From aea299ac4a3bd9453a769c48f455dddd66f8f3a4 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 24 Jun 2025 22:48:00 -0700
Subject: [PATCH 01/53] Adding class sero_mod_output to run_mod output

---
 R/Run_Mod.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/Run_Mod.R b/R/Run_Mod.R
index 98e904c3..78310318 100644
--- a/R/Run_Mod.R
+++ b/R/Run_Mod.R
@@ -196,4 +196,6 @@ run_mod <- function(data,
       structure(jags.post = jags_post_final)
   } 
   jags_out
+  class(jags_out) <- "sero_mod_output"
+  
 }

From a13db942c5e590e8fabf26a64426da37d6b51424 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 24 Jun 2025 23:21:27 -0700
Subject: [PATCH 02/53] Specifying class in run_mod

---
 R/Run_Mod.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/Run_Mod.R b/R/Run_Mod.R
index 78310318..2f0ed78f 100644
--- a/R/Run_Mod.R
+++ b/R/Run_Mod.R
@@ -195,7 +195,7 @@ run_mod <- function(data,
     jags_out <- jags_out |>
       structure(jags.post = jags_post_final)
   } 
-  jags_out
   class(jags_out) <- "sero_mod_output"
+  jags_out
   
 }

From eef3d8ed527cbef310098b7b06c386e1910e871d Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 24 Jun 2025 23:21:53 -0700
Subject: [PATCH 03/53] creating default print function method for
 sero_mod_output objects

---
 R/print_sero_mod_output.R | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 R/print_sero_mod_output.R

diff --git a/R/print_sero_mod_output.R b/R/print_sero_mod_output.R
new file mode 100644
index 00000000..dc950058
--- /dev/null
+++ b/R/print_sero_mod_output.R
@@ -0,0 +1,32 @@
+#' @title Default print method for run_mod output
+#' @author Sam Schildhauer
+#' @description
+#'  Will print a default output for a run_mod object that specifies the median
+#'  value of the posterior distribution for serokinetic curve parameters (y0,
+#'  y1, t1, alpha, shape) by stratification (if specified) and antigen/iso type.
+#' @param obj A [serodynamics::sero_mod_output] object.
+#' @returns A [dplyr::tbl_df] that contains the median value of the posterior
+#' distribution of stratifications (if any specified), antigen/iso type, and
+#' parameter value.
+#' @export
+#' @example inst/examples/run_mod-examples.R
+
+print.sero_mod_output <- function(obj) {
+
+  # Summarizing results
+  df_obj <- data.frame("Parameter" = obj$Parameter, "Iso_type" = obj$Iso_type,
+                       "Stratification" = obj$Stratification, 
+                       "Value" = obj$value)
+  if (unique(df_obj$Stratification == "None")) {
+  to_print <- df_obj |>
+    dplyr::group_by(Iso_type, Parameter) |>
+    dplyr::summarize(median = median(Value)) |>
+    tidyr::spread(Parameter, median)
+  } else {
+    to_print <- df_obj |>
+      dplyr::group_by(Stratification, Iso_type, Parameter) |>
+      dplyr::summarize(median = median(Value)) |>
+      tidyr::spread(Parameter, median)
+  }
+  to_print
+}

From 147ae9ec1e9b240dd2f2563c3f43ddc8b9f14036 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 24 Jun 2025 23:22:53 -0700
Subject: [PATCH 04/53] Adding S3 method to NameSpace

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index 09e6f3bd..022010b0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(autoplot,case_data)
+S3method(print,sero_mod_output)
 export(as_case_data)
 export(autoplot)
 export(get_biomarker_levels)

From ea74517c908b6c366c07dfe0e9fc96011be284a7 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 24 Jun 2025 23:23:07 -0700
Subject: [PATCH 05/53] Documentation for default print method

