Add some model components

.Rbuildignore

@@ -2,3 +2,5 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -42,6 +42,11 @@ jobs:
           extra-packages: any::pkgdown local::.
           needs: website
 
+      - name: "Install cmdstan via cmdstanr"
+        uses: epinowcast/actions/install-cmdstan@v1
+        with:
+          cmdstan-version: "latest"
+
       - name: Build site
         run: "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
         shell: Rscript {0}

.gitignore

@@ -1,6 +1,10 @@
 #####
 # Exclude many data and output file types by default
 
+# Exclude stan compiled model
+
+inst/stan/wwinference
+
 # Data
 *.csv
 *.tsv
@@ -235,6 +239,8 @@ cython_debug/
 # RStudio files
 .Rproj.user/
 
+*.Rproj
+
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf

.pre-commit-config.yaml

@@ -37,7 +37,6 @@ repos:
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style,
                --cache-root=styler-perm]
-    -   id: roxygenize
     -   id: use-tidy-description
     -   id: lintr
     -   id: readme-rmd-rendered
@@ -46,6 +45,7 @@ repos:
     -   id: no-print-statement
     -   id: no-debug-statement
     -   id: deps-in-desc
+        exclude: data-raw
 #####
 # Java
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks

DESCRIPTION

@@ -60,5 +60,24 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Suggests:
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    bookdown
 Config/testthat/edition: 3
+LazyData: true
+Imports:
+    fs,
+    dplyr,
+    lubridate,
+    glue,
+    RcppTOML,
+    cli,
+    tibble,
+    tidybayes,
+    tidyr,
+    purrr,
+    withr,
+    cmdstanr (>= 0.8.0),
+    rlang,
+    scales
+Remotes:
+    stan-dev/cmdstanr

NAMESPACE

@@ -1,3 +1,70 @@
 # Generated by roxygen2: do not edit by hand
 
 export(add_pmfs)
+export(add_time_indexing)
+export(compile_model)
+export(convert_to_logmean)
+export(convert_to_logsd)
+export(create_dir)
+export(drop_first_and_renormalize)
+export(flag_ww_outliers)
+export(generate_simulated_data)
+export(get_count_data_sizes)
+export(get_count_indices)
+export(get_count_values)
+export(get_draws_df)
+export(get_ind_m)
+export(get_mcmc_options)
+export(get_model_diagnostic_flags)
+export(get_model_spec)
+export(get_params)
+export(get_plot_forecasted_counts)
+export(get_plot_global_rt)
+export(get_plot_subpop_rt)
+export(get_plot_ww_conc)
+export(get_stan_data)
+export(get_subpop_data)
+export(get_ww_data_indices)
+export(get_ww_data_sizes)
+export(get_ww_values)
+export(indicate_ww_exclusions)
+export(preprocess_hosp_data)
+export(preprocess_ww_data)
+export(to_simplex)
+export(validate_paramlist)
+export(wwinference)
+importFrom(cmdstanr,cmdstan_model)
+importFrom(dplyr,arrange)
+importFrom(dplyr,as_tibble)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
+importFrom(dplyr,row_number)
+importFrom(dplyr,select)
+importFrom(dplyr,ungroup)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_ribbon)
+importFrom(ggplot2,geom_vline)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_colour_discrete)
+importFrom(ggplot2,scale_fill_discrete)
+importFrom(ggplot2,scale_x_date)
+importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,theme)
+importFrom(lubridate,ymd)
+importFrom(tidybayes,spread_draws)
+importFrom(tidybayes,stat_halfeye)
+importFrom(tidybayes,stat_slab)
+importFrom(tidyr,pivot_longer)
+importFrom(tidyr,pivot_wider)

R/checkers.R

@@ -0,0 +1,45 @@
+#' Check that all dates in dataframe passed in are before a specified date
+#'
+#' @param df dataframe with `date` column
+#' @param max_date string indicating the maximum date in ISO8601 convention
+#' e.g. YYYY-MM-DD
+#' @param call Calling environment to be passed to the type checker
+#'
+#' @return NULL, invisibly
+check_date <- function(df, max_date, call = rlang::caller_env()) {
+  if (max(df$date) > max_date) {
+    cli::cli_abort(
+      c(
+        "The data passed in has observations beyond the specified",
+        "maximum date. Either this is the incorrect vintaged",
+        "data, or the data needs to be filtered to only contain",
+        "observations before the maximum date"
+      ),
+      call = call,
+      class = "wwinference_input_data_error"
+    )
+  }
+  invisible()
+}
+
+#' Check that all elements of a vector are non-negative
+#'
+#' @param x vector of arguments to check for negativity
+#' @param call Calling environment to be passed to the type checker
+#'
+#' @return NULL, invisibly
+check_elements_non_neg <- function(x, arg = "x", call = rlang::caller_env()) {
+  # Greater than or equal to 0 or is NA
+  is_non_neg <- (x >= 0) | is.na(x)
+  if (!all(is_non_neg)) {
+    cli::cli_abort(
+      c("{.arg {arg}} has negative elements",
+        "!" = "All elements must be 0 or greater",
+        "i" = "Elements {.val {which(!is_non_neg)}} are negative"
+      ),
+      class = "wwinference_input_data_error",
+      call = call
+    )
+  }
+  invisible()
+}

R/compile_model.R

@@ -0,0 +1,95 @@
+#' Compile a stan model while pointing at the package default
+#' include directory (`stan`) for #include statements
+#'
+#' @description
+#' This function reads in and optionally compiles a Stan model.
+#' It is written to search the installed package `stan` directory
+#' for additional source files to include. Within each stan file,
+#' use #include {path to your file with the `stan` directory}.stan
+#'
+#' @details The code for this function has been adapted
+#' from code written (under an MIT license) as part of
+#' the [`epinowcast`](https://github.com/epinowcast/epinowcast)
+#' R package.
+#'
+#' @param model_filepath path to .stan file defining the model, default is
+#' `system.file("stan", "wwinference.stan", package = "wwinference")
+#' @param include_paths path(s) to directories to search for files
+#' specified in #include statements. Passed to [cmdstanr::cmdstan_model()].
+#' Defaults to the `stan` subdirectory of the installed
+#' `wwinference` package.
+#' @param threads Number of threads to use in model compilation,
+#' as an integer. Passed to [cmdstanr::cmdstan_model()].
+#' Default `FALSE` (use single-threaded compilation).
+#' @param target_dir Directory in which to save the compiled
+#' stan model binary. Passed as the `dir` keyword argument to
+#' [cmdstanr::cmdstan_model()]. Defaults to a temporary directory
+#' for the R session (the output of [tempdir()]).
+#' @param stanc_options Options for the stan compiler passed to
+#' [cmdstanr::cmdstan_model()], as a list. See that function's
+#' documentation for more details. Default `list()` (use default
+#' options).
+#' @param cpp_options Options for the C++ compiler passed to
+#' [cmdstanr::cmdstan_model()], as a list. See that function's
+#' documentation for more details. Default `list()` (use default
+#' options).
+#' @param verbose Write detailed output to the terminal while
+#' executing the function? Boolean, default `TRUE`.
+#' @param ... Additional keyword arguments passed to
+#' [cmdstanr::cmdstan_model()].
+#'
+#' @return The resulting `cmdstanr` model object, as the output
+#' of [cmdstanr::cmdstan_model()].
+#' @export
+compile_model <- function(model_filepath = system.file("stan",
+                            "wwinference.stan",
+                            package = "wwinference"
+                          ),
+                          include_paths = system.file(
+                            "stan",
+                            package = "wwinference"
+                          ),
+                          threads = FALSE,
+                          target_dir = tempdir(),
+                          stanc_options = list(),
+                          cpp_options = list(),
+                          verbose = TRUE,
+                          ...) {
+  if (verbose) {
+    cli::cli_inform(
+      glue::glue(paste0(
+        "Using model source file: ",
+        "{model_filepath}"
+      ))
+    )
+    cli::cli_inform(
+      sprintf(
+        "Using include paths: %s",
+        toString(include_paths)
+      )
+    )
+  }
+
+  create_dir(target_dir)
+
+  model <- cmdstanr::cmdstan_model(
+    model_filepath,
+    include_paths = include_paths,
+    compile = TRUE,
+    stanc_options = stanc_options,
+    cpp_options = cpp_options,
+    threads = threads,
+    dir = target_dir,
+    ...
+  )
+
+  if (verbose) {
+    cli::cli_inform(paste0(
+      "Model compiled or loaded successfully; ",
+      "model executable binary located at: ",
+      "{model$exe_file()}"
+    ))
+  }
+
+  return(model)
+}