From 08551cc76b7e6fe1a12765b41fcd8f7fe18c75ea Mon Sep 17 00:00:00 2001
From: Adam Howes <xwg3@cdc.gov>
Date: Sun, 23 Jun 2024 16:17:02 +0100
Subject: [PATCH] Issue #126: Import stats functions (#128)

* Add importing stats functions

* Fix lint
---
 DESCRIPTION                    | 3 ++-
 NAMESPACE                      | 8 ++++++++
 R/fitting-and-postprocessing.R | 1 +
 R/latent_individual.R          | 1 +
 R/plot-helpers.R               | 1 +
 R/preprocess.R                 | 1 +
 R/simulate.R                   | 4 ++++
 7 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e436288ea..be76232d8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -31,7 +31,8 @@ Imports:
     posterior,
     purrr,
     ggridges,
-    here
+    here,
+    stats
 Suggests:
     bookdown,
     epinowcast,
diff --git a/NAMESPACE b/NAMESPACE
index 6e16137af..9f0551e7c 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/fitting-and-postprocessing.R b/R/fitting-and-postprocessing.R
index 47dda7dae..d43931105 100644
--- a/R/fitting-and-postprocessing.R
+++ b/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)) {
diff --git a/R/latent_individual.R b/R/latent_individual.R
index a20174f1b..f7cf5d9f1 100644
--- a/R/latent_individual.R
+++ b/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, ...) {
diff --git a/R/plot-helpers.R b/R/plot-helpers.R
index 164eccc26..41cc17bc1 100644
--- a/R/plot-helpers.R
+++ b/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) {
diff --git a/R/preprocess.R b/R/preprocess.R
index 93b43fb35..4c92fe91a 100644
--- a/R/preprocess.R
+++ b/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)
diff --git a/R/simulate.R b/R/simulate.R
index 8e9f9bdea..500ca0d5e 100644
--- a/R/simulate.R
+++ b/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,