Issue #341: Add cli and checkmate functions to namespace (#344)

* Put checkmate functions into NAMESPACE * Put cli functions into NAMESPACE * Add assert_numeric
epinowcast · Sep 19, 2024 · bc10a37 · bc10a37
1 parent 21784f4
commit bc10a37
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Showing 7 changed files with 39 additions and 28 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -41,6 +41,14 @@ import(cmdstanr)
 import(ggplot2)
 importFrom(brms,bf)
 importFrom(brms,prior)
+importFrom(checkmate,assert_data_frame)
+importFrom(checkmate,assert_factor)
+importFrom(checkmate,assert_integer)
+importFrom(checkmate,assert_names)
+importFrom(checkmate,assert_numeric)
+importFrom(checkmate,assert_true)
+importFrom(cli,cli_abort)
+importFrom(cli,cli_inform)
 importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
diff --git a/R/defaults.R b/R/defaults.R
@@ -5,7 +5,7 @@
 #' @family defaults
 #' @export
 epidist_validate.default <- function(data, ...) {
-  cli::cli_abort(
+  cli_abort(
     "No epidist_validate method implemented for the class ", class(data), "\n",
     "See methods(epidist_validate) for available methods"
   )
@@ -18,7 +18,7 @@ epidist_validate.default <- function(data, ...) {
 #' @family defaults
 #' @export
 epidist_formula.default <- function(data, ...) {
-  cli::cli_abort(
+  cli_abort(
     "No epidist_formula method implemented for the class ", class(data), "\n",
     "See methods(epidist_formula) for available methods"
   )
@@ -31,7 +31,7 @@ epidist_formula.default <- function(data, ...) {
 #' @family defaults
 #' @export
 epidist_family.default <- function(data, ...) {
-  cli::cli_abort(
+  cli_abort(
     "No epidist_family method implemented for the class ", class(data), "\n",
     "See methods(epidist_family) for available methods"
   )
@@ -44,7 +44,7 @@ epidist_family.default <- function(data, ...) {
 #' @family defaults
 #' @export
 epidist_stancode.default <- function(data, ...) {
-  cli::cli_abort(
+  cli_abort(
     "No epidist_stancode method implemented for the class ", class(data), "\n",
     "See methods(epidist_stancode) for available methods"
   )

diff --git a/R/diagnostics.R b/R/diagnostics.R
@@ -22,12 +22,12 @@
 #' @export
 epidist_diagnostics <- function(fit) {
   if (!inherits(fit, "epidist_fit")) {
-    cli::cli_abort(c(
+    cli_abort(c(
       "!" = "Diagnostics only supported for objects of class epidist_fit"
     ))
   }
   if (fit$algorithm %in% c("laplace", "meanfield", "fullrank", "pathfinder")) {
-    cli::cli_abort(c(
+    cli_abort(c(
       "!" = paste0(
         "Diagnostics not yet supported for the algorithm: ", fit$algorithm
       )
@@ -50,7 +50,7 @@ epidist_diagnostics <- function(fit) {
         per_at_max_treedepth = no_at_max_treedepth / samples
       )
   } else {
-    cli::cli_abort(c(
+    cli_abort(c(
       "!" = paste0("Unrecognised algorithm: ", fit$algorithm)
     ))
   }

diff --git a/R/epidist-package.R b/R/epidist-package.R
@@ -7,5 +7,8 @@
 ## usethis namespace: start
 #' @importFrom dplyr filter select
 #' @importFrom brms bf prior
+#' @importFrom checkmate assert_data_frame assert_names assert_integer
+#'   assert_true assert_factor assert_numeric
+#' @importFrom cli cli_abort cli_inform
 ## usethis namespace: end
 NULL
diff --git a/R/latent_individual.R b/R/latent_individual.R
@@ -8,20 +8,20 @@ as_latent_individual <- function(data) {
 }
 
