From 33627abc07551b3284779d874fd082b7899db206 Mon Sep 17 00:00:00 2001
From: Matthew Carroll <28577806+MJC598@users.noreply.github.com>
Date: Wed, 3 Dec 2025 11:21:47 -0500
Subject: [PATCH 1/3] adding lintr and air

---
 Syndemics/.lintr                         |  31 +++++
 Syndemics/R/buildLifeTables.R            | 168 +++++++++++++---------
 Syndemics/R/compare_moud.R               | 128 +++++++++--------
 Syndemics/R/compare_oud.R                | 132 ++++++++++--------
 Syndemics/R/crc.R                        | 163 ++++++++++++----------
 Syndemics/R/fetch_sas.R                  |  38 +++--
 Syndemics/R/internal_crcTools.R          | 168 +++++++++++++---------
 Syndemics/R/loadOutputFiles.R            |  35 +++--
 Syndemics/R/residential_admissions.R     |  63 +++++----
 Syndemics/R/respond_inputManipulations.R | 170 ++++++++++++++---------
 Syndemics/air.toml                       |  11 ++
 11 files changed, 661 insertions(+), 446 deletions(-)
 create mode 100644 Syndemics/.lintr
 create mode 100644 Syndemics/air.toml

diff --git a/Syndemics/.lintr b/Syndemics/.lintr
new file mode 100644
index 0000000..36a9512
--- /dev/null
+++ b/Syndemics/.lintr
@@ -0,0 +1,31 @@
+linters: all_linters(
+    assignment_linter = assignment_linter(operator = c("<-"), allow_trailing = FALSE),
+    backport_linter = backport_linter("4.0.0"),
+    brace_linter = brace_linter(allow_single_line = TRUE),
+    indentation_linter = indentation_linter(indent = 4L),
+    line_length_linter = line_length_linter(length = 80L),
+    object_name_linter = object_name_linter(styles = c("snake_case", "lowercase", "SNAKE_CASE")),
+    return_linter = return_linter(return_style = "explicit", allow_implicit_else = FALSE),
+    cyclocomp_linter = cyclocomp_linter(complexity_limit = 10L),
+    pipe_consistency_linter = pipe_consistency_linter("auto"),
+    unused_import_linter = unused_import_linter(interpret_glue = TRUE),
+    undesirable_function_linter = undesirable_function_linter(
+        fun = modify_defaults(
+            defaults = default_undesirable_functions,
+            source = NULL,
+            library = NULL,
+            require = NULL)),
+    object_usage_linter = NULL, # This doesn't work well with dplyr
+    condition_call_linter = NULL,
+    condition_message_linter = NULL,
+    consecutive_mutate_linter = NULL,
+    expect_identical_linter = NULL,
+    implicit_integer_linter = NULL,
+    library_call_linter = NULL,
+    literal_coercion_linter = NULL,
+    print_linter = NULL, # This one is the opposite of our style guide
+    sample_int_linter = NULL, # I disagree with this one in terms of clarity
+    strings_as_factors_linter = NULL, # Not relevant given > R 4.0.0
+    unnecessary_placeholder_linter = NULL # I disagree with the style
+    )
+exclusions: list()
diff --git a/Syndemics/R/buildLifeTables.R b/Syndemics/R/buildLifeTables.R
index cd801d1..a0c5397 100644
--- a/Syndemics/R/buildLifeTables.R
+++ b/Syndemics/R/buildLifeTables.R
@@ -14,21 +14,31 @@
 #' @importFrom utils write.csv
 #' @export
 
-build_background_mortality_file <- function(files,
-                                            outputfile,
-                                            races = c("black", "hispanic", "white"),
-                                            sexes = c("female", "male"),
-                                            age_groups = c("1_20", "21_40", "41_60", "61_80", "81_100"),
-                                            bin_size = 20) {
-
-  background_mortality <- lapply(files, extract_background_mortality,
-                                 bin_size = bin_size, age_groups = age_groups)
-  result_table <- create_and_fill_table(background_mortality, races, sexes, age_groups)
-  if (!missing(outputfile)) {
-    write.csv(result_table, outputfile, row.names = FALSE)
-  }
-
-  return(result_table)
+build_background_mortality_file <- function(
+    files,
+    outputfile,
+    races = c("black", "hispanic", "white"),
+    sexes = c("female", "male"),
+    age_groups = c("1_20", "21_40", "41_60", "61_80", "81_100"),
+    bin_size = 20
+) {
+    background_mortality <- lapply(
+        files,
+        extract_background_mortality,
+        bin_size = bin_size,
+        age_groups = age_groups
+    )
+    result_table <- create_and_fill_table(
+        background_mortality,
+        races,
+        sexes,
+        age_groups
+    )
+    if (!missing(outputfile)) {
+        write.csv(result_table, outputfile, row.names = FALSE)
+    }
+
+    return(result_table)
 }
 
 #' Function used to extract background mortality values based on age from a single yearly CDC NVSS life table
@@ -41,33 +51,48 @@ build_background_mortality_file <- function(files,
 #' @importFrom readxl read_excel
 #' @keywords internal
 
-extract_background_mortality <- function(file_path, bin_size = 20, age_groups = c("1_20", "21_40", "41_60", "61_80", "81_100")) {
-  data <- readxl::read_excel(file_path, skip = 1)
-  dt <- as.data.table(data)[(2:101)]
-
-  # Rename columns to standard names
-  setnames(dt, "Probability of dying between ages x and x + 1", "year_prob", skip_absent = TRUE)
-  setnames(dt, "Number dying between ages x and x + 1", "year_deaths", skip_absent = TRUE)
-  
-  #Data table bindings
-  year_prob <- year_deaths <- V1 <- NULL
-
-  dt[, year_prob := as.numeric(year_prob)
-     ][, year_deaths := as.numeric(year_deaths)]
-
-  bin_groups <- (seq(nrow(dt)) - 1) %/% bin_size
-  deaths_by_group <- dt[, sum(year_deaths), by = bin_groups][, V1]
-
-  # 100k originates from the CDC NVSS data - reported in rates per 100,000 persons
-  weekly_rates <- (deaths_by_group / 100000) / 52
-  weekly_probs <- 1 - exp(-weekly_rates)
-
-  result <- data.table(
-    agegrp = age_groups,
-    weekly_probability = weekly_probs
-  )
-
-  return(result)
+extract_background_mortality <- function(
+    file_path,
+    bin_size = 20,
+    age_groups = c("1_20", "21_40", "41_60", "61_80", "81_100")
+) {
+    data <- readxl::read_excel(file_path, skip = 1)
+    dt <- as.data.table(data)[(2:101)]
+
+    # Rename columns to standard names
+    setnames(
+        dt,
+        "Probability of dying between ages x and x + 1",
+        "year_prob",
+        skip_absent = TRUE
+    )
+    setnames(
+        dt,
+        "Number dying between ages x and x + 1",
+        "year_deaths",
+        skip_absent = TRUE
+    )
+
+    #Data table bindings
+    year_prob <- year_deaths <- V1 <- NULL
+
+    dt[, year_prob := as.numeric(year_prob)][,
+        year_deaths := as.numeric(year_deaths)
+    ]
+
+    bin_groups <- (seq(nrow(dt)) - 1) %/% bin_size
+    deaths_by_group <- dt[, sum(year_deaths), by = bin_groups][, V1]
+
+    # 100k originates from the CDC NVSS data - reported in rates per 100,000 persons
+    weekly_rates <- (deaths_by_group / 100000) / 52
+    weekly_probs <- 1 - exp(-weekly_rates)
+
+    result <- data.table(
+        agegrp = age_groups,
+        weekly_probability = weekly_probs
+    )
+
+    return(result)
 }
 
 #' Create and fill the table with mortality values for all demographic combinations
@@ -80,29 +105,38 @@ extract_background_mortality <- function(file_path, bin_size = 20, age_groups =
 #' @import data.table
 #' @keywords internal
 
