extending graph.decay.curves()

.Rbuildignore

@@ -21,6 +21,8 @@ allpopsamples_hlye.csv$
 ^serocalculator.*\.tgz$
 ^inst/extdata
 ^CRAN-SUBMISSION$
+^vignettes/rsconnect$
+^rsconnect$
 ^README\.qmd$
 ^codecov\.yml$
 ^_quarto\.yml$

.gitignore

@@ -13,6 +13,7 @@ src-x64
 serocalculator.Rcheck/
 serocalculator*.tar.gz
 serocalculator*.tgz
+rsconnect
 README.html
 README_files
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.2.0.9018
+Version: 1.2.0.9019
 Authors@R: c(
     person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

NAMESPACE

@@ -33,6 +33,7 @@ export(load_curve_params)
 export(load_noise_params)
 export(load_pop_data)
 export(log_likelihood)
+export(plot_curve_params_one_ab)
 export(sim.cs)
 export(sim.cs.multi)
 importFrom(Rcpp,sourceCpp)

R/autoplot.curve_params.R

@@ -6,15 +6,17 @@
 #' @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,
+#' 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`.
+#' 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`.
 #' @return a [ggplot2::ggplot()] object
 #' @export
 #' @examples
@@ -25,7 +27,7 @@
 #'
 #' 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 this example
+#'   slice(1:100, .by = antigen_iso) %>% # Reduce dataset for this example
 #'   autoplot()
 #'
 #' curve

R/graph.decay.curves.R

@@ -68,11 +68,11 @@
   layer_function <- function(cur_row) {
     cur_params <- object[cur_row, ]
     ggplot2::geom_function(
       alpha = alpha,
       fun = ab0,
       args = list(curve_params = cur_params),
-      n = n_points
-    )
+      n = n_points,
+      ...)
   }
 
   layers <-