---
 man/print.sero_mod_output.Rd | 50 ++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 man/print.sero_mod_output.Rd

diff --git a/man/print.sero_mod_output.Rd b/man/print.sero_mod_output.Rd
new file mode 100644
index 00000000..0dd8540f
--- /dev/null
+++ b/man/print.sero_mod_output.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/print_sero_mod_output.R
+\name{print.sero_mod_output}
+\alias{print.sero_mod_output}
+\title{Default print method for run_mod output}
+\usage{
+\method{print}{sero_mod_output}(obj)
+}
+\arguments{
+\item{obj}{A \link{sero_mod_output} object.}
+}
+\value{
+A \link[dplyr:tbl_df]{dplyr::tbl_df} that contains the median value of the posterior
+distribution of stratifications (if any specified), antigen/iso type, and
+parameter value.
+}
+\description{
+Will print a default output for a run_mod object that specifies the median
+value of the posterior distribution for serokinetic curve parameters (y0,
+y1, t1, alpha, shape) by stratification (if specified) and antigen/iso type.
+}
+\examples{
+if (!is.element(runjags::findjags(), c("", NULL))) {
+  library(runjags)
+  set.seed(1)
+  library(dplyr)
+  strat1 <- serocalculator::typhoid_curves_nostrat_100 |>
+    sim_case_data(n = 100) |>
+    mutate(strat = "stratum 2")
+  strat2 <- serocalculator::typhoid_curves_nostrat_100 |>
+    sim_case_data(n = 100) |>
+    mutate(strat = "stratum 1")
+
+  dataset <- bind_rows(strat1, strat2)
+
+  fitted_model <- run_mod(
+    data = dataset, # The data set input
+    file_mod = serodynamics_example("model.jags"),
+    nchain = 4, # Number of mcmc chains to run
+    nadapt = 100, # Number of adaptations to run
+    nburn = 100, # Number of unrecorded samples before sampling begins
+    nmc = 1000,
+    niter = 2000, # Number of iterations
+    strat = "strat"
+  ) # Variable to be stratified
+}
+}
+\author{
+Sam Schildhauer
+}

From 102cb808b695691268eeb1622ada71c2cea46d97 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:12:24 -0700
Subject: [PATCH 06/53] Creating default print for run_mod objects

---
 R/print.sr_model.R | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 R/print.sr_model.R

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
new file mode 100644
index 00000000..0ba453b6
--- /dev/null
+++ b/R/print.sr_model.R
@@ -0,0 +1,29 @@
+#' @title Default print for run_mod object of class sr_model
+#' @author Sam Schildhauer
+#' @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 data A [serodynamics::sr_model] object output from the
+#' [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
+#' @example
+#' print.sr_model(nepal_sees_output)
+print.sr_model <- function(data) {
+  data_group <- data |>
+    dplyr::group_by(Stratification, Iso_type, Parameter) |>
+    dplyr::summarise(mean_val = mean(value)) |>
+    tidyr::spread(Parameter, mean_val)
+  # Taking out stratification column if not specified
+  if(unique(data$Stratification == "None")) {
+    data_group <- data_group[,2:7]
+  } 
+  data_group
+}
+    
+  
+  
+  
\ No newline at end of file

From 7323fda893e188968f65ef1a0b00f0e061996e90 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:15:51 -0700
Subject: [PATCH 07/53] Creating a test for default run_mod object print

---
 tests/testthat/test-print.sr_model.R | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 tests/testthat/test-print.sr_model.R

diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
new file mode 100644
index 00000000..3f0d0e11
--- /dev/null
+++ b/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_data("default-print-runmod-object")
+        
+  }
+)

From 88b96aff66c11de4f1f3831e2eec69cfe67c3aba Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:16:23 -0700
Subject: [PATCH 08/53] Updating example for print default

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 0ba453b6..2b48f933 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -11,7 +11,7 @@
 #' parameters by `Iso_type` and `Stratification` (if specified).
 #' @export
 #' @example
-#' print.sr_model(nepal_sees_output)
+#' print.sr_model(nepal_sees_jags_output)
 print.sr_model <- function(data) {
   data_group <- data |>
     dplyr::group_by(Stratification, Iso_type, Parameter) |>