-create_and_fill_table <- function(background_mortality,
-                                  races = c("black", "hispanic", "white"),
-                                  sexes = c("female", "male"),
-                                  age_groups = c("1_20", "21_40", "41_60", "61_80", "81_100")) {
-  #Data table bindings
-  agegrp <- NULL
-  
-  combinations <- expand.grid(races = races, sexes = sexes, stringsAsFactors = FALSE)
-  combinations <- as.data.table(combinations)
-  result_table <- combinations[rep(seq_len(nrow(combinations)), each = length(age_groups))]
-  result_table[, agegrp := rep(age_groups, times = nrow(combinations))]
-  n_race_sex_combos <- length(races) * length(sexes)
-
-  mortality_data <- data.table()
-  for (i in seq_along(background_mortality)) {
-    group_index <- ((i - 1) %% n_race_sex_combos) + 1
-    bg_mort <- background_mortality[[i]]
-    demo_info <- combinations[group_index]
-    mortality_group <- cbind(demo_info[rep(1, nrow(bg_mort))], bg_mort)
-    mortality_data <- rbind(mortality_data, mortality_group)
-  }
-
-  setorder(mortality_data, races, sexes, agegrp)
-
-  return(mortality_data)
+create_and_fill_table <- function(
+    background_mortality,
+    races = c("black", "hispanic", "white"),
+    sexes = c("female", "male"),
+    age_groups = c("1_20", "21_40", "41_60", "61_80", "81_100")
+) {
+    #Data table bindings
+    agegrp <- NULL
+
+    combinations <- expand.grid(
+        races = races,
+        sexes = sexes,
+        stringsAsFactors = FALSE
+    )
+    combinations <- as.data.table(combinations)
+    result_table <- combinations[rep(
+        seq_len(nrow(combinations)),
+        each = length(age_groups)
+    )]
+    result_table[, agegrp := rep(age_groups, times = nrow(combinations))]
+    n_race_sex_combos <- length(races) * length(sexes)
+
+    mortality_data <- data.table()
+    for (i in seq_along(background_mortality)) {
+        group_index <- ((i - 1) %% n_race_sex_combos) + 1
+        bg_mort <- background_mortality[[i]]
+        demo_info <- combinations[group_index]
+        mortality_group <- cbind(demo_info[rep(1, nrow(bg_mort))], bg_mort)
+        mortality_data <- rbind(mortality_data, mortality_group)
+    }
+
+    setorder(mortality_data, races, sexes, agegrp)
+
+    return(mortality_data)
 }
diff --git a/Syndemics/R/compare_moud.R b/Syndemics/R/compare_moud.R
index a634512..472fa20 100644
--- a/Syndemics/R/compare_moud.R
+++ b/Syndemics/R/compare_moud.R
@@ -23,71 +23,87 @@
 #' @export
 
 compare_moud <- function(old_path, new_path) {
-  N_ID <- treatment <- new_count <- old_count <- difference <- NULL
+    N_ID <- treatment <- new_count <- old_count <- difference <- NULL
 
-  # read and label the datasets
-  old <- read.csv(old_path, stringsAsFactors = FALSE)
-  new <- read.csv(new_path, stringsAsFactors = FALSE)
+    # read and label the datasets
+    old <- read.csv(old_path, stringsAsFactors = FALSE)
+    new <- read.csv(new_path, stringsAsFactors = FALSE)
 
-  old_df <- old %>%
-    dplyr::mutate(version = "Old")
-  new_df <- new %>%
-    dplyr::mutate(version = "New")
+    old_df <- old %>%
+        dplyr::mutate(version = "Old")
+    new_df <- new %>%
+        dplyr::mutate(version = "New")
 
-  # combine datasets and add date
-  combined <- dplyr::bind_rows(old_df, new_df) %>%
-  dplyr::mutate(date = as.Date(paste(year, month, "01", sep = "-")))
+    # combine datasets and add date
+    combined <- dplyr::bind_rows(old_df, new_df) %>%
+        dplyr::mutate(date = as.Date(paste(year, month, "01", sep = "-")))
 
-
-  # plot 1: time series of MOUD counts by treatment
-  count_plot <- ggplot2::ggplot(combined, ggplot2::aes(x = date, y = N_ID, color = version, linetype = version)) +
-    ggplot2::geom_line(linewidth = 1) +
-    ggplot2::facet_wrap(~ treatment, scales = "free_y") +
-    ggplot2::labs(
-      title = "Monthly MOUD Counts by Treatment Type: Old vs New Dataset",
-      x = "Date",
-      y = "MOUD Count",
-      color = "Version",
-      linetype = "Version"
+    # plot 1: time series of MOUD counts by treatment
+    count_plot <- ggplot2::ggplot(
+        combined,
+        ggplot2::aes(x = date, y = N_ID, color = version, linetype = version)
     ) +
-    ggplot2::scale_color_manual(values = c("Old" = "grey", "New" = "purple")) +
-    ggplot2::theme_minimal() +
-    ggplot2::theme(
-      legend.position = "top",
-      axis.text.x = ggplot2::element_text(angle = 45, hjust = 1)
-    )
-
-  # prepare difference dataset
-  old_df2 <- old %>%
-    dplyr::select(treatment, month, year, N_ID) %>%
-    dplyr::rename(old_count = N_ID)
+        ggplot2::geom_line(linewidth = 1) +
+        ggplot2::facet_wrap(~treatment, scales = "free_y") +
+        ggplot2::labs(
+            title = "Monthly MOUD Counts by Treatment Type: Old vs New Dataset",
+            x = "Date",
+            y = "MOUD Count",
+            color = "Version",
+            linetype = "Version"
+        ) +
+        ggplot2::scale_color_manual(
+            values = c("Old" = "grey", "New" = "purple")
+        ) +
+        ggplot2::theme_minimal() +
+        ggplot2::theme(
+            legend.position = "top",
+            axis.text.x = ggplot2::element_text(angle = 45, hjust = 1)
+        )
 
-  new_df2 <- new %>%
-    dplyr::select(treatment, month, year, N_ID) %>%
-    dplyr::rename(new_count = N_ID)
+    # prepare difference dataset
+    old_df2 <- old %>%
+        dplyr::select(treatment, month, year, N_ID) %>%
+        dplyr::rename(old_count = N_ID)
 
-  diff_df <- dplyr::left_join(old_df2, new_df2, by = c("treatment", "month", "year")) %>%
-    dplyr::mutate(
-      difference = new_count - old_count,
-      date = as.Date(paste(year, month, "01", sep = "-"))
-    )
+    new_df2 <- new %>%
+        dplyr::select(treatment, month, year, N_ID) %>%
+        dplyr::rename(new_count = N_ID)
 
+    diff_df <- dplyr::left_join(
+        old_df2,
+        new_df2,
+        by = c("treatment", "month", "year")
+    ) %>%
+        dplyr::mutate(
+            difference = new_count - old_count,
+            date = as.Date(paste(year, month, "01", sep = "-"))
+        )
 
-  # plot 2: difference in MOUD counts
-  difference_plot <- ggplot2::ggplot(diff_df, ggplot2::aes(x = date, y = difference, fill = difference > 0)) +
-    ggplot2::geom_col(show.legend = FALSE) +
-    ggplot2::facet_wrap(~ treatment, scales = "free_y") +
-    ggplot2::scale_fill_manual(values = c("TRUE" = "darkgreen", "FALSE" = "firebrick")) +
-    ggplot2::geom_hline(yintercept = 0, linetype = "dashed") +
-    ggplot2::labs(
-      title = "Change in MOUD Counts by Treatment Type: New vs Old",
-      x = "Date",
-      y = "Difference in MOUD Count (New vs Old)"
+    # plot 2: difference in MOUD counts
+    difference_plot <- ggplot2::ggplot(
+        diff_df,
+        ggplot2::aes(x = date, y = difference, fill = difference > 0)
     ) +
-    ggplot2::theme_minimal() +
-    ggplot2::theme(
-      axis.text.x = ggplot2::element_text(angle = 45, hjust = 1)
-    )
+        ggplot2::geom_col(show.legend = FALSE) +
+        ggplot2::facet_wrap(~treatment, scales = "free_y") +
+        ggplot2::scale_fill_manual(
+            values = c("TRUE" = "darkgreen", "FALSE" = "firebrick")
+        ) +
+        ggplot2::geom_hline(yintercept = 0, linetype = "dashed") +
+        ggplot2::labs(
+            title = "Change in MOUD Counts by Treatment Type: New vs Old",
+            x = "Date",
+            y = "Difference in MOUD Count (New vs Old)"
+        ) +
+        ggplot2::theme_minimal() +
+        ggplot2::theme(
+            axis.text.x = ggplot2::element_text(angle = 45, hjust = 1)
+        )
 
