Updating density diagnostic function

NEWS.md

@@ -4,6 +4,7 @@
 
 ## New features
 
+* Updating density diagnostic function (#71)
 * Changes to `run_mod()` (#79):
    - `jags.post` now optionally included in output, as specified by argument
    `with_post`

R/plot_jags_densitydx.R

@@ -26,7 +26,7 @@
 #' - `y1` = posterior estimate of peak antibody concentration
 #' @param strat Specify [character] string to produce plots of specific
 #' stratification entered in quotes.
-#' @return A [base::list()] of [ggplot2::ggplot()] objects producing density
+#' @return A [list] of [ggplot2::ggplot] objects producing density
 #' plots for all the specified input.
 #' @export
 #' @example inst/examples/examples-plot_jags_densitydx.R
@@ -61,18 +61,23 @@
         # Changing parameter name to reflect the input
         dplyr::mutate(Parameter = paste0("iso = ", j, ", parameter = ",
                                          .data$Parameter_sub, ", strat = ",
-                                         i),
-                      value = log(.data$value))
+                                         i))
       # Assigning attributes, which are needed to run ggs_density
       attributes(visualize_jags_plot) <- c(attributes(visualize_jags_plot),
                                            attributes_jags)
       # Creating density plot
       densplot <- ggmcmc::ggs_density(visualize_jags_plot) +
         ggplot2::theme_bw() +
-        ggplot2::labs(x = "log(value)")
+        ggplot2::labs(x = "parameter value") +
+        ggplot2::scale_x_log10(labels = scales::label_comma())
       density_out[[j]] <- densplot
     }
+
     dens_strat_list[[i]] <- density_out
   }
+  #Printing only one plot if only one exists.
+  if (length(dens_strat_list) == 1) {
+    dens_strat_list <- dens_strat_list[[1]][[iso]]
+  } 
   dens_strat_list
 }

inst/examples/examples-plot_jags_densitydx.R

@@ -1,7 +1,7 @@
 
+
 data <- serodynamics::nepal_sees_jags_output
 
-# Specifying isotype and stratification for traceplot.
 plot_jags_dens(
                data = data,
                iso = "HlyE_IgA",

tests/testthat/test-plot_jags_densitydx.R

@@ -3,11 +3,8 @@ test_that(
   desc = "results are consistent with ggplot output",
   code = {
     skip_if(getRversion() < "4.4.1") # 4.3.3 had issues
-    library(runjags)
-    library(dplyr)
 
-    data <- serodynamics::nepal_sees_jags_output |>
-      suppressWarnings()
+    data <- serodynamics::nepal_sees_jags_output
 
     # Testing for any errors:
     results <- plot_jags_dens(data) |> expect_no_error()

tests/testthat/test-run_mod.R

@@ -12,7 +12,7 @@ test_that(
       sim_case_data(n = 100,
                     antigen_isos = "HlyE_IgA") |>
       mutate(strat = "stratum 1")
-    dataset <- bind_rows(strat1, strat2)
+    dataset <- dplyr::bind_rows(strat1, strat2)
     withr::with_seed(
       1,
       code = {