Merge branch 'main' into add-user-error-message-for-missing-strata

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: serocalculator
 Type: Package
 Title: Estimating Infection Rates from Serological Data
-Version: 1.3.0
+Version: 1.2.0.9002
 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")), 

R/autoplot.curve_params.R

@@ -2,27 +2,37 @@
 #'
 #' @inheritParams plot_curve_params_one_ab
 #' @inheritDotParams plot_curve_params_one_ab
-#' @param antigen_isos antigen isotypes to analyze (can be used to subset `curve_params`)
+#' @param antigen_isos antigen isotypes to analyze (can subset `curve_params`)
 #' @param ncol how many columns of subfigures to use in panel plot
 #' @details
 #' ## `rows_to_graph`
-#' Note that if you directly specify `rows_to_graph` when calling this function, the row numbers are enumerated separately for each antigen isotype; in other words, for the purposes of this argument, row numbers start over at 1 for each antigen isotype. There is currently no way to specify different row numbers for different antigen isotypes; if you want to do that, you will could call [plot_curve_params_one_ab()] directly for each antigen isotype and combine the resulting panels yourself. Or you could subset `curve_params` manually, before passing it to this function, and set the `n_curves` argument to `Inf`.
+#' Note that if you directly specify `rows_to_graph` when calling this function,
+#' the row numbers are enumerated separately for each antigen isotype;
+#' in other words, for the purposes of this argument,
+#' row numbers start over at 1 for each antigen isotype. There is currently
+#' no way to specify different row numbers for different antigen isotypes;
+#' if you want to do that, you could call [plot_curve_params_one_ab()]
+#' directly for each antigen isotype and combine the resulting panels yourself.
+#' Or you could subset `curve_params` manually, before passing it to this
+#' function, and set the `n_curves` argument to `Inf`.
 #' @return a [ggplot2::ggplot()] object
 #' @export
 #' @examples
+#' \donttest{
 #' library(dplyr)
 #' library(ggplot2)
+#' library(magrittr)
 #'
 #' curve = load_curve_params("https://osf.io/download/rtw5k/") %>%
 #'   filter(antigen_iso %in% c("HlyE_IgA", "HlyE_IgG")) %>%
-#'   slice(1:100, .by = antigen_iso)  %>% # Reduce dataset for the purposes of this example
+#'   slice(1:100, .by = antigen_iso)  %>% # Reduce dataset for this example
 #'   autoplot()
 #'
 #' curve
-#'
-autoplot.curve_params = function(
+#'}
+autoplot.curve_params <- function(
     object,
-    antigen_isos = object$antigen_iso %>% unique(),
+    antigen_isos = unique(object$antigen_iso),
     ncol = min(3, length(antigen_isos)),
     ...) {
   split_data <- object %>%
@@ -34,8 +44,7 @@ autoplot.curve_params = function(
   figs <- split_data %>%
     lapply(FUN = plot_curve_params_one_ab, ...)
 
-  for (i in 1:length(figs))
-  {
+  for (i in seq_along(figs)) {
     figs[[i]] <- figs[[i]] + ggplot2::ggtitle(labels[i])
   }