-  return(list(count_plot = count_plot, difference_plot = difference_plot, difference_data = diff_df))
+    return(list(
+        count_plot = count_plot,
+        difference_plot = difference_plot,
+        difference_data = diff_df
+    ))
 }
diff --git a/Syndemics/R/compare_oud.R b/Syndemics/R/compare_oud.R
index fd47db0..2072837 100644
--- a/Syndemics/R/compare_oud.R
+++ b/Syndemics/R/compare_oud.R
@@ -11,16 +11,16 @@
 #' @importFrom data.table fread rbindlist
 #' @export
 combine_files <- function(path) {
-  source_file <- NULL
-  files <- list.files(path, full.names = TRUE)
-  rbindlist(
-    lapply(files, function(f) {
-      d <- fread(f)
-      d[, source_file := basename(f)]
-      d
-    }),
-    fill = TRUE
-  )
+    source_file <- NULL
+    files <- list.files(path, full.names = TRUE)
+    rbindlist(
+        lapply(files, function(f) {
+            d <- fread(f)
+            d[, source_file := basename(f)]
+            d
+        }),
+        fill = TRUE
+    )
 }
 
 #' Plot OUD Counts Over Time
@@ -36,22 +36,27 @@ combine_files <- function(path) {
 #' @importFrom scales label_comma
 #' @export
 time_trends <- function(data) {
-  N_ID <- source_file <- total <- NULL
-  yearly_totals <- data[, list(total = sum(N_ID, na.rm = TRUE)), by = c(year, source_file)]
+    N_ID <- source_file <- total <- NULL
+    yearly_totals <- data[,
+        list(total = sum(N_ID, na.rm = TRUE)),
+        by = c(year, source_file)
+    ]
 
-  p <- ggplot(yearly_totals, aes(x = year, y = total, color = source_file)) +
-    geom_line(size = 1) +
-    geom_point(size = 2) +
-    labs(title = "OUD Counts Over Time",
-         x = "Year",
-         y = "Total Count",
-         color = "Data Source") +
-    scale_y_continuous(labels = scales::label_comma()) +
-    theme_minimal() +
-    theme(legend.position = "bottom")
+    p <- ggplot(yearly_totals, aes(x = year, y = total, color = source_file)) +
+        geom_line(size = 1) +
+        geom_point(size = 2) +
+        labs(
+            title = "OUD Counts Over Time",
+            x = "Year",
+            y = "Total Count",
+            color = "Data Source"
+        ) +
+        scale_y_continuous(labels = scales::label_comma()) +
+        theme_minimal() +
+        theme(legend.position = "bottom")
 
-  print(p)
-  return(p)
+    print(p)
+    return(p)
 }
 
 #' Compare Annual OUD Counts Across Files
@@ -66,26 +71,33 @@ time_trends <- function(data) {
 #' @importFrom data.table dcast
 #' @export
 compare_by_year <- function(data) {
-  N_ID <- total <- source_file <- NULL
-  yearly_totals <- data[, list(total = sum(N_ID, na.rm = TRUE)), by = c(year, source_file)]
-  comparison_table <- dcast(yearly_totals, year ~ source_file, value.var = "total")
-  print(comparison_table)
-  return(comparison_table)
+    N_ID <- total <- source_file <- NULL
+    yearly_totals <- data[,
+        list(total = sum(N_ID, na.rm = TRUE)),
+        by = c(year, source_file)
+    ]
+    comparison_table <- dcast(
+        yearly_totals,
+        year ~ source_file,
+        value.var = "total"
+    )
+    print(comparison_table)
+    return(comparison_table)
 }
 #' Filter OUD Data by Source File Pattern
 #'
 #' Extracts rows from the dataset where the source_file column matches a specified pattern.
 #'
 #' @param data A \code{data.table} containing a \code{source_file} column.
-#' @param pattern A character string containing a regular expression pattern to match 
+#' @param pattern A character string containing a regular expression pattern to match
 #'   against the \code{source_file} column.
 #' @param ignore_case Logical; if TRUE, pattern matching is case-insensitive. Default is TRUE.
 #'
 #' @return A filtered \code{data.table} containing only rows where source_file matches the pattern.
 #' @export
 get_filtered_data <- function(data, pattern, ignore_case = TRUE) {
-  source_file <- NULL
-  return(data[grepl(pattern, source_file, ignore.case = ignore_case)])
+    source_file <- NULL
+    return(data[grepl(pattern, source_file, ignore.case = ignore_case)])
 }
 
 #' Plot OUD Counts by Demographic Category
@@ -104,23 +116,23 @@ get_filtered_data <- function(data, pattern, ignore_case = TRUE) {
 #' @importFrom scales label_comma
 #' @export
 plot_oud_data <- function(data, group_col, labels, title, legend_title) {
-  N_ID <- total <- group_name <- NULL
-  totals <- data[, list(total = sum(N_ID, na.rm = TRUE)), by = c("year", group_col)]
-  totals$group_name <- labels[as.character(totals[[group_col]])]
-  
-  p <- ggplot(totals, aes(x = year, y = total, color = group_name)) +
-    geom_line(size = 1) +
-    geom_point(size = 2) +
-    labs(title = title,
-         x = "Year",
-         y = "Count",
-         color = legend_title) +
-    scale_y_continuous(labels = scales::label_comma()) +
-    theme_minimal() +
-    theme(legend.position = "bottom")
-  
-  print(p)
-  return(p)
+    N_ID <- total <- group_name <- NULL
+    totals <- data[,
+        list(total = sum(N_ID, na.rm = TRUE)),
+        by = c("year", group_col)
+    ]
+    totals$group_name <- labels[as.character(totals[[group_col]])]
+
+    p <- ggplot(totals, aes(x = year, y = total, color = group_name)) +
+        geom_line(size = 1) +
+        geom_point(size = 2) +
+        labs(title = title, x = "Year", y = "Count", color = legend_title) +
+        scale_y_continuous(labels = scales::label_comma()) +
+        theme_minimal() +
+        theme(legend.position = "bottom")
+
+    print(p)
+    return(p)
 }
 
 #' Histogram of OUD Counts
@@ -135,15 +147,17 @@ plot_oud_data <- function(data, group_col, labels, title, legend_title) {
 #' @importFrom scales label_comma
 #' @export
 histogram <- function(data) {
-  N_ID <- NULL
-  p <- ggplot(data, aes(x = N_ID)) +
-    geom_histogram(bins = 30, fill = "lightblue", color = "black") +
-    labs(title = "Distribution of OUD Counts",
-         x = "Count",
-         y = "Frequency") +
-    scale_y_continuous(labels = scales::label_comma()) +
-    theme_minimal()
+    N_ID <- NULL
+    p <- ggplot(data, aes(x = N_ID)) +
+        geom_histogram(bins = 30, fill = "lightblue", color = "black") +
+        labs(
+            title = "Distribution of OUD Counts",
+            x = "Count",
+            y = "Frequency"
+        ) +
+        scale_y_continuous(labels = scales::label_comma()) +
+        theme_minimal()
 
-  print(p)
-  return(p)
+    print(p)
+    return(p)
 }
diff --git a/Syndemics/R/crc.R b/Syndemics/R/crc.R
index 540a706..1291eea 100644
--- a/Syndemics/R/crc.R
+++ b/Syndemics/R/crc.R
@@ -17,87 +17,108 @@
 #' @importFrom stats AIC coef confint formula glm poisson
 #' @export
 
-crc <- function(data, freq.column, binary.variables, method = "poisson", formula.selection = "stepwise", formula = NULL,
-                opts.stepwise = list(
-                  direction = "both",
-                  threshold = 0.05,
-                  verbose = TRUE
-                )) {
-  if (!(method %in% c("poisson", "negbin"))) {
-    stop("Method must be either 'poisson' or 'negbin'")
-  }
-
-  if (!(formula.selection %in% c("aic", "stepwise"))) {
-    stop("Formula selection must be either 'aic' or 'stepwise'")
-  }
-
-  dt <- setDT(data)
+crc <- function(
+    data,
+    freq.column,
+    binary.variables,
+    method = "poisson",
+    formula.selection = "stepwise",
+    formula = NULL,
+    opts.stepwise = list(
+        direction = "both",
+        threshold = 0.05,
+        verbose = TRUE
+    )
+) {
+    if (!(method %in% c("poisson", "negbin"))) {
+        stop("Method must be either 'poisson' or 'negbin'")
+    }
 
