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test: adapt integration tests to latest CroptimizR version #29

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test: adapt integration tests to latest CroptimizR version #29

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56 changes: 23 additions & 33 deletions tests/testthat/test-estim_param.R
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Original file line number Diff line number Diff line change
Expand Up @@ -120,10 +120,10 @@ nlo <- lapply(nlo, function(x) {
})

test_that("Test Vignette simple_case", {
expect_equal(nlo_new[[1]]$x0, c(0.0023862966, 118.3769), tolerance = 1e-7)
expect_equal(nlo_new[[2]]$x0, c(0.0008777006, 290.9086), tolerance = 1e-7)
expect_equal(sapply(nlo_new, "[[", "solution"), sapply(nlo, "[[", "solution"), tolerance = 1e-4)
expect_equal(sapply(nlo_new, "[[", "objective"), sapply(nlo, "[[", "objective"), tolerance = 1e-4)
expect_equal(as.numeric(res$init_values[1,]), c(0.0023862966, 118.3769), tolerance = 1e-7)
expect_equal(as.numeric(res$init_values[2,]), c(0.0008777006, 290.9086), tolerance = 1e-7)
expect_equivalent(t(res$est_values), sapply(nlo, "[[", "solution"), tolerance = 1e-4)
expect_equal(res$crit_values, sapply(nlo, "[[", "objective"), tolerance = 1e-4)
expect_true(file.exists(file.path(data_dir, "EstimatedVSinit.pdf")))
expect_true(file.exists(file.path(data_dir, "ValuesVSit.pdf")))
expect_true(file.exists(file.path(data_dir, "ValuesVSit_2D.pdf")))
Expand Down Expand Up @@ -226,21 +226,16 @@ source(file.path(tmpdir, "Parameter_estimation_Specific_and_Varietal.R"))

## load the results
load(file.path(data_dir, "optim_results.Rdata"))
nlo_new <- lapply(res$nlo, function(x) {
x$call <- NULL
x
}) # remove "call" since it may change between code versions ...
res_new <- res
rm(res)
load(system.file(file.path("extdata", "ResSpecVar_2rep4it", stics_version), "optim_results.Rdata", package = "CroptimizR"))
nlo <- lapply(res$nlo, function(x) {
x$call <- NULL
x
}) # remove "call" since it may change between code versions ...
res_ref <- res

test_that("Test Vignette specific and varietal", {
expect_equal(nlo_new[[1]]$x0, c(0.001386297, 293.3769, 299.3398), tolerance = 1e-7)
expect_equal(nlo_new[[2]]$x0, c(0.001877701, 115.9086, 162.9456), tolerance = 1e-7)
expect_equal(sapply(nlo_new, "[[", "solution"), sapply(nlo, "[[", "solution"), tolerance = 1e-4)
expect_equal(sapply(nlo_new, "[[", "objective"), sapply(nlo, "[[", "objective"), tolerance = 1e-4)
expect_equal(as.numeric(res_new$init_values[1,]), c(0.001386297, 293.3769, 299.3398), tolerance = 1e-7)
expect_equal(as.numeric(res_new$init_values[2,]), c(0.001877701, 115.9086, 162.9456), tolerance = 1e-7)
expect_equal(res_new$est_values, res$est_values, tolerance = 1e-4)
expect_equal(res_new$crit_values, res$crit_values, tolerance = 1e-4)
expect_true(file.exists(file.path(data_dir, "EstimatedVSinit.pdf")))
expect_true(file.exists(file.path(data_dir, "ValuesVSit.pdf")))
expect_true(file.exists(file.path(data_dir, "ValuesVSit_2D.pdf")))
Expand Down Expand Up @@ -610,13 +605,13 @@ test_that("Test rotation", {



# Test Vignette AgMIP phase III protocol
# --------------------------------------
# Test Vignette Parameter selection
# ---------------------------------

tmpdir <- normalizePath(tempdir(), winslash = "/", mustWork = FALSE)
vignette_rmd <- file.path(tmpdir, "AgMIP_Calibration_Phenology_protocol.Rmd")
download.file(
"https://raw.github.com/SticsRPacks/CroptimizR/main/vignettes/AgMIP_Calibration_Phenology_protocol.Rmd",
"https://raw.github.com/SticsRPacks/CroptimizR/main/vignettes/Parameter_selection.Rmd",
vignette_rmd
)

Expand Down Expand Up @@ -676,7 +671,7 @@ if (Sys.getenv("CI") != "") {
## generate the R script
knitr::purl(
input = vignette_rmd,
output = file.path(tmpdir, "AgMIP_Calibration_Phenology_protocol.R"), documentation = 2
output = file.path(tmpdir, "Parameter_selection.R"), documentation = 2
)

## Seems that optim_options and optim_results.Rdata are not overwritten => try to remove them before run
Expand All @@ -686,19 +681,14 @@ if (file.exists(file.path(data_dir, "optim_results.Rdata"))) {
rm(optim_options, param_info)

## run it
source(file.path(tmpdir, "AgMIP_Calibration_Phenology_protocol.R"))
source(file.path(tmpdir, "Parameter_selection.R"))

## load the results
load(file.path(data_dir, "optim_results.Rdata"))
nlo_new <- lapply(res$nlo, function(x) {
x$call <- NULL
x
}) # remove "call" since it may change between code versions ...
res_new <- res
rm(res)
load(system.file(file.path("extdata", "ResAgmipPheno_2rep4it", stics_version), "optim_results.Rdata", package = "CroptimizR"))
nlo <- lapply(res$nlo, function(x) {
x$call <- NULL
x
}) # remove "call" since it may change between code versions ...
res_ref <- res

test_that("Test Vignette AgMIP Phase III protocol", {
expect_equal(optim_options$nb_rep, 2)
Expand All @@ -713,10 +703,10 @@ test_that("Test Vignette AgMIP Phase III protocol", {
tdmax = c(30.67603, 27.26267)
)
)
expect_equal(nlo_new[[1]]$x0, c(138.2656, 506.3340), tolerance = 1e-4)
expect_equal(nlo_new[[2]]$x0, c(446.0060, 639.4217), tolerance = 1e-4)
expect_equal(sapply(nlo_new, "[[", "solution"), sapply(nlo, "[[", "solution"), tolerance = 1e-4)
expect_equal(sapply(nlo_new, "[[", "objective"), sapply(nlo, "[[", "objective"), tolerance = 1e-4)
expect_equal(as.numeric(res_new$init_values[1,]), c(138.2656, 506.3340), tolerance = 1e-4)
expect_equal(as.numeric(res_new$init_values[2,]), c(446.0060, 639.4217), tolerance = 1e-4)
expect_equal(res_new$est_values, res$est_values, tolerance = 1e-4)
expect_equal(res_new$crit_values, res$crit_values, tolerance = 1e-4)
expect_true(file.exists(file.path(data_dir, "param_selection_steps.csv")))
for (i in 1:4) {
expect_true(file.exists(file.path(data_dir, paste0("param_select_step", i), "optim_results.Rdata")))
Expand Down
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