Creating default print methods for class sr_model

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(autoplot,case_data)
+S3method(print,sr_model)
 export(as_case_data)
 export(autoplot)
 export(get_biomarker_levels)

NEWS.md

@@ -4,6 +4,7 @@
 
 ## New features
 
+* Creating default print.sr_model function for sr_model class (#114)
 * Added `plot_predicted_curve()`  (#68)
 * Replacing old data object with new run_mod output (#102)
 * Adding class assignment to run_mod output (#76)

R/Run_Mod.R

@@ -200,4 +200,5 @@ run_mod <- function(data,
   jags_out <- jags_out |>
     structure(class = union("sr_model", class(jags_out)))
   jags_out
+
 }

R/print.sr_model.R

@@ -0,0 +1,28 @@
+#' @title Default print for [serodynamics::run_mod()] output object of class
+#' `sr_model`
+#' @description
+#'  A default print method for class `sr_model` that includes the mean posterior
+#'  distribution for antibody kinetic curve parameters by `Iso_type` and
+#'  `Stratification` (if specified).
+#' @param x An `sr_model` output object from [run_mod()].
+#' @param ... Additional arguments affecting the summary produced.
+#' [serodynamics::run_mod()] function.
+#' @returns A [dplyr::grouped_df] that
+#' contains the mean posterior distribution for antibody kinetic curve
+#' parameters by `Iso_type` and `Stratification` (if specified).
+#' @export
+#' @examples
+#' print(nepal_sees_jags_output)
+print.sr_model <- function(x, ...) { # nolint
+  x <- x |>
+    dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |>
+    dplyr::summarise(mean_val = mean(.data$value)) |>
+    tidyr::pivot_wider(names_from = .data$Parameter, 
+                       values_from = .data$mean_val) |>
+    dplyr::arrange(.data$Iso_type)
+  # Taking out stratification column if not specified
+  if (unique(data$Stratification == "None")) {
+    x <- x |> select(-all_of(Stratification))
+  } 
+  invisible(x)
+}

inst/WORDLIST

@@ -1,6 +1,8 @@
+Biomarker
 CMD
 CodeFactor
 Codecov
+Hyperpriors
 JAGs
 Lifecycle
 Postprocess
@@ -9,29 +11,37 @@ Traceplots
 behaviour
 biomarker
 biomarkers
+bmatrix
+cdot
 dobson
 dotplots
 geoms
 ggproto
 hyp
 hyperprior
 hyperpriors
+ij
 iso
 isotype
 isotypes
+mathcal
 mcmc
 nmc
+overfit
 params
 prec
+pred
 rhat
 sd
 seroconversion
 serocourse
 seroresponse
 seroresponses
+sr
 strat
 stratifications
 tbl
+tibble
 unstratified
 wishdf
 dayssincefeveronset

pkgdown/_pkgdown.yml

@@ -42,6 +42,7 @@ reference:
 - title: Summarize seroresponse model estimates
   contents:
   - post_summ
+  - print.sr_model
 - title: Example data sets
   contents:
   - serodynamics_example

tests/testthat/_snaps/print.sr_model/default-print-runmod-object.csv

@@ -0,0 +1,5 @@
+Stratification,Iso_type,alpha,shape,t1,y0,y1
+paratyphi,HlyE_IgA,0.00228672,1.66482,3.85028,2.55072,1024.3
+typhi,HlyE_IgA,0.00290543,1.61299,7.3068,2.9673,1031.9
+paratyphi,HlyE_IgG,0.00256872,1.36053,4.7794,1.72131,833.105
+typhi,HlyE_IgG,0.00153667,1.40846,8.72891,2.31451,338.572

tests/testthat/test-print.sr_model.R

@@ -0,0 +1,9 @@
+test_that(
+  desc = "results are consistent with printed output for sr_model class",
+  code = {
+    withr::local_seed(1)
+    results <- print(nepal_sees_jags_output) |>
+      ssdtools:::expect_snapshot("default-print-runmod-object")
+
+  }
+)