-  if (is.null(formula)) {
-    if (formula.selection == "aic") {
-      form <- formula_list(freq.column, binary.variables)
-    } else if (formula.selection == "stepwise") {
-      form <- NULL
+    if (!(formula.selection %in% c("aic", "stepwise"))) {
+        stop("Formula selection must be either 'aic' or 'stepwise'")
     }
-  } else if (!is.formula(formula)) {
-    stop("Expected Formula Object when Specifying Formula")
-  } else {
-    form <- formula
-  }
 
-  if (formula.selection == "aic") {
-    results <- list()
+    dt <- setDT(data)
 
-    for (i in seq_along(form)) {
-      result <- tryCatch({
-        if (method == "poisson") {
-          model <- stats::glm(form[[i]], data = dt, family = "poisson")
-        } else {
-          model <- MASS::glm.nb(formula = form[[i]], data = dt)
+    if (is.null(formula)) {
+        if (formula.selection == "aic") {
+            form <- formula_list(freq.column, binary.variables)
+        } else if (formula.selection == "stepwise") {
+            form <- NULL
         }
+    } else if (!is.formula(formula)) {
+        stop("Expected Formula Object when Specifying Formula")
+    } else {
+        form <- formula
+    }
 
-        intercept <- exp(stats::coef(model)["(Intercept)"])
-        aic <- stats::AIC(model)
+    if (formula.selection == "aic") {
+        results <- list()
 
-        ci <- suppressMessages(stats::confint(model, "(Intercept)", level = 0.95))
-        lower_ci <- exp(ci[1])
-        upper_ci <- exp(ci[2])
+        for (i in seq_along(form)) {
+            result <- tryCatch(
+                {
+                    if (method == "poisson") {
+                        model <- stats::glm(
+                            form[[i]],
+                            data = dt,
+                            family = "poisson"
+                        )
+                    } else {
+                        model <- MASS::glm.nb(formula = form[[i]], data = dt)
+                    }
 
-        data.frame(
-          formula = paste(deparse(form[[i]]), collapse = " "),
-          estimate = round(intercept, 2),
-          AIC = round(aic, 2),
-          lower_ci = unname(round(lower_ci, 2)),
-          upper_ci = unname(round(upper_ci, 2)),
-          error = NA,
-          row.names = NULL
-        )
-      }, error = function(e) {
-        data.frame(
-          formula = paste(deparse(form[[i]]), collapse = " "),
-          estimate = NA,
-          AIC = NA,
-          lower_ci = NA,
-          upper_ci = NA,
-          error = toString(e$message),
-          row.names = NULL
-        )
-      })
+                    intercept <- exp(stats::coef(model)["(Intercept)"])
+                    aic <- stats::AIC(model)
 
-      results[[i]] <- result
-    }
+                    ci <- suppressMessages(stats::confint(
+                        model,
+                        "(Intercept)",
+                        level = 0.95
+                    ))
+                    lower_ci <- exp(ci[1])
+                    upper_ci <- exp(ci[2])
 
-    model <- do.call(rbind, results)
-    model <- model[order(model$AIC), ]
+                    data.frame(
+                        formula = paste(deparse(form[[i]]), collapse = " "),
+                        estimate = round(intercept, 2),
+                        AIC = round(aic, 2),
+                        lower_ci = unname(round(lower_ci, 2)),
+                        upper_ci = unname(round(upper_ci, 2)),
+                        error = NA,
+                        row.names = NULL
+                    )
+                },
+                error = function(e) {
+                    data.frame(
+                        formula = paste(deparse(form[[i]]), collapse = " "),
+                        estimate = NA,
+                        AIC = NA,
+                        lower_ci = NA,
+                        upper_ci = NA,
+                        error = toString(e$message),
+                        row.names = NULL
+                    )
+                }
+            )
+
+            results[[i]] <- result
+        }
 
-  } else if (formula.selection == "stepwise") {
-    model <- step_regression(data, freq.column, binary.variables,
-                             p.threshold = opts.stepwise$threshold,
-                             direction = opts.stepwise$direction,
-                             method = method,
-                             verbose = opts.stepwise$verbose,
-                             k = 2)
-  }
+        model <- do.call(rbind, results)
+        model <- model[order(model$AIC), ]
+    } else if (formula.selection == "stepwise") {
+        model <- step_regression(
+            data,
+            freq.column,
+            binary.variables,
+            p.threshold = opts.stepwise$threshold,
+            direction = opts.stepwise$direction,
+            method = method,
+            verbose = opts.stepwise$verbose,
+            k = 2
+        )
+    }
 
-  return(model)
+    return(model)
 }
diff --git a/Syndemics/R/fetch_sas.R b/Syndemics/R/fetch_sas.R
index f7d725f..abbeec3 100644
--- a/Syndemics/R/fetch_sas.R
+++ b/Syndemics/R/fetch_sas.R
@@ -4,17 +4,33 @@
 #' @importFrom httr GET stop_for_status content config
 #'
 #' @export
-fetch_sas <- function(){
-  if(!dir.exists("SAS")) dir.create("SAS")
-  req <- httr::GET("https://api.github.com/repos/SyndemicsLab/PHD/git/trees/main?recursive=1")
-  httr::stop_for_status(req)
+fetch_sas <- function() {
+    if (!dir.exists("SAS")) {
+        dir.create("SAS")
+    }
+    req <- httr::GET(
+        "https://api.github.com/repos/SyndemicsLab/PHD/git/trees/main?recursive=1"
+    )
+    httr::stop_for_status(req)
 
-  file_list <- grep(".sas", unlist(lapply(httr::content(req)$tree, "[", "path"), use.names = FALSE),
-                    value = TRUE, fixed = TRUE)
+    file_list <- grep(
+        ".sas",
+        unlist(lapply(httr::content(req)$tree, "[", "path"), use.names = FALSE),
+        value = TRUE,
+        fixed = TRUE
+    )
 
-  for(i in seq_along(file_list)){
-    response <- httr::GET(paste0("https://raw.githubusercontent.com/SyndemicsLab/PHD/main/", file_list[i]),
-                    config = config(ssl_verifypeer = FALSE))
-    writeBin(content(response, "raw"), paste0("SAS/", gsub(".*/", "", file_list[i])))
-  }
+    for (i in seq_along(file_list)) {
+        response <- httr::GET(
+            paste0(
+                "https://raw.githubusercontent.com/SyndemicsLab/PHD/main/",
+                file_list[i]
+            ),
+            config = config(ssl_verifypeer = FALSE)
+        )
+        writeBin(
+            content(response, "raw"),
+            paste0("SAS/", gsub(".*/", "", file_list[i]))
+        )
+    }
 }
diff --git a/Syndemics/R/internal_crcTools.R b/Syndemics/R/internal_crcTools.R
index b7df361..ed4567f 100644
--- a/Syndemics/R/internal_crcTools.R
+++ b/Syndemics/R/internal_crcTools.R
@@ -5,8 +5,8 @@
 #'
 #' @export
 
-is.formula <- function(x){
-  inherits(x, "formula")
+is.formula <- function(x) {
+    inherits(x, "formula")
 }
 