From 91a887f03e7ecfb64933b20ad9e3f4b49051fa25 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:16:46 -0700
Subject: [PATCH 09/53] Updating documentation for default print

---
 NAMESPACE             |  1 +
 man/print.sr_model.Rd | 25 +++++++++++++++++++++++++
 2 files changed, 26 insertions(+)
 create mode 100644 man/print.sr_model.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 022010b0..0bd66d02 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,7 @@
 
 S3method(autoplot,case_data)
 S3method(print,sero_mod_output)
+S3method(print,sr_model)
 export(as_case_data)
 export(autoplot)
 export(get_biomarker_levels)
diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd
new file mode 100644
index 00000000..6b14d968
--- /dev/null
+++ b/man/print.sr_model.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/print.sr_model.R
+\name{print.sr_model}
+\alias{print.sr_model}
+\title{Default print for run_mod object of class sr_model}
+\usage{
+\method{print}{sr_model}(data)
+}
+\arguments{
+\item{data}{A \link{sr_model} object output from the
+\code{\link[=run_mod]{run_mod()}} function.}
+}
+\value{
+A \link[dplyr:grouped_df]{dplyr::grouped_df} that
+contains the mean posterior distribution for antibody kinetic curve
+parameters by \code{Iso_type} and \code{Stratification} (if specified).
+}
+\description{
+A default print method for class \code{sr_model} that includes the mean posterior
+distribution for antibody kinetic curve parameters by \code{Iso_type} and
+\code{Stratification} (if specified).
+}
+\author{
+Sam Schildhauer
+}

From a7afd630bdaf134d4ac27c9a89570e8f586dcb59 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:20:26 -0700
Subject: [PATCH 10/53] Arranging data by Iso_type to allow for easy comparison
 between stratifications

---
 R/print.sr_model.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 2b48f933..90c47bf7 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -16,7 +16,8 @@ print.sr_model <- function(data) {
   data_group <- data |>
     dplyr::group_by(Stratification, Iso_type, Parameter) |>
     dplyr::summarise(mean_val = mean(value)) |>
-    tidyr::spread(Parameter, mean_val)
+    tidyr::spread(Parameter, mean_val) |>
+    dplyr::arrange(Iso_type)
   # Taking out stratification column if not specified
   if(unique(data$Stratification == "None")) {
     data_group <- data_group[,2:7]

From f5be2b33313b844cea051a8c74ece9559989087e Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:21:42 -0700
Subject: [PATCH 11/53] Adding test snap for run_mod object default print

---
 .../_snaps/print.sr_model/default-print-runmod-object.csv    | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 tests/testthat/_snaps/print.sr_model/default-print-runmod-object.csv

diff --git a/tests/testthat/_snaps/print.sr_model/default-print-runmod-object.csv b/tests/testthat/_snaps/print.sr_model/default-print-runmod-object.csv
new file mode 100644
index 00000000..75d8a137
--- /dev/null
+++ b/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

From ba5973fa2f5f84a028787030b0c5c9ca2ccc7391 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:25:53 -0700
Subject: [PATCH 12/53] Updating default sr_model print documentation

---
 R/print.sr_model.R    | 6 +++---
 man/print.sr_model.Rd | 8 +++-----
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 90c47bf7..f4c6f40b 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -1,10 +1,10 @@
-#' @title Default print for run_mod object of class sr_model
-#' @author Sam Schildhauer
+#' @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 data A [serodynamics::sr_model] object output from the
+#' @param data An `sr_model` output object from the
 #' [serodynamics::run_mod()] function.
 #' @returns A [dplyr::grouped_df] that
 #' contains the mean posterior distribution for antibody kinetic curve
diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd
index 6b14d968..847320bb 100644
--- a/man/print.sr_model.Rd
+++ b/man/print.sr_model.Rd
@@ -2,12 +2,13 @@
 % Please edit documentation in R/print.sr_model.R
 \name{print.sr_model}
 \alias{print.sr_model}
-\title{Default print for run_mod object of class sr_model}
+\title{Default print for \code{\link[=run_mod]{run_mod()}} output object of class
+\code{sr_model}}
 \usage{
 \method{print}{sr_model}(data)
 }
 \arguments{
-\item{data}{A \link{sr_model} object output from the
+\item{data}{An \code{sr_model} output object from the
 \code{\link[=run_mod]{run_mod()}} function.}
 }
 \value{
@@ -20,6 +21,3 @@ A default print method for class \code{sr_model} that includes the mean posterio
 distribution for antibody kinetic curve parameters by \code{Iso_type} and
 \code{Stratification} (if specified).
 }
-\author{
-Sam Schildhauer
-}

