UCD-SERG · sschildhauer · Jul 5, 2025 · Jul 5, 2025 · Jul 5, 2025 · Jul 5, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: serodynamics
 Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9034
+Version: 0.0.0.9035
 Authors@R: c(
     person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,7 @@
 
 ## New features
 
+* Updating run_mod description specifying data input values (#105)
 * Replacing old data object with new run_mod output (#102)
 * Adding class assignment to run_mod output (#76)
 * Making prep_priors modifiable (#78)

diff --git a/R/Run_Mod.R b/R/Run_Mod.R
@@ -11,7 +11,14 @@
 #'  - t1 = time to peak
 #'  - shape = shape parameter
 #'  - alpha = decay rate
-#' @param data A [base::data.frame()] with the following columns.
+#' @param data A [base::data.frame()] with the following columns. These values
+#' can be clarified as inputs using [serodynamics::as_case_data()] if not
+#' explicitly labeled as so.
+#'  - id_var = The ID of individuals included
+#'  - biomarker_var = The different antigen isotype combinations that are being
+#'  measured
+#'  - timeindays = The amount of time in days since symptom onset
+#'  - value_var = The measured assay value
-#'  - id_var = The ID of individuals included
-#'  - biomarker_var = The different antigen isotype combinations that are being
-#'  measured
-#'  - timeindays = The amount of time in days since symptom onset
-#'  - value_var = The measured assay value
+#' - id_var = Unique identifier for each individual.
+#' - biomarker_var = Antigen-isotype combinations being measured (e.g., "~ IgG").
+#' - timeindays = Time since symptom onset, in days.
+#' - value_var = Measured assay value (e.g., MFI-bg, OD, or concentration).
-#'  - id_var = The ID of individuals included
-#'  - biomarker_var = The different antigen isotype combinations that are being
-#'  measured
-#'  - timeindays = The amount of time in days since symptom onset
-#'  - value_var = The measured assay value
+#' - id_var = Unique identifier for each individual.
+#' - biomarker_var = Antigen-isotype combinations being measured (e.g., "~ IgG").
+#' - timeindays = Time since symptom onset, in days.
+#' - value_var = Measured assay value (e.g., MFI-bg, OD, or concentration).
 #' @param file_mod The name of the file that contains model structure.
 #' @param nchain An [integer] between 1 and 4 that specifies
 #' the number of MCMC chains to be run per jags model.

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,6 +1,8 @@
+Biomarker
 CMD
 CodeFactor
 Codecov
+Hyperpriors
 JAGs
 Lifecycle
 Postprocess
@@ -9,20 +11,26 @@ 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
@@ -32,5 +40,7 @@ seroresponses
 strat
 stratifications
 tbl
+tibble
+timeindays
 unstratified
 wishdf
diff --git a/man/run_mod.Rd b/man/run_mod.Rd