 #' Generates All Possible Combination of Interaction Terms
@@ -20,33 +20,45 @@ is.formula <- function(x){
 #' @export
 
 formula_list <- function(y, x) {
-  n <- length(x)
-  all_formulas <- list()
-
-  for (i in 1:n) {
-    all_formulas <- c(all_formulas, paste0(y, "~", x[i]))
-  }
-
-  for (i in 2:n) {
-    combinations <- combn(x, i)
-    for (j in 1:ncol(combinations)) {
-      combination <- combinations[,j]
-
-      all_formulas <- c(all_formulas, paste0(y, "~", paste(combination, collapse="+")))
-      interaction_formula <- paste(combination, collapse="*")
-      all_formulas <- c(all_formulas, paste0(y, "~", interaction_formula))
-
-      for (k in 1:(i-1)) {
-        combinations_additive <- combn(combination, k)
-        for (l in 1:ncol(combinations_additive)) {
-          combination_additive <- combinations_additive[,l]
-          all_formulas <- c(all_formulas, paste0(y, "~", paste(combination_additive, collapse="+"), "+", interaction_formula))
+    n <- length(x)
+    all_formulas <- list()
+
+    for (i in 1:n) {
+        all_formulas <- c(all_formulas, paste0(y, "~", x[i]))
+    }
+
+    for (i in 2:n) {
+        combinations <- combn(x, i)
+        for (j in 1:ncol(combinations)) {
+            combination <- combinations[, j]
+
+            all_formulas <- c(
+                all_formulas,
+                paste0(y, "~", paste(combination, collapse = "+"))
+            )
+            interaction_formula <- paste(combination, collapse = "*")
+            all_formulas <- c(all_formulas, paste0(y, "~", interaction_formula))
+
+            for (k in 1:(i - 1)) {
+                combinations_additive <- combn(combination, k)
+                for (l in 1:ncol(combinations_additive)) {
+                    combination_additive <- combinations_additive[, l]
+                    all_formulas <- c(
+                        all_formulas,
+                        paste0(
+                            y,
+                            "~",
+                            paste(combination_additive, collapse = "+"),
+                            "+",
+                            interaction_formula
+                        )
+                    )
+                }
+            }
         }
-      }
     }
-  }
 
-  return(lapply(unique(all_formulas), as.formula))
+    return(lapply(unique(all_formulas), as.formula))
 }
 
 #' Helper function for stepwise regression
@@ -64,50 +76,68 @@ formula_list <- function(y, x) {
 #' @importFrom utils capture.output
 #' @importFrom stats AIC coef confint formula glm poisson step
 
-step_regression <- function(data, y, x, method = "poisson", direction = "both",
-                            p.threshold = 0.05, k = 2, verbose = TRUE) {
-  formula_init <- as.formula(paste(y, "~", paste(x, collapse = " + ")))
-  formula_max <- as.formula(paste(y, "~ (", paste(x, collapse = " + "), ")^", k))
-
-  if (!verbose) {
-    capture.output({
-      if (method == "poisson") {
-        init_mod <- glm(formula_init, family = poisson, data = data)
-      } else {
-        init_mod <- MASS::glm.nb(formula_init, data = data)
-      }
-
-      final_mod <- suppressWarnings(step(init_mod,
-                                         scope = list(upper = formula_max, lower = formula_init),
-                                         direction = direction,
-                                         k = log(nrow(data))))
-    })
-  } else {
-    if (method == "poisson") {
-      init_mod <- glm(formula_init, family = poisson, data = data)
+step_regression <- function(
+    data,
+    y,
+    x,
+    method = "poisson",
+    direction = "both",
+    p.threshold = 0.05,
+    k = 2,
+    verbose = TRUE
+) {
+    formula_init <- as.formula(paste(y, "~", paste(x, collapse = " + ")))
+    formula_max <- as.formula(paste(
+        y,
+        "~ (",
+        paste(x, collapse = " + "),
+        ")^",
+        k
+    ))
+
+    if (!verbose) {
+        capture.output({
+            if (method == "poisson") {
+                init_mod <- glm(formula_init, family = poisson, data = data)
+            } else {
+                init_mod <- MASS::glm.nb(formula_init, data = data)
+            }
+
+            final_mod <- suppressWarnings(step(
+                init_mod,
+                scope = list(upper = formula_max, lower = formula_init),
+                direction = direction,
+                k = log(nrow(data))
+            ))
+        })
     } else {
-      init_mod <- MASS::glm.nb(formula_init, data = data)
+        if (method == "poisson") {
+            init_mod <- glm(formula_init, family = poisson, data = data)
+        } else {
+            init_mod <- MASS::glm.nb(formula_init, data = data)
+        }
+
+        final_mod <- step(
+            init_mod,
+            scope = list(upper = formula_max, lower = formula_init),
+            direction = direction,
+            k = log(nrow(data))
+        )
     }
 
-    final_mod <- step(init_mod,
-                      scope = list(upper = formula_max, lower = formula_init),
-                      direction = direction,
-                      k = log(nrow(data)))
-  }
-
-  intercept <- coef(final_mod)[1]
-  estimate <- exp(intercept)
-  ci <- exp(confint(final_mod)[1, ])
-
-  results <- list(
-    model = method,
-    formula = formula(final_mod),
-    summary = summary(final_mod),
-    estimate = unname(round(estimate, 2)),
-    lower_ci = unname(round(ci[1], 2)),
-    upper_ci = unname(round(ci[2], 2)),
-    AIC = AIC(final_mod)
-  )
-
-  return(results)
+    intercept <- coef(final_mod)[1]
+    estimate <- exp(intercept)
+    ci <- exp(confint(final_mod)[1, ])
+
+    results <- list(
+        model = method,
+        formula = formula(final_mod),
+        summary = summary(final_mod),
+        estimate = unname(round(estimate, 2)),
+        lower_ci = unname(round(ci[1], 2)),
+        upper_ci = unname(round(ci[2], 2)),
+        AIC = AIC(final_mod)
+    )
+
+    return(results)
 }
diff --git a/Syndemics/R/loadOutputFiles.R b/Syndemics/R/loadOutputFiles.R
index a0028d3..33b6529 100644
--- a/Syndemics/R/loadOutputFiles.R
+++ b/Syndemics/R/loadOutputFiles.R
@@ -24,20 +24,25 @@
 #'
 #' @export
 loadOutputFiles <- function(N, outputFileNames, pathPrefix = "") {
-  # append the trailing slash if the prefix does not already
-  if (pathPrefix != "" && !endsWith(pathPrefix, "/")) {
-    pathPrefix <- paste0(pathPrefix, "/")
-  }
-  outputNumbers <- 1:N
-  outputTables <- list()
-  # read files and store them in outputTables
-  for (index in seq_along(outputNumbers)) {
-    outputFolder <- paste0("output", index)
-    currentOutputTables <- list()
-    for (outputFile in outputFileNames) {
-      currentOutputTables[[outputFile]] <- read.csv(paste0(pathPrefix, outputFolder, "/", outputFile))
+    # append the trailing slash if the prefix does not already
+    if (pathPrefix != "" && !endsWith(pathPrefix, "/")) {
+        pathPrefix <- paste0(pathPrefix, "/")
     }
-    outputTables[[outputFolder]] <- currentOutputTables
-  }
-  return(outputTables)
+    outputNumbers <- 1:N
+    outputTables <- list()
+    # read files and store them in outputTables
+    for (index in seq_along(outputNumbers)) {
+        outputFolder <- paste0("output", index)
+        currentOutputTables <- list()
+        for (outputFile in outputFileNames) {
+            currentOutputTables[[outputFile]] <- read.csv(paste0(
+                pathPrefix,
+                outputFolder,
+                "/",
+                outputFile
+            ))
+        }
+        outputTables[[outputFolder]] <- currentOutputTables
+    }
+    return(outputTables)
 }
diff --git a/Syndemics/R/residential_admissions.R b/Syndemics/R/residential_admissions.R
index 3e83674..89be6c2 100644
--- a/Syndemics/R/residential_admissions.R
+++ b/Syndemics/R/residential_admissions.R
@@ -16,42 +16,41 @@
 #'   print(monthly_avg)
 #' }
 process_teds_year <- function(year, data_path) {
+    # Construct file path and object name
+    file_name <- paste0("tedsa_puf_", year, "_R.rdata")
+    full_path <- file.path(data_path, file_name)
+    object_name <- paste0("TEDSA_PUF_", year)
 
-  # Construct file path and object name
-  file_name <- paste0("tedsa_puf_", year, "_R.rdata")
-  full_path <- file.path(data_path, file_name)
-  object_name <- paste0("TEDSA_PUF_", year)
+    # Load data
+    load(full_path)
 
-  # Load data
-  load(full_path)
+    # Convert to tibble
+    teds <- as_tibble(get(object_name))
 
-  # Convert to tibble
-  teds <- as_tibble(get(object_name))
+    # Filter for Massachusetts
+    teds <- teds %>%
+        filter(STFIPS == 25)
 
