Merge branch 'main' into auto-document

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: serocalculator
 Type: Package
 Title: Estimating Infection Rates from Serological Data
-Version: 1.1.0
+Version: 1.1.0.9000
 Authors@R: c(
   person(given = "Peter", family = "Teunis", email = "[email protected]", role = c("aut", "cph"), comment = "Author of the method and original code."),
   person(given = "Kristina", family = "Lai", email = "[email protected]", role = c("aut", "cre")), 

NEWS.md

@@ -1,3 +1,8 @@
+# serocalculator (development version)
+
+* Added `verbose` option for `check_pop_data()`, changing default behavior
+to avoid printing an OK message.
+
 # serocalculator 1.1.0
 
 * Renamed `llik()` to `log_likelihood()`

R/check_pop_data.R

@@ -1,7 +1,7 @@
 #' Check the formatting of a cross-sectional antibody survey dataset.
 #'
 #' @param pop_data dataset to check
-#'
+#' @param verbose whether to print an "OK" message when all checks pass
 #' @returns NULL (invisibly)
 #' @export
 #' @examples
@@ -10,7 +10,8 @@
 #' xs_data <- load_pop_data("https://osf.io/download//n6cp3/") %>%
 #'   check_pop_data()
 #'
-check_pop_data <- function(pop_data) {
+check_pop_data <- function(pop_data,
+                           verbose = FALSE) {
   if (!is.data.frame(pop_data)) {
     cli::cli_abort(message = .pasteN(
       "Argument `pop_data` is not a `data.frame()`.",
@@ -30,6 +31,6 @@ check_pop_data <- function(pop_data) {
     cli::cli_abort(message = paste("Argument `pop_data` is missing column", attributes(pop_data)$value_var, "(antibody measurement)"))
   }
 
-  message("data format is as expected.")
+  if(verbose) message("data format is as expected.")
   invisible(NULL)
 }

_pkgdown.yml

@@ -1,4 +1,5 @@
 url: https://ucd-serg.github.io/serocalculator/
 template:
   bootstrap: 5
+  light-switch: true
 

vignettes/articles/enteric_fever_example.Rmd

@@ -114,7 +114,7 @@ xs_data <-
 We can check that `xs_data` has the correct formatting using the `check_pop_data()` function:
 
 ```{r, message = TRUE}
-xs_data %>% check_pop_data()
+xs_data %>% check_pop_data(verbose = TRUE)
 ```
 
 #### Summarize antibody data

vignettes/articles/scrubTyphus_example.Rmd

@@ -105,7 +105,7 @@ xs_data <- load_pop_data(
 We can check that `xs_data` has the correct formatting using the `check_pop_data()` function:
 
 ```{r, message = TRUE}
-xs_data %>% check_pop_data()
+xs_data %>% check_pop_data(verbose = TRUE)
 ```
 
 #### Summarize antibody data