From 4ed27e68009a4c0c21b41ef1eacd3a89a7db499e Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:28:08 -0700
Subject: [PATCH 13/53] Updating example for print.sr_model

---
 R/print.sr_model.R    | 4 ++--
 man/print.sr_model.Rd | 3 +++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index f4c6f40b..887ddabf 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -10,8 +10,8 @@
 #' contains the mean posterior distribution for antibody kinetic curve
 #' parameters by `Iso_type` and `Stratification` (if specified).
 #' @export
-#' @example
-#' print.sr_model(nepal_sees_jags_output)
+#' @examples
+#' print(nepal_sees_jags_output)
 print.sr_model <- function(data) {
   data_group <- data |>
     dplyr::group_by(Stratification, Iso_type, Parameter) |>
diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd
index 847320bb..eb91c2a4 100644
--- a/man/print.sr_model.Rd
+++ b/man/print.sr_model.Rd
@@ -21,3 +21,6 @@ A default print method for class \code{sr_model} that includes the mean posterio
 distribution for antibody kinetic curve parameters by \code{Iso_type} and
 \code{Stratification} (if specified).
 }
+\examples{
+print(nepal_sees_jags_output)
+}

From 8e5eba79442677d5f39502d2d20cee1da9cf5a35 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:28:21 -0700
Subject: [PATCH 14/53] Increment version number to 0.0.0.9035

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index bb07d694..5409ade5 100644
--- 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."),

From f377d5c9e55be420f4b59a1e0ccfca5171348e4b Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:29:03 -0700
Subject: [PATCH 15/53] Updating news

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 1867fca0..a51dca5d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 ## New features
 
+* Creating default print.sr_model function for sr_model class (#)
 * Replacing old data object with new run_mod output (#102)
 * Adding class assignment to run_mod output (#76)
 * Making prep_priors modifiable (#78)

From 9711df67d111cd291ead51bfbaa02b8e49af949c Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:29:32 -0700
Subject: [PATCH 16/53] Adding print.sr_model to pkgdown

---
 pkgdown/_pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 39698daf..1c1ef43b 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -41,6 +41,7 @@ reference:
 - title: Summarize seroresponse model estimates
   contents:
   - post_summ
+  - print.sr_model
 - title: Example data sets
   contents:
   - serodynamics_example

From ff9ee850044a34b340d32e0d46322d9d1b6f6644 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:33:18 -0700
Subject: [PATCH 17/53] Deleting a previous default print method that was being
 created

---
 R/print_sero_mod_output.R | 32 --------------------------------
 1 file changed, 32 deletions(-)
 delete mode 100644 R/print_sero_mod_output.R