 assert_latent_individual_input <- function(data) {
-  checkmate::assert_data_frame(data)
-  checkmate::assert_names(
+  assert_data_frame(data)
+  assert_names(
     names(data),
     must.include = c("case", "ptime_lwr", "ptime_upr",
                      "stime_lwr", "stime_upr", "obs_at")
   )
-  checkmate::assert_integer(data$case, lower = 0)
-  checkmate::assert_numeric(data$ptime_lwr, lower = 0)
-  checkmate::assert_numeric(data$ptime_upr, lower = 0)
-  checkmate::assert_true(all(data$ptime_upr - data$ptime_lwr > 0))
-  checkmate::assert_numeric(data$stime_lwr, lower = 0)
-  checkmate::assert_numeric(data$stime_upr, lower = 0)
-  checkmate::assert_true(all(data$stime_upr - data$stime_lwr > 0))
-  checkmate::assert_numeric(data$obs_at, lower = 0)
+  assert_integer(data$case, lower = 0)
+  assert_numeric(data$ptime_lwr, lower = 0)
+  assert_numeric(data$ptime_upr, lower = 0)
+  assert_true(all(data$ptime_upr - data$ptime_lwr > 0))
+  assert_numeric(data$stime_lwr, lower = 0)
+  assert_numeric(data$stime_upr, lower = 0)
+  assert_true(all(data$stime_upr - data$stime_lwr > 0))
+  assert_numeric(data$obs_at, lower = 0)
 }
 
 #' Prepare latent individual model
@@ -76,23 +76,23 @@ as_latent_individual.data.frame <- function(data) {
 #' @family latent_individual
 #' @export
 epidist_validate.epidist_latent_individual <- function(data) {
-  checkmate::assert_true(is_latent_individual(data))
+  assert_true(is_latent_individual(data))
   assert_latent_individual_input(data)
-  checkmate::assert_names(
+  assert_names(
     names(data),
     must.include = c("case", "ptime_lwr", "ptime_upr",
                      "stime_lwr", "stime_upr", "obs_at",
                      "obs_t", "pwindow", "woverlap",
                      "swindow", "delay", "row_id")
   )
   if (nrow(data) > 1) {
-    checkmate::assert_factor(data$row_id)
+    assert_factor(data$row_id)
   }
-  checkmate::assert_numeric(data$obs_t, lower = 0)
-  checkmate::assert_numeric(data$pwindow, lower = 0)
-  checkmate::assert_numeric(data$woverlap, lower = 0)
-  checkmate::assert_numeric(data$swindow, lower = 0)
-  checkmate::assert_numeric(data$delay, lower = 0)
+  assert_numeric(data$obs_t, lower = 0)
+  assert_numeric(data$pwindow, lower = 0)
+  assert_numeric(data$woverlap, lower = 0)
+  assert_numeric(data$swindow, lower = 0)
+  assert_numeric(data$delay, lower = 0)
 }
 
 #' Check if data has the `epidist_latent_individual` class

diff --git a/R/postprocess.R b/R/postprocess.R
@@ -51,7 +51,7 @@ add_mean_sd <- function(data, ...) {
 #' @method add_mean_sd default
 #' @export
 add_mean_sd.default <- function(data, ...) {
-  cli::cli_inform(c(
+  cli_inform(c(
     "!" = "Natural scale mean and standard deviation parameter columns not
     added: no method available for this family",
     "Consider submitting an issue to https:/github.com/epinowcast/epidist"

diff --git a/R/utils.R b/R/utils.R
@@ -38,7 +38,7 @@
 #' @param f A positive number specifying the multiple to be rounded down to
 #' @keywords internal
 .floor_mult <- function(x, f = 1) {
-  checkmate::assert_numeric(f, lower = 0)
+  assert_numeric(f, lower = 0)
   ifelse(f == 0, x, floor(x / f) * f)
 }
 
@@ -75,7 +75,7 @@
       "i" = "No available prior to replace in old_prior found for:",
       missing_prior
     )
-    cli::cli_abort(message = msg)
+    cli_abort(message = msg)
   }
 
   prior <- prior |>