e_p1[1]", "s_e_p1[2] ~ dunif(0, sqrt(meane_p1[2] * (1 - meane_p1[2])))", model_string_jags, fixed = TRUE) } if(dist_e %in% c("gamma", "logis")) {model_string_jags <- gsub("s_e_p1[2] <- s_e_p1[1]", "s_e_p1[2] ~ dunif(0, 10000)", model_string_jags, fixed = TRUE) } @@ -983,10 +983,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d1 <- ifelse(d1 == 4, 2, d1) if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p1[2] <- meanc_p1[2]", "mu_c_p1[2] <- meanc_p1[2] + Delta_c[1]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.0000001)", "beta_p1[1, 2] <- beta_p1[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.0000001)", "beta_p1[j, 2] <- beta_p1[j, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[1, 2] ~ dnorm(0, 0.001)", "beta_p1[1, 2] <- beta_p1[1, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 2] ~ dnorm(0, 0.001)", "beta_p1[j, 2] <- beta_p1[j, 1]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.0000001)", "beta_p1[2] <- beta_p1[1]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[2] ~ dnorm(0, 0.001)", "beta_p1[2] <- beta_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p1[2] ~ dunif(-5, 10)", "ls_c_p1[2] <- ls_c_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p1[2] ~ dunif(0, 100)", "ls_c_p1[2] <- ls_c_p1[1]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p1[2] ~ dunif(0, 10000)", "s_c_p1[2] <- s_c_p1[1]", model_string_jags, fixed = TRUE) } @@ -1021,10 +1021,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d1 <- ifelse(d1 == 4, 1, d1) if(type == "MNAR" | type == "MNAR_eff") {model_string_jags <- gsub("mu_e_p1[1] <- meane_p1[1]", "mu_e_p1[1] <- meane_p1[1] + Delta_e[1]", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.0000001)", "alpha_p1[1, 1] <- alpha_p1[1, 3]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.0000001)", "alpha_p1[j, 1] <- alpha_p1[j, 3]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[1, 1] ~ dnorm(0, 0.001)", "alpha_p1[1, 1] <- alpha_p1[1, 3]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 1] ~ dnorm(0, 0.001)", "alpha_p1[j, 1] <- alpha_p1[j, 3]", model_string_jags, fixed = TRUE) } - if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.0000001)", "alpha_p1[1] <- alpha_p1[3]", model_string_jags, fixed = TRUE) } + if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p1[1] ~ dnorm(0, 0.001)", "alpha_p1[1] <- alpha_p1[3]", model_string_jags, fixed = TRUE) } if(dist_e == "norm") {model_string_jags <- gsub("ls_e_p1[1] ~ dunif(-5, 10)", "ls_e_p1[1] <- ls_e_p1[3]", model_string_jags, fixed = TRUE) } if(dist_e == "beta") {model_string_jags <- gsub("s_e_p1[1] ~ dunif(0, sqrt(meane_p1[1] * (1 - meane_p1[1])))", "s_e_p1[1] <- s_e_p1[3]", model_string_jags, fixed = TRUE) } if(dist_e %in% c("gamma", "logis")) {model_string_jags <- gsub("s_e_p1[1] ~ dunif(0, 10000)", "s_e_p1[1] <- s_e_p1[3]", model_string_jags, fixed = TRUE) } @@ -1035,10 +1035,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(dist_e == "nbinom") {model_string_jags <- gsub("tau_e_p1[1] ~ dunif(0, 100)", "tau_e_p1[1] <- tau_e_p1[3]", model_string_jags, fixed = TRUE) } if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p1[1] <- meanc_p1[1]", "mu_c_p1[1] <- meanc_p1[1] + Delta_c[1]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001)", "beta_p1[1, 1] <- beta_p1[1, 2]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001)", "beta_p1[j, 1] <- beta_p1[j, 2]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001)", "beta_p1[1, 1] <- beta_p1[1, 2]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001)", "beta_p1[j, 1] <- beta_p1[j, 2]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001)", "beta_p1[1] <- beta_p1[2]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001)", "beta_p1[1] <- beta_p1[2]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p1[1] ~ dunif(-5, 10)", "ls_c_p1[1] <- ls_c_p1[2]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p1[1] ~ dunif(0, 100)", "ls_c_p1[1] <- ls_c_p1[2]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p1[1] ~ dunif(0, 10000)", "s_c_p1[1] <- s_c_p1[2]", model_string_jags, fixed = TRUE) } @@ -1051,13 +1051,13 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p1[3] <- meanc_p1[3] + Delta_c[1]", "", model_string_jags, fixed = TRUE) } if(type == "MNAR" | type == "MNAR_eff") {model_string_jags <- gsub("mu_e_p1[3] <- meane_p1[3]", "", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[1, 3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p1[1, 2] <- alpha_p1[1, 3]", "alpha_p1[1, 2] <- alpha_p1[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[j, 3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p1[j, 2] <- alpha_p1[j, 3]", "alpha_p1[j, 2] <- alpha_p1[j, 1]", model_string_jags, fixed = TRUE) } if(pe_fixed == 1) { - model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p1[3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p1[2] <- alpha_p1[3]", "alpha_p1[2] <- alpha_p1[1]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { @@ -1104,10 +1104,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(ind_fixed == FALSE) {model_string_jags <- gsub("beta_f_p1[3] <- beta_f_p1[1]" , "", model_string_jags, fixed = TRUE) } if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p1[1] <- meanc_p1[1]", "mu_c_p1[1] <- meanc_p1[1] + Delta_c[1]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.0000001)", "beta_p1[1, 1] <- beta_p1[1, 2]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.0000001)", "beta_p1[j, 1] <- beta_p1[j, 2]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[1, 1] ~ dnorm(0, 0.001)", "beta_p1[1, 1] <- beta_p1[1, 2]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p1[j, 1] ~ dnorm(0, 0.001)", "beta_p1[j, 1] <- beta_p1[j, 2]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.0000001)", "beta_p1[1] <- beta_p1[2]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p1[1] ~ dnorm(0, 0.001)", "beta_p1[1] <- beta_p1[2]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p1[1] ~ dunif(-5, 10)", "ls_c_p1[1] <- ls_c_p1[2]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p1[1] ~ dunif(0, 100)", "ls_c_p1[1] <- ls_c_p1[2]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p1[1] ~ dunif(0, 10000)", "s_c_p1[1] <- s_c_p1[2]", model_string_jags, fixed = TRUE) } @@ -1141,10 +1141,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d2 <- ifelse(d2 == 4, 3, d2) if(type == "MNAR" | type == "MNAR_eff") {model_string_jags <- gsub("mu_e_p2[3] <- meane_p2[3]", "mu_e_p2[3] <- meane_p2[3] + Delta_e[2]", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.0000001)", "alpha_p2[1, 3] <- alpha_p2[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.0000001)", "alpha_p2[j, 3] <- alpha_p2[j, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.001)", "alpha_p2[1, 3] <- alpha_p2[1, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.001)", "alpha_p2[j, 3] <- alpha_p2[j, 1]", model_string_jags, fixed = TRUE) } - if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.0000001)", "alpha_p2[3] <- alpha_p2[1]", model_string_jags, fixed = TRUE) } + if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.001)", "alpha_p2[3] <- alpha_p2[1]", model_string_jags, fixed = TRUE) } if(dist_e == "norm") {model_string_jags <- gsub("ls_e_p2[3] ~ dunif(-5, 10)", "ls_e_p2[3] <- ls_e_p2[1]", model_string_jags, fixed = TRUE) } if(dist_e == "beta") {model_string_jags <- gsub("s_e_p2[3] ~ dunif(0, sqrt(meane_p2[3] * (1 - meane_p2[3])))", "s_e_p2[3] <- s_e_p2[1]", model_string_jags, fixed = TRUE) } if(dist_e %in% c("gamma", "logis")) {model_string_jags <- gsub("s_e_p2[3] ~ dunif(0, 10000)", "s_e_p2[3] <- s_e_p2[1]", model_string_jags, fixed = TRUE) } @@ -1157,10 +1157,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d2 <- ifelse(d2 == 4, 2, d2) if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p2[2] <- meanc_p2[2]", "mu_c_p2[2] <- meanc_p2[2] + Delta_c[2]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001)", "beta_p2[1, 2] <- beta_p2[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001)", "beta_p2[j, 2] <- beta_p2[j, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001)", "beta_p2[1, 2] <- beta_p2[1, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001)", "beta_p2[j, 2] <- beta_p2[j, 1]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001)", "beta_p2[2] <- beta_p2[1]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001)", "beta_p2[2] <- beta_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p2[2] ~ dunif(-5, 10)", "ls_c_p2[2] <- ls_c_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p2[2] ~ dunif(0, 100)", "ls_c_p2[2] <- ls_c_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p2[2] ~ dunif(0, 10000)", "s_c_p2[2] <- s_c_p2[1]", model_string_jags, fixed = TRUE) } @@ -1172,10 +1172,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p2[3] <- meanc_p2[3] + Delta_c[2]", "", model_string_jags, fixed = TRUE) } if(type == "MNAR" | type == "MNAR_eff") {model_string_jags <- gsub("mu_e_p2[3] <- meane_p2[3]", "", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) } - if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) } + if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { model_string_jags <- gsub("beta_p2[1, 3] <- beta_p2[1, 1]", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("beta_p2[j, 3] <- beta_p2[j, 1]", "", model_string_jags, fixed = TRUE) @@ -1196,18 +1196,18 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d2 <- ifelse(d2 == 3, 2, d2) if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p2[2] <- meanc_p2[2]", "mu_c_p2[2] <- meanc_p2[2] + Delta_c[2]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001)", "beta_p2[1, 2] <- beta_p2[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001)", "beta_p2[j, 2] <- beta_p2[j, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001)", "beta_p2[1, 2] <- beta_p2[1, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001)", "beta_p2[j, 2] <- beta_p2[j, 1]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001)", "beta_p2[2] <- beta_p2[1]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001)", "beta_p2[2] <- beta_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p2[2] ~ dunif(-5, 10)", "ls_c_p2[2] <- ls_c_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p2[2] ~ dunif(0, 100)", "ls_c_p2[2] <- ls_c_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p2[2] ~ dunif(0, 10000)", "s_c_p2[2] <- s_c_p2[1]", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p2[1, 2] <- alpha_p2[1, 1]", "alpha_p2[1, 2] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[j, 2] <- alpha_p2[j, 1]", "alpha_p2[j, 2] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[1, 2] <- alpha_p2[1, 1]", "alpha_p2[1, 2] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 2] <- alpha_p2[j, 1]", "alpha_p2[j, 2] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) } - if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p2[2] <- alpha_p2[1]", "alpha_p2[2] ~ dnorm(0, 0.0000001)", model_string_jags, fixed = TRUE) } + if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p2[2] <- alpha_p2[1]", "alpha_p2[2] ~ dnorm(0, 0.001)", model_string_jags, fixed = TRUE) } if(dist_e == "norm") {model_string_jags <- gsub("ls_e_p2[2] <- ls_e_p2[1]", "ls_e_p2[2] ~ dunif(-5, 10)", model_string_jags, fixed = TRUE) } if(dist_e == "beta") {model_string_jags <- gsub("s_e_p2[2] <- s_e_p2[1]", "s_e_p2[2] ~ dunif(0, sqrt(meane_p2[2] * (1 - meane_p2[2])))", model_string_jags, fixed = TRUE) } if(dist_e %in% c("gamma", "logis")) {model_string_jags <- gsub("s_e_p2[2] <- s_e_p2[1]", "s_e_p2[2] ~ dunif(0, 10000)", model_string_jags, fixed = TRUE) } @@ -1220,10 +1220,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d2 <- ifelse(d2 == 4, 2, d2) if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p2[2] <- meanc_p2[2]", "mu_c_p2[2] <- meanc_p2[2] + Delta_c[2]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.0000001)", "beta_p2[1, 2] <- beta_p2[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.0000001)", "beta_p2[j, 2] <- beta_p2[j, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[1, 2] ~ dnorm(0, 0.001)", "beta_p2[1, 2] <- beta_p2[1, 1]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 2] ~ dnorm(0, 0.001)", "beta_p2[j, 2] <- beta_p2[j, 1]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.0000001)", "beta_p2[2] <- beta_p2[1]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[2] ~ dnorm(0, 0.001)", "beta_p2[2] <- beta_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p2[2] ~ dunif(-5, 10)", "ls_c_p2[2] <- ls_c_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p2[2] ~ dunif(0, 100)", "ls_c_p2[2] <- ls_c_p2[1]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p2[2] ~ dunif(0, 10000)", "s_c_p2[2] <- s_c_p2[1]", model_string_jags, fixed = TRUE) } @@ -1258,10 +1258,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p d2 <- ifelse(d2 == 4, 1, d2) if(type == "MNAR" | type == "MNAR_eff") {model_string_jags <- gsub("mu_e_p2[1] <- meane_p2[1]", "mu_e_p2[1] <- meane_p2[1] + Delta_e[2]", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.0000001)", "alpha_p2[1, 1] <- alpha_p2[1, 3]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.0000001)", "alpha_p2[j, 1] <- alpha_p2[j, 3]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[1, 1] ~ dnorm(0, 0.001)", "alpha_p2[1, 1] <- alpha_p2[1, 3]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 1] ~ dnorm(0, 0.001)", "alpha_p2[j, 1] <- alpha_p2[j, 3]", model_string_jags, fixed = TRUE) } - if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.0000001)", "alpha_p2[1] <- alpha_p2[3]", model_string_jags, fixed = TRUE) } + if(pe_fixed == 1) {model_string_jags <- gsub("alpha_p2[1] ~ dnorm(0, 0.001)", "alpha_p2[1] <- alpha_p2[3]", model_string_jags, fixed = TRUE) } if(dist_e == "norm") {model_string_jags <- gsub("ls_e_p2[1] ~ dunif(-5, 10)", "ls_e_p2[1] <- ls_e_p2[3]", model_string_jags, fixed = TRUE) } if(dist_e == "beta") {model_string_jags <- gsub("s_e_p2[1] ~ dunif(0, sqrt(meane_p2[1] * (1 - meane_p2[1])))", "s_e_p2[1] <- s_e_p2[3]", model_string_jags, fixed = TRUE) } if(dist_e %in% c("gamma", "logis")) {model_string_jags <- gsub("s_e_p2[1] ~ dunif(0, 10000)", "s_e_p2[1] <- s_e_p2[3]", model_string_jags, fixed = TRUE) } @@ -1272,10 +1272,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(dist_e == "nbinom") {model_string_jags <- gsub("tau_e_p2[1] ~ dunif(0, 100)", "tau_e_p2[1] <- tau_e_p2[3]", model_string_jags, fixed = TRUE) } if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p2[1] <- meanc_p2[1]", "mu_c_p2[1] <- meanc_p2[1] + Delta_c[2]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001)", "beta_p2[1, 1] <- beta_p2[1, 2]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001)", "beta_p2[j, 1] <- beta_p2[j, 2]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001)", "beta_p2[1, 1] <- beta_p2[1, 2]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001)", "beta_p2[j, 1] <- beta_p2[j, 2]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001)", "beta_p2[1] <- beta_p2[2]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001)", "beta_p2[1] <- beta_p2[2]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p2[1] ~ dunif(-5, 10)", "ls_c_p2[1] <- ls_c_p2[2]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p2[1] ~ dunif(0, 100)", "ls_c_p2[1] <- ls_c_p2[2]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p2[1] ~ dunif(0, 10000)", "s_c_p2[1] <- s_c_p2[2]", model_string_jags, fixed = TRUE) } @@ -1288,13 +1288,13 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p2[3] <- meanc_p2[3] + Delta_c[2]", "", model_string_jags, fixed = TRUE) } if(type == "MNAR" | type == "MNAR_eff") {model_string_jags <- gsub("mu_e_p2[3] <- meane_p2[3]", "", model_string_jags, fixed = TRUE) } if(pe_fixed > 1) { - model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[1, 3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p2[1, 2] <- alpha_p2[1, 3]", "alpha_p2[1, 2] <- alpha_p2[1, 1]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[j, 3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p2[j, 2] <- alpha_p2[j, 3]", "alpha_p2[j, 2] <- alpha_p2[j, 1]", model_string_jags, fixed = TRUE) } if(pe_fixed == 1) { - model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha_p2[3] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("alpha_p2[2] <- alpha_p2[3]", "alpha_p2[2] <- alpha_p2[1]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { @@ -1341,10 +1341,10 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p if(ind_fixed == FALSE) {model_string_jags <- gsub("beta_f_p2[3] <- beta_f_p2[1]" , "", model_string_jags, fixed = TRUE) } if(type == "MNAR" | type == "MNAR_cost") {model_string_jags <- gsub("mu_c_p2[1] <- meanc_p2[1]", "mu_c_p2[1] <- meanc_p2[1] + Delta_c[2]", model_string_jags, fixed = TRUE) } if(pc_fixed > 1) { - model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.0000001)", "beta_p2[1, 1] <- beta_p2[1, 2]", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.0000001)", "beta_p2[j, 1] <- beta_p2[j, 2]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[1, 1] ~ dnorm(0, 0.001)", "beta_p2[1, 1] <- beta_p2[1, 2]", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_p2[j, 1] ~ dnorm(0, 0.001)", "beta_p2[j, 1] <- beta_p2[j, 2]", model_string_jags, fixed = TRUE) } - if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.0000001)", "beta_p2[1] <- beta_p2[2]", model_string_jags, fixed = TRUE) } + if(pc_fixed == 1) {model_string_jags <- gsub("beta_p2[1] ~ dnorm(0, 0.001)", "beta_p2[1] <- beta_p2[2]", model_string_jags, fixed = TRUE) } if(dist_c == "norm") {model_string_jags <- gsub("ls_c_p2[1] ~ dunif(-5, 10)", "ls_c_p2[1] <- ls_c_p2[2]", model_string_jags, fixed = TRUE) } if(dist_c == "lnorm") {model_string_jags <- gsub("ls_c_p2[1] ~ dunif(0, 100)", "ls_c_p2[1] <- ls_c_p2[2]", model_string_jags, fixed = TRUE) } if(dist_c == "gamma") {model_string_jags <- gsub("s_c_p2[1] ~ dunif(0, 10000)", "s_c_p2[1] <- s_c_p2[2]", model_string_jags, fixed = TRUE) } @@ -1356,4 +1356,4 @@ write_pattern <- function(type, dist_e, dist_c, pe_fixed, pc_fixed, ind_fixed, p writeLines(model_string_jags, "pattern.txt") model_string <- "pattern.txt" return(model_string) -})) \ No newline at end of file +})) diff --git a/R/write_selection.R b/R/write_selection.R index 2781736..4c0622a 100644 --- a/R/write_selection.R +++ b/R/write_selection.R @@ -132,16 +132,16 @@ write_selection <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, #priors for mean regression coefficients for (j in 2:pe_fixed) {#begin alpha priors effects - for(t in 1:2) {alpha[j, t] ~ dnorm(0, 0.0000001) } + for(t in 1:2) {alpha[j, t] ~ dnorm(0, 0.001) } }#end alpha priors effects - alpha[1, 1] ~ dnorm(0, 0.0000001) - alpha[1, 2] ~ dnorm(0, 0.0000001) + alpha[1, 1] ~ dnorm(0, 0.001) + alpha[1, 2] ~ dnorm(0, 0.001) for (j in 2:pc_fixed) {#begin beta priors costs - for(t in 1:2) {beta[j, t] ~ dnorm(0, 0.0000001) } + for(t in 1:2) {beta[j, t] ~ dnorm(0, 0.001) } }#end beta priors costs - beta[1, 1] ~ dnorm(0, 0.0000001) - beta[1, 2] ~ dnorm(0, 0.0000001) + beta[1, 1] ~ dnorm(0, 0.001) + beta[1, 2] ~ dnorm(0, 0.001) #priors for mean regression random coefficients for (j in 1:pe_random) {#begin a1 priors effects @@ -164,7 +164,7 @@ write_selection <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, ls_e[t] ~ dunif(-5, 10) #correlation - beta_f[t] ~ dnorm(0, 0.0000001) + beta_f[t] ~ dnorm(0, 0.001) # mean and sd mean regression random coefficients priors for(j in 1:pc_random) {mu_b_hat[j, t] ~ dnorm(0, 0.001) @@ -564,7 +564,7 @@ write_selection <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, if(ind_fixed == TRUE) { model_string_jags <- gsub(" + beta_f[1] * (eff1[i] - mu_e[1])", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub(" + beta_f[2] * (eff2[i] - mu_e[2])", "", model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta_f[t] ~ dnorm(0, 0.0000001)", "", model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta_f[t] ~ dnorm(0, 0.001)", "", model_string_jags, fixed = TRUE) model_string_jags <- gsub("#correlation", "", model_string_jags, fixed = TRUE) } if(dist_c == "norm") { @@ -792,17 +792,17 @@ write_selection <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, begin_prior_beta <- "#begin alpha priors effects" prior_beta <- "#" end_prior_beta <- "#end alpha priors effects" - prior_beta_e1 <- "alpha[1] ~ dnorm(0, 0.0000001)" - prior_beta_e2 <- "alpha[2] ~ dnorm(0, 0.0000001)" + prior_beta_e1 <- "alpha[1] ~ dnorm(0, 0.001)" + prior_beta_e2 <- "alpha[2] ~ dnorm(0, 0.001)" model_string_jags <- gsub("inprod(X1_e_fixed[i, ], alpha[, 