-  # Filter for Massachusetts
-  teds <- teds %>%
-    filter(STFIPS == 25)
+    # Define strata filters (currently commented for customization)
+    # when GENDER is 2 this represents females,
+    # when RACE is 5 and ETHNIC is 4 this represents non-Hispanic White individuals,
+    # when RACE is 4 or 5 and ETHNIC is 1, 2, 3, or 5 this represents Hispanic/Latino individuals that also identify as White or African American/Black,
+    # when AGE is between 8 - 11 this represents individuals that are 40-64 years old at admission
+    # when AGE is 12 this represents individuals that are 65 years old or older at admission
+    # True is a placeholder to ensure code runs if filters are commented out
+    teds_strat <- teds %>%
+        filter(
+            TRUE
+        )
 
-  # Define strata filters (currently commented for customization)
-  # when GENDER is 2 this represents females,
-  # when RACE is 5 and ETHNIC is 4 this represents non-Hispanic White individuals,
-  # when RACE is 4 or 5 and ETHNIC is 1, 2, 3, or 5 this represents Hispanic/Latino individuals that also identify as White or African American/Black,
-  # when AGE is between 8 - 11 this represents individuals that are 40-64 years old at admission
-  # when AGE is 12 this represents individuals that are 65 years old or older at admission
-  # True is a placeholder to ensure code runs if filters are commented out
-  teds_strat <- teds %>%
-    filter(
-      TRUE
-    )
+    # Final filtering for service type, opioids, and IDU status
+    teds_final <- teds_strat %>%
+        filter(
+            SERVICES %in% c(4, 5),
+            (SUB1 %in% 5:7 | SUB2 %in% 5:7),
+            IDU == 1
+        )
 
-  # Final filtering for service type, opioids, and IDU status
-  teds_final <- teds_strat %>%
-    filter(
-      SERVICES %in% c(4, 5),
-      (SUB1 %in% 5:7 | SUB2 %in% 5:7),
-      IDU == 1
-    )
-
-  # Return monthly admissions number
-  return(nrow(teds_final) / 12)
+    # Return monthly admissions number
+    return(nrow(teds_final) / 12)
 }
diff --git a/Syndemics/R/respond_inputManipulations.R b/Syndemics/R/respond_inputManipulations.R
index 1754a35..73f54f7 100644
--- a/Syndemics/R/respond_inputManipulations.R
+++ b/Syndemics/R/respond_inputManipulations.R
@@ -6,14 +6,25 @@
 #'
 #' @import data.table
 #' @export
-DSA <- function(data, filter, cycle, pct_change){
-  data <- as.data.table(data)
-  initial_block <- NULL
-  for(c in cycle){
-    DT <- data[initial_block == filter, paste0("to_", filter, "_cycle", c) := get(paste0("to_", filter, "_cycle", c))*pct_change
-               ][, paste0("to_corresponding_post_trt_cycle", c) := 1 - get(paste0("to_", filter, "_cycle", c))]
-  }
-  return(DT)
+DSA <- function(data, filter, cycle, pct_change) {
+    data <- as.data.table(data)
+    initial_block <- NULL
+    for (c in cycle) {
+        DT <- data[
+            initial_block == filter,
+            paste0("to_", filter, "_cycle", c) := get(paste0(
+                "to_",
+                filter,
+                "_cycle",
+                c
+            )) *
+                pct_change
+        ][,
+            paste0("to_corresponding_post_trt_cycle", c) := 1 -
+                get(paste0("to_", filter, "_cycle", c))
+        ]
+    }
+    return(DT)
 }
 
 #' A function to change default age groups from RESPOND shell tables
@@ -25,48 +36,71 @@ DSA <- function(data, filter, cycle, pct_change){
 #'
 #' @import data.table
 #' @export
-change_agegrp_chunk <- function(data, size.out, transformation, cols, grouping){
-  DT <- as.data.table(data)
-  agegrp <- age <- NULL
-  age_min <- age_max <- NULL
-  if(!cols %in% names(DT)) stop("Column names in 'cols' do not match names in 'data'")
-  if(missing(grouping)) grouping <- names(DT)[!c(names(DT) %in% c(cols, "agegrp"))]
+change_agegrp_chunk <- function(
+    data,
+    size.out,
+    transformation,
+    cols,
+    grouping
+) {
+    DT <- as.data.table(data)
+    agegrp <- age <- NULL
+    age_min <- age_max <- NULL
+    if (!cols %in% names(DT)) {
+        stop("Column names in 'cols' do not match names in 'data'")
+    }
+    if (missing(grouping)) {
+        grouping <- names(DT)[!c(names(DT) %in% c(cols, "agegrp"))]
+    }
 
-  DT <- DT[, `:=` (age_min = as.integer(sub("_(.*)", "", agegrp)),
-                   age_max = as.integer(sub("^(.*?)_", "", agegrp)),
-                   agegrp = NULL)]
+    DT <- DT[, `:=`(
+        age_min = as.integer(sub("_(.*)", "", agegrp)),
+        age_max = as.integer(sub("^(.*?)_", "", agegrp)),
+        agegrp = NULL
+    )]
 
-  chunk.diffs <- unique(DT[["age_min"]] - DT[["age_max"]])
-  if(length(chunk.diffs) > 1){
-    stop("Chunk differences non-uniform")
-  } else size.in <- chunk.diffs*-1 + 1
+    chunk.diffs <- unique(DT[["age_min"]] - DT[["age_max"]])
+    if (length(chunk.diffs) > 1) {
+        stop("Chunk differences non-uniform")
+    } else {
+        size.in <- chunk.diffs * -1 + 1
+    }
 
-  # A more efficient method would be to Map(seq, age_min, age_max),
-  # although unlisting seems to be a problem.... will work on this in the future
+    # A more efficient method would be to Map(seq, age_min, age_max),
+    # although unlisting seems to be a problem.... will work on this in the future
 
-  expanded <- merge(DT, expand.grid(block = unique(DT[["block"]]),
-                                    sex = unique(DT[["sex"]]),
-                                    oud = unique(DT[["oud"]]),
-                                    age = as.integer(c(min(DT[["age_min"]]):max(DT[["age_max"]])))),
-                    by = grouping,
-                    allow.cartesian = TRUE)[age >= age_min & age <= age_max,
-                    ][, `:=` (age_min = NULL,
-                              age_max = NULL,
-                              agegrp = cut(age, seq(9, 100, size.out),
-                                           labels = paste0(seq(10, 98, size.out),
-                                                           "_",
-                                                           seq(11, 99, size.out))),
-                              age = NULL)
-                    ]
-  if(transformation == "sum"){
-    out <- expanded[, (cols) := lapply(cols, function(x) get(x)/size.in),
-    ][, (cols) := lapply(cols, function(x) sum(get(x))), by = c("agegrp", "block", "oud", "sex")]
-    return(unique(out))
-
-  } else if(transformation == "mean"){
-    out <- expanded[, (cols) := lapply(cols, function(x) mean(x))]
-    return(unique(out))
-  }
+    expanded <- merge(
+        DT,
+        expand.grid(
+            block = unique(DT[["block"]]),
+            sex = unique(DT[["sex"]]),
+            oud = unique(DT[["oud"]]),
+            age = as.integer(c(min(DT[["age_min"]]):max(DT[["age_max"]])))
+        ),
+        by = grouping,
+        allow.cartesian = TRUE
+    )[age >= age_min & age <= age_max, ][, `:=`(
+        age_min = NULL,
+        age_max = NULL,
+        agegrp = cut(
+            age,
+            seq(9, 100, size.out),
+            labels = paste0(seq(10, 98, size.out), "_", seq(11, 99, size.out))
+        ),
+        age = NULL
+    )]
+    if (transformation == "sum") {
+        out <- expanded[,
+            (cols) := lapply(cols, function(x) get(x) / size.in),
+        ][,
+            (cols) := lapply(cols, function(x) sum(get(x))),
+            by = c("agegrp", "block", "oud", "sex")
+        ]
+        return(unique(out))
+    } else if (transformation == "mean") {
+        out <- expanded[, (cols) := lapply(cols, function(x) mean(x))]
+        return(unique(out))
+    }
 }
 
 #' A function to create new blocks for RESPOND (clones 'No_Treatment' blocks and reassigns the name)
@@ -76,17 +110,19 @@ change_agegrp_chunk <- function(data, size.out, transformation, cols, grouping){
 #'
 #' @import data.table
 #' @export
-new_block <- function(data, names, column="block"){
-  if(!column %in% names(data)) stop(paste(column, "is not in original data"))
-  data <- as.data.table(data)
-  data_list <- list()
+new_block <- function(data, names, column = "block") {
+    if (!column %in% names(data)) {
+        stop(paste(column, "is not in original data"))
+    }
+    data <- as.data.table(data)
+    data_list <- list()
 
-  for(n in seq_along(names)){
-    DT <- copy(data)[get(column) == "No_Treatment", ]
-    data_list[[n]] <- DT[, (column) := rep.int(names[n], .N)]
-  }
-  out <- data.table::rbindlist(append(data_list, list(data)))
-  return(out)
+    for (n in seq_along(names)) {
+        DT <- copy(data)[get(column) == "No_Treatment", ]
+        data_list[[n]] <- DT[, (column) := rep.int(names[n], .N)]
+    }
+    out <- data.table::rbindlist(append(data_list, list(data)))
+    return(out)
 }
 
 #' A function to change values to another block; follows the format \code{data$x[column == "a", ] <- data$y[column == "b", ]}
@@ -99,15 +135,17 @@ new_block <- function(data, names, column="block"){
 #' @import data.table
 #' @export
 
-replace_vals <- function(data, column="block", x, y, a, b) {
-  if (length(a) != length(b)) {
-    stop("Vectors 'a' and 'b' must be of the same length")
-  }
-  setDT(data)
-  for (i in seq_along(a)) {
-    data[, (x) := as.numeric(get(x))
-    ][get(column) == a[i], (x) := data[get(column) == b[i], y, with = FALSE][[1]]]
-  }
+replace_vals <- function(data, column = "block", x, y, a, b) {
+    if (length(a) != length(b)) {
+        stop("Vectors 'a' and 'b' must be of the same length")
+    }
+    setDT(data)
+    for (i in seq_along(a)) {
+        data[, (x) := as.numeric(get(x))][
+            get(column) == a[i],
+            (x) := data[get(column) == b[i], y, with = FALSE][[1]]
+        ]
+    }
 
-  return(data)
+    return(data)
 }
diff --git a/Syndemics/air.toml b/Syndemics/air.toml
new file mode 100644
index 0000000..ca2605b
--- /dev/null
+++ b/Syndemics/air.toml
@@ -0,0 +1,11 @@
+[format]
+line-width = 80
+indent-width = 4
+indent-style = "space"
+line-ending = "auto"
+persistent-line-breaks = true
+exclude = []
+default-exclude = true
+skip = []
+table = []
+default-table = true
\ No newline at end of file

From 6ee30f947cf1cb23072a8a6ec6ec844df3a4a8f0 Mon Sep 17 00:00:00 2001
From: Matthew Carroll <28577806+MJC598@users.noreply.github.com>
Date: Wed, 3 Dec 2025 11:36:17 -0500
Subject: [PATCH 2/3] fixing file names and man pages

---
 Syndemics/.Rbuildignore                                         | 1 +
 Syndemics/NAMESPACE                                             | 1 +
 Syndemics/R/{buildLifeTables.R => build_life_tables.R}          | 2 +-
 Syndemics/R/{internal_crcTools.R => internal_crc_tools.R}       | 0
 Syndemics/R/{loadOutputFiles.R => load_output_files.R}          | 0
 Syndemics/R/residential_admissions.R                            | 1 +
 ...spond_inputManipulations.R => respond_input_manipulations.R} | 0
 Syndemics/man/DSA.Rd                                            | 2 +-
 Syndemics/man/Syndemics-package.Rd                              | 2 +-
 Syndemics/man/build_background_mortality_file.Rd                | 2 +-
 Syndemics/man/change_agegrp_chunk.Rd                            | 2 +-
 Syndemics/man/create_and_fill_table.Rd                          | 2 +-
 Syndemics/man/extract_background_mortality.Rd                   | 2 +-
 Syndemics/man/formula_list.Rd                                   | 2 +-
 Syndemics/man/get_filtered_data.Rd                              | 2 +-
 Syndemics/man/is.formula.Rd                                     | 2 +-
 Syndemics/man/loadOutputFiles.Rd                                | 2 +-
 Syndemics/man/new_block.Rd                                      | 2 +-
 Syndemics/man/replace_vals.Rd                                   | 2 +-
 Syndemics/man/step_regression.Rd                                | 2 +-
 20 files changed, 17 insertions(+), 14 deletions(-)
 rename Syndemics/R/{buildLifeTables.R => build_life_tables.R} (98%)
 rename Syndemics/R/{internal_crcTools.R => internal_crc_tools.R} (100%)
 rename Syndemics/R/{loadOutputFiles.R => load_output_files.R} (100%)
 rename Syndemics/R/{respond_inputManipulations.R => respond_input_manipulations.R} (100%)

diff --git a/Syndemics/.Rbuildignore b/Syndemics/.Rbuildignore
index f0b429d..617bb64 100644
--- a/Syndemics/.Rbuildignore
+++ b/Syndemics/.Rbuildignore
@@ -3,3 +3,4 @@
 ^LICENSE\.md$
 ^\.github$
 inst/data
+.air.toml
diff --git a/Syndemics/NAMESPACE b/Syndemics/NAMESPACE
index 345dde9..9c8b27c 100644
--- a/Syndemics/NAMESPACE
+++ b/Syndemics/NAMESPACE
@@ -31,6 +31,7 @@ importFrom(data.table,dcast)
 importFrom(data.table,fread)
 importFrom(data.table,rbindlist)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,rename)
diff --git a/Syndemics/R/buildLifeTables.R b/Syndemics/R/build_life_tables.R
similarity index 98%
rename from Syndemics/R/buildLifeTables.R
rename to Syndemics/R/build_life_tables.R
index a0c5397..6426b08 100644
--- a/Syndemics/R/buildLifeTables.R
+++ b/Syndemics/R/build_life_tables.R
@@ -80,7 +80,7 @@ extract_background_mortality <- function(
         year_deaths := as.numeric(year_deaths)
     ]
 
-    bin_groups <- (seq(nrow(dt)) - 1) %/% bin_size
+    bin_groups <- (seq_len(nrow(dt)) - 1) %/% bin_size
     deaths_by_group <- dt[, sum(year_deaths), by = bin_groups][, V1]
 
     # 100k originates from the CDC NVSS data - reported in rates per 100,000 persons
diff --git a/Syndemics/R/internal_crcTools.R b/Syndemics/R/internal_crc_tools.R
similarity index 100%
rename from Syndemics/R/internal_crcTools.R
rename to Syndemics/R/internal_crc_tools.R
diff --git a/Syndemics/R/loadOutputFiles.R b/Syndemics/R/load_output_files.R
similarity index 100%
rename from Syndemics/R/loadOutputFiles.R
rename to Syndemics/R/load_output_files.R
diff --git a/Syndemics/R/residential_admissions.R b/Syndemics/R/residential_admissions.R
index 89be6c2..942cfc1 100644
--- a/Syndemics/R/residential_admissions.R
+++ b/Syndemics/R/residential_admissions.R
@@ -8,6 +8,7 @@
 #'
 #' @return Numeric. Average number of filtered admissions per month.
 #' @importFrom tibble as_tibble
+#' @importFrom dplyr filter
 #' @export
 #'
 #' @examples
diff --git a/Syndemics/R/respond_inputManipulations.R b/Syndemics/R/respond_input_manipulations.R
similarity index 100%
rename from Syndemics/R/respond_inputManipulations.R
rename to Syndemics/R/respond_input_manipulations.R
diff --git a/Syndemics/man/DSA.Rd b/Syndemics/man/DSA.Rd
index ccbd8d9..618b71d 100644
--- a/Syndemics/man/DSA.Rd
+++ b/Syndemics/man/DSA.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/respond_inputManipulations.R
+% Please edit documentation in R/respond_input_manipulations.R
 \name{DSA}
 \alias{DSA}
 \title{A Function to Change RESPOND inputs from base-case by some percent change}
diff --git a/Syndemics/man/Syndemics-package.Rd b/Syndemics/man/Syndemics-package.Rd
index 1394ace..ed7d603 100644
--- a/Syndemics/man/Syndemics-package.Rd
+++ b/Syndemics/man/Syndemics-package.Rd
@@ -24,7 +24,7 @@ Authors:
   \item Ryan O'Dea \email{ryan.odea@bmc.org}
   \item Dimitri Baptiste \email{dimitri.baptiste@bmc.org}
   \item Hana Zwick \email{hana.zwick@bmc.org}
-  \item Alexandra Purdy \email{alexandra.purdy@bmc.org}
+  \item Alexandra Purdy
 }
 
 }
diff --git a/Syndemics/man/build_background_mortality_file.Rd b/Syndemics/man/build_background_mortality_file.Rd
index 3e0ddd3..57bba7c 100644
--- a/Syndemics/man/build_background_mortality_file.Rd
+++ b/Syndemics/man/build_background_mortality_file.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/buildLifeTables.R
+% Please edit documentation in R/build_life_tables.R
 \name{build_background_mortality_file}
 \alias{build_background_mortality_file}
 \title{Taking in the CDC NVSS Yearly life tables, extract and build the background mortality table expected by RESPOND}
diff --git a/Syndemics/man/change_agegrp_chunk.Rd b/Syndemics/man/change_agegrp_chunk.Rd
index d86b62b..77fd4db 100644
--- a/Syndemics/man/change_agegrp_chunk.Rd
+++ b/Syndemics/man/change_agegrp_chunk.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/respond_inputManipulations.R
+% Please edit documentation in R/respond_input_manipulations.R
 \name{change_agegrp_chunk}
 \alias{change_agegrp_chunk}
 \title{A function to change default age groups from RESPOND shell tables}
diff --git a/Syndemics/man/create_and_fill_table.Rd b/Syndemics/man/create_and_fill_table.Rd
index 244f25b..5617d4e 100644
--- a/Syndemics/man/create_and_fill_table.Rd
+++ b/Syndemics/man/create_and_fill_table.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/buildLifeTables.R
+% Please edit documentation in R/build_life_tables.R
 \name{create_and_fill_table}
 \alias{create_and_fill_table}
 \title{Create and fill the table with mortality values for all demographic combinations}
diff --git a/Syndemics/man/extract_background_mortality.Rd b/Syndemics/man/extract_background_mortality.Rd
index 11a73b6..6c53c57 100644
--- a/Syndemics/man/extract_background_mortality.Rd
+++ b/Syndemics/man/extract_background_mortality.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/buildLifeTables.R
+% Please edit documentation in R/build_life_tables.R
 \name{extract_background_mortality}
 \alias{extract_background_mortality}
 \title{Function used to extract background mortality values based on age from a single yearly CDC NVSS life table}
diff --git a/Syndemics/man/formula_list.Rd b/Syndemics/man/formula_list.Rd
index 73b5c00..a1bd313 100644
--- a/Syndemics/man/formula_list.Rd
+++ b/Syndemics/man/formula_list.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/internal_crcTools.R
+% Please edit documentation in R/internal_crc_tools.R
 \name{formula_list}
 \alias{formula_list}
 \title{Generates All Possible Combination of Interaction Terms
diff --git a/Syndemics/man/get_filtered_data.Rd b/Syndemics/man/get_filtered_data.Rd
index e8f2681..d2326a4 100644
--- a/Syndemics/man/get_filtered_data.Rd
+++ b/Syndemics/man/get_filtered_data.Rd
@@ -9,7 +9,7 @@ get_filtered_data(data, pattern, ignore_case = TRUE)
 \arguments{
 \item{data}{A \code{data.table} containing a \code{source_file} column.}
 
-\item{pattern}{A character string containing a regular expression pattern to match 
+\item{pattern}{A character string containing a regular expression pattern to match
 against the \code{source_file} column.}
 
 \item{ignore_case}{Logical; if TRUE, pattern matching is case-insensitive. Default is TRUE.}
diff --git a/Syndemics/man/is.formula.Rd b/Syndemics/man/is.formula.Rd
index 41092d9..b73d780 100644
--- a/Syndemics/man/is.formula.Rd
+++ b/Syndemics/man/is.formula.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/internal_crcTools.R
+% Please edit documentation in R/internal_crc_tools.R
 \name{is.formula}
 \alias{is.formula}
 \title{Formula Objects
diff --git a/Syndemics/man/loadOutputFiles.Rd b/Syndemics/man/loadOutputFiles.Rd
index ed95c0d..f150d74 100644
--- a/Syndemics/man/loadOutputFiles.Rd
+++ b/Syndemics/man/loadOutputFiles.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/loadOutputFiles.R
+% Please edit documentation in R/load_output_files.R
 \name{loadOutputFiles}
 \alias{loadOutputFiles}
 \title{Aggregate selected tables from a set of RESPOND simulation runs}
diff --git a/Syndemics/man/new_block.Rd b/Syndemics/man/new_block.Rd
index 8eaceed..d65d26e 100644
--- a/Syndemics/man/new_block.Rd
+++ b/Syndemics/man/new_block.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/respond_inputManipulations.R
+% Please edit documentation in R/respond_input_manipulations.R
 \name{new_block}
 \alias{new_block}
 \title{A function to create new blocks for RESPOND (clones 'No_Treatment' blocks and reassigns the name)}
diff --git a/Syndemics/man/replace_vals.Rd b/Syndemics/man/replace_vals.Rd
index 9caf1ce..e59ff80 100644
--- a/Syndemics/man/replace_vals.Rd
+++ b/Syndemics/man/replace_vals.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/respond_inputManipulations.R
+% Please edit documentation in R/respond_input_manipulations.R
 \name{replace_vals}
 \alias{replace_vals}
 \title{A function to change values to another block; follows the format \code{data$x[column == "a", ] <- data$y[column == "b", ]}}
diff --git a/Syndemics/man/step_regression.Rd b/Syndemics/man/step_regression.Rd
index 8f0a5c2..ed32aac 100644
--- a/Syndemics/man/step_regression.Rd
+++ b/Syndemics/man/step_regression.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/internal_crcTools.R
+% Please edit documentation in R/internal_crc_tools.R
 \name{step_regression}
 \alias{step_regression}
 \title{Helper function for stepwise regression}

From 5401a7ee89b11105d90bd90fded4dc161e5948b3 Mon Sep 17 00:00:00 2001
From: Matthew Carroll <28577806+MJC598@users.noreply.github.com>
Date: Wed, 3 Dec 2025 12:12:55 -0500
Subject: [PATCH 3/3] Saving a basic test for proof of concept

---
 .gitignore                                        |  3 +++
 Syndemics/DESCRIPTION                             |  4 +++-
 Syndemics/tests/testthat.R                        | 12 ++++++++++++
 Syndemics/tests/testthat/test-build_life_tables.R | 15 +++++++++++++++
 4 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 Syndemics/tests/testthat.R
 create mode 100644 Syndemics/tests/testthat/test-build_life_tables.R

diff --git a/.gitignore b/.gitignore
index b9fc0ff..ef82ca8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+# Editors
+.vscode/
+
 # History files
 .Rhistory
 .Rapp.history
diff --git a/Syndemics/DESCRIPTION b/Syndemics/DESCRIPTION
index 1ecbcf9..44a2ea0 100644
--- a/Syndemics/DESCRIPTION
+++ b/Syndemics/DESCRIPTION
@@ -52,7 +52,9 @@ Suggests:
     doParallel,
     foreach,
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
 URL: https://github.com/SyndemicsLab/Syndemics
 BugReports: https://github.com/SyndemicsLab/Syndemics/issues
+Config/testthat/edition: 3
diff --git a/Syndemics/tests/testthat.R b/Syndemics/tests/testthat.R
new file mode 100644
index 0000000..2bafbdc
--- /dev/null
+++ b/Syndemics/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(Syndemics)
+
+test_check("Syndemics")
diff --git a/Syndemics/tests/testthat/test-build_life_tables.R b/Syndemics/tests/testthat/test-build_life_tables.R
new file mode 100644
index 0000000..ebae8b6
--- /dev/null
+++ b/Syndemics/tests/testthat/test-build_life_tables.R
@@ -0,0 +1,15 @@
+################################################################################
+# File: test-build_life_tables.R                                               #
+# Project: Syndemics                                                           #
+# Created Date: 2025-12-03                                                     #
+# Author: Matthew Carroll                                                      #
+# -----                                                                        #
+# Last Modified: 2025-12-03                                                    #
+# Modified By: Matthew Carroll                                                 #
+# -----                                                                        #
+# Copyright (c) 2025 Syndemics Lab at Boston Medical Center                    #
+################################################################################
+
+test_that("extract_background_mortality", {
+    expect_equal(2 * 2, 4)
+})