Tabulate parameters alphabetically, ignoring case

vignettes/evidence-for-parameter-values.Rmd

@@ -32,23 +32,12 @@ suppressPackageStartupMessages(library(here))
 
 output_dir <- here("outputs")
 
+# Remove non-scalar derived parameters, such as the initial red blood cell
+# populations.
 remove_nonscalar_derived_parameters <- function(x) {
   x[sapply(x, function(x) length(x) == 1)]
 }
 
-# Convert the baseline parameters for both species into data frames.
-pf <- baseline_parameters(species = "Pf") |> #, derived = FALSE) |>
-  remove_nonscalar_derived_parameters() |>
-  as.data.frame() |>
-  dplyr::mutate(species = NULL, nospleen = NULL, Scenario = NULL) |>
-  tidyr::pivot_longer(everything(), names_to = "Parameter", values_to = "Pf")
-
-pv <- baseline_parameters(species = "Pv") |> #, derived = FALSE) |>
-  remove_nonscalar_derived_parameters() |>
-  as.data.frame() |>
-  dplyr::mutate(species = NULL, nospleen = NULL, Scenario = NULL) |>
-  tidyr::pivot_longer(everything(), names_to = "Parameter", values_to = "Pv")
-
 # Define how to format parameter values of different magnitudes.
 format_value <- function(x, nsmall=4, min=1e-3, max=1e3) {
   scientific <- x < min || x > max
@@ -69,12 +58,40 @@ format_value <- function(x, nsmall=4, min=1e-3, max=1e3) {
   }
 }
 
-# Join the baseline parameters into a single data frame.
-baseline <- dplyr::inner_join(pf, pv, by = "Parameter") |>
-  dplyr::mutate(
-    Pf = sapply(Pf, format_value),
-    Pv = sapply(Pv, format_value)
-  )
+# Return the baseline parameters for a species as a long data frame.
+get_baseline_parameters <- function(species) {
+  baseline_parameters(species = species) |>
+    remove_nonscalar_derived_parameters() |>
+    as.data.frame() |>
+    dplyr::mutate(
+      species = NULL,
+      nospleen = NULL,
+      Scenario = NULL
+    ) |>
+    tidyr::pivot_longer(
+      everything(),
+      names_to = "Parameter",
+    ) |>
+    dplyr::mutate(
+      value = sapply(value, format_value)
+    )
+}
+
+# Convert the baseline parameters for both species into data frames.
+baseline <- dplyr::inner_join(
+  get_baseline_parameters("Pf") |>
+    dplyr::rename(Pf = value),
+  get_baseline_parameters("Pv") |>
+    dplyr::rename(Pv = value),
+  by = "Parameter"
+) |>
+  # Sort by parameter name (case-insensitive).
+  dplyr::arrange(tolower(Parameter)) |>
+  # Highlight parameters whose values differ between species.
+  dplyr::mutate(Parameter = dplyr::case_when(
+    .default = Parameter,
+    Pf != Pv ~ paste0("**", Parameter, "**")
+  ))
 ```
 
 ```{r define-evidence, class.source = 'fold-hide'}
@@ -83,10 +100,16 @@ baseline <- dplyr::inner_join(pf, pv, by = "Parameter") |>
 baseline <- baseline |>
   dplyr::mutate(Evidence = dplyr::case_when(
     .default = "",
-    Parameter == "MaxFold" ~ "[Maximum fold increase in RBC production]" # "@Watson17"
+    Parameter == "MaxFold" ~ "[Maximum fold increase in RBC production]"
   ))
 
-knitr::kable(baseline)
+knitr::kable(
+  baseline,
+  caption=paste(
+    "Evidence for chosen parameter values.",
+    "Parameters that differ between species are shown **in bold**."
+  )
+)
 ```
 
 ## Maximum fold increase in RBC production