diff --git a/R/print_sero_mod_output.R b/R/print_sero_mod_output.R
deleted file mode 100644
index dc950058..00000000
--- a/R/print_sero_mod_output.R
+++ /dev/null
@@ -1,32 +0,0 @@
-#' @title Default print method for run_mod output
-#' @author Sam Schildhauer
-#' @description
-#'  Will print a default output for a run_mod object that specifies the median
-#'  value of the posterior distribution for serokinetic curve parameters (y0,
-#'  y1, t1, alpha, shape) by stratification (if specified) and antigen/iso type.
-#' @param obj A [serodynamics::sero_mod_output] object.
-#' @returns A [dplyr::tbl_df] that contains the median value of the posterior
-#' distribution of stratifications (if any specified), antigen/iso type, and
-#' parameter value.
-#' @export
-#' @example inst/examples/run_mod-examples.R
-
-print.sero_mod_output <- function(obj) {
-
-  # Summarizing results
-  df_obj <- data.frame("Parameter" = obj$Parameter, "Iso_type" = obj$Iso_type,
-                       "Stratification" = obj$Stratification, 
-                       "Value" = obj$value)
-  if (unique(df_obj$Stratification == "None")) {
-  to_print <- df_obj |>
-    dplyr::group_by(Iso_type, Parameter) |>
-    dplyr::summarize(median = median(Value)) |>
-    tidyr::spread(Parameter, median)
-  } else {
-    to_print <- df_obj |>
-      dplyr::group_by(Stratification, Iso_type, Parameter) |>
-      dplyr::summarize(median = median(Value)) |>
-      tidyr::spread(Parameter, median)
-  }
-  to_print
-}

From 8eed4a7c768d4813421c4390e44f18258f97d8a7 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:34:27 -0700
Subject: [PATCH 18/53] Updating function for pivot_wider

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 887ddabf..00780c98 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -16,7 +16,7 @@ print.sr_model <- function(data) {
   data_group <- data |>
     dplyr::group_by(Stratification, Iso_type, Parameter) |>
     dplyr::summarise(mean_val = mean(value)) |>
-    tidyr::spread(Parameter, mean_val) |>
+    pivot_wider(Parameter, mean_val) |>
     dplyr::arrange(Iso_type)
   # Taking out stratification column if not specified
   if(unique(data$Stratification == "None")) {

From 7a5ec6266efb9f9e3491ea5476e4759522f6dd1a Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Tue, 8 Jul 2025 23:35:14 -0700
Subject: [PATCH 19/53] Updating documentation to take out old print function

---
 NAMESPACE                    |  1 -
 man/print.sero_mod_output.Rd | 50 ------------------------------------
 2 files changed, 51 deletions(-)
 delete mode 100644 man/print.sero_mod_output.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 0bd66d02..c45e1ccf 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(autoplot,case_data)
-S3method(print,sero_mod_output)
 S3method(print,sr_model)
 export(as_case_data)
 export(autoplot)
diff --git a/man/print.sero_mod_output.Rd b/man/print.sero_mod_output.Rd
deleted file mode 100644
index 0dd8540f..00000000
--- a/man/print.sero_mod_output.Rd
+++ /dev/null
@@ -1,50 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/print_sero_mod_output.R
-\name{print.sero_mod_output}
-\alias{print.sero_mod_output}
-\title{Default print method for run_mod output}
-\usage{
-\method{print}{sero_mod_output}(obj)
-}
-\arguments{
-\item{obj}{A \link{sero_mod_output} object.}
-}
-\value{
-A \link[dplyr:tbl_df]{dplyr::tbl_df} that contains the median value of the posterior
-distribution of stratifications (if any specified), antigen/iso type, and
-parameter value.
-}
-\description{
-Will print a default output for a run_mod object that specifies the median
-value of the posterior distribution for serokinetic curve parameters (y0,
-y1, t1, alpha, shape) by stratification (if specified) and antigen/iso type.
-}
-\examples{
-if (!is.element(runjags::findjags(), c("", NULL))) {
-  library(runjags)
-  set.seed(1)
-  library(dplyr)
-  strat1 <- serocalculator::typhoid_curves_nostrat_100 |>
-    sim_case_data(n = 100) |>
-    mutate(strat = "stratum 2")
-  strat2 <- serocalculator::typhoid_curves_nostrat_100 |>
-    sim_case_data(n = 100) |>
-    mutate(strat = "stratum 1")
-
-  dataset <- bind_rows(strat1, strat2)
-
-  fitted_model <- run_mod(
-    data = dataset, # The data set input
-    file_mod = serodynamics_example("model.jags"),
-    nchain = 4, # Number of mcmc chains to run
-    nadapt = 100, # Number of adaptