Issue #126: Import stats functions (#128)

* Add importing stats functions

* Fix lint

DESCRIPTION

@@ -31,7 +31,8 @@ Imports:
     posterior,
     purrr,
     ggridges,
-    here
+    here,
+    stats
 Suggests:
     bookdown,
     epinowcast,

NAMESPACE

@@ -60,3 +60,11 @@ import(cmdstanr)
 import(data.table)
 import(ggplot2)
 importFrom(posterior,as_draws_df)
+importFrom(stats,as.formula)
+importFrom(stats,ecdf)
+importFrom(stats,integrate)
+importFrom(stats,median)
+importFrom(stats,quantile)
+importFrom(stats,rexp)
+importFrom(stats,runif)
+importFrom(stats,t.test)

R/fitting-and-postprocessing.R

@@ -276,6 +276,7 @@ make_relative_to_truth <- function(draws, secondary_dist, by = "parameter") {
 #' @param not_by ...
 #' @param by A vector of columns to group by
 #' @family postprocess
+#' @importFrom stats median quantile
 #' @export
 summarise_draws <- function(draws, sf, not_by = "value", by) {
   if (missing(by)) {

R/latent_individual.R

@@ -32,6 +32,7 @@ epidist_prepare.epidist_latent_individual <- function(data, ...) {
 #' @param ... ...
 #' @method epidist_formula epidist_latent_individual
 #' @family latent_individual
+#' @importFrom stats as.formula
 #' @export
 epidist_formula.epidist_latent_individual <- function(data, delay_central = ~ 1,
                                                       sigma = ~ 1, ...) {

R/plot-helpers.R

@@ -33,6 +33,7 @@ calculate_cohort_mean <- function(data, type = c("cohort", "cumulative"),
 #' @param ptime ...
 #' @param distribution ...
 #' @family plot
+#' @importFrom stats integrate
 #' @export
 calculate_truncated_means <- function(draws, obs_at, ptime,
                                       distribution = function(x, y, z) {

R/preprocess.R

@@ -138,6 +138,7 @@ combine_obs <- function(truncated_obs, obs) {
 #' @param additional_by ...
 #' @family preprocess
 #' @autoglobal
+#' @importFrom stats t.test
 #' @export
 calculate_censor_delay <- function(truncated_obs, additional_by = c()) {
   truncated_obs_psumm <- data.table::copy(truncated_obs)

R/simulate.R

@@ -11,6 +11,7 @@
 #' (primary event time).
 #'
 #' @family simulate
+#' @importFrom stats runif
 #' @export
 simulate_uniform_cases <- function(sample_size = 1000, t = 60) {
   data.table::data.table(
@@ -34,6 +35,7 @@ simulate_uniform_cases <- function(sample_size = 1000, t = 60) {
 #' (primary event time).
 #'
 #' @family simulate
+#' @importFrom stats runif
 #' @export
 simulate_exponential_cases <- function(r = 0.2,
                                        sample_size = 10000,
@@ -74,6 +76,7 @@ simulate_exponential_cases <- function(r = 0.2,
 #' (primary event time).
 #'
 #' @family simulate
+#' @importFrom stats rexp
 #' @export
 simulate_gillespie <- function(r = 0.2,
                                gamma = 1 / 7,
@@ -166,6 +169,7 @@ simulate_secondary <- function(linelist, dist = rlnorm, ...) {
 #' delays.
 #'
 #' @family simulate
+#' @importFrom stats runif ecdf
 #' @export
 simulate_double_censored_pmf <- function(
   alpha, beta, max, n = 1000,