1])", inprod_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X2_e_fixed[i, ], alpha[, 2])", inprod_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_e1_fixed[], alpha[, 1])", inprod_mean_e1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_e2_fixed[], alpha[, 2])", inprod_mean_e2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pe_fixed) {#begin alpha priors effects", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("for(t in 1:2) {alpha[j, t] ~ dnorm(0, 0.0000001) }", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("for(t in 1:2) {alpha[j, t] ~ dnorm(0, 0.001) }", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end alpha priors effects", end_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_e1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("alpha[1, 2] ~ dnorm(0, 0.0000001)", prior_beta_e2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha[1, 1] ~ dnorm(0, 0.001)", prior_beta_e1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("alpha[1, 2] ~ dnorm(0, 0.001)", prior_beta_e2, model_string_jags, fixed = TRUE) } if(length(model_e_random) != 0 & pe_random == 1) { model_string_jags <- gsub("inprod(X1_e_random[i, ], a1[, clus1_e[i]])", "X1_e_random[i] * a1[clus1_e[i]]", model_string_jags, fixed = TRUE) @@ -828,17 +828,17 @@ write_selection <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, begin_prior_beta <- "#begin beta priors costs" prior_beta <- "#" end_prior_beta <- "#end beta priors costs" - prior_beta_c1 <- "beta[1] ~ dnorm(0, 0.0000001)" - prior_beta_c2 <- "beta[2] ~ dnorm(0, 0.0000001)" + prior_beta_c1 <- "beta[1] ~ dnorm(0, 0.001)" + prior_beta_c2 <- "beta[2] ~ dnorm(0, 0.001)" model_string_jags <- gsub("inprod(X1_c_fixed[i, ], beta[, 1])", inprod_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(X2_c_fixed[i, ], beta[, 2])", inprod_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_c1_fixed[], beta[, 1])", inprod_mean_c1, model_string_jags, fixed = TRUE) model_string_jags <- gsub("inprod(mean_cov_c2_fixed[], beta[, 2])", inprod_mean_c2, model_string_jags, fixed = TRUE) model_string_jags <- gsub("for (j in 2:pc_fixed) {#begin beta priors costs", begin_prior_beta, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("for(t in 1:2) {beta[j, t] ~ dnorm(0, 0.0000001) }", prior_beta, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("for(t in 1:2) {beta[j, t] ~ dnorm(0, 0.001) }", prior_beta, model_string_jags, fixed = TRUE) model_string_jags <- gsub("}#end beta priors costs", end_prior_beta,model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta[1, 1] ~ dnorm(0, 0.0000001)", prior_beta_c1, model_string_jags, fixed = TRUE) - model_string_jags <- gsub("beta[1, 2] ~ dnorm(0, 0.0000001)", prior_beta_c2, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, 1] ~ dnorm(0, 0.001)", prior_beta_c1, model_string_jags, fixed = TRUE) + model_string_jags <- gsub("beta[1, 2] ~ dnorm(0, 0.001)", prior_beta_c2, model_string_jags, fixed = TRUE) } if(length(model_c_random) != 0 & pc_random == 1) { model_string_jags <- gsub("inprod(X1_c_random[i, ], b1[, clus1_c[i]])", "X1_c_random[i] * b1[clus1_c[i]]", model_string_jags, fixed = TRUE) @@ -966,4 +966,4 @@ write_selection <- function(dist_e , dist_c, type, pe_fixed, pc_fixed, ze_fixed, writeLines(model_string_jags, "selection.txt") model_string <- "selection.txt" return(model_string) - })) \ No newline at end of file + })) diff --git a/vignettes/Model_customisation_in_missingHE.Rmd b/vignettes/Model_customisation_in_missingHE.Rmd index bcf7feb..63dd573 100644 --- a/vignettes/Model_customisation_in_missingHE.Rmd +++ b/vignettes/Model_customisation_in_missingHE.Rmd @@ -141,9 +141,9 @@ Prior values can be modified by first creating a list object which, for example, ```{r prior_hurdle1, eval=TRUE, echo=TRUE, comment=NA,warning=FALSE,error=FALSE,message=FALSE} my.prior <- list( - "alpha0.prior" = c(0 , 0.0000001), - "alpha.prior" = c(0, 0.0000001), - "beta0.prior" = c(0, 0.0000001), + "alpha0.prior" = c(0 , 0.001), + "alpha.prior" = c(0, 0.001), + "beta0.prior" = c(0, 0.001), "gamma0.prior.c"= c(0, 1), "gamma.prior.c" = c(0, 0.01), "mu.b0.prior" = c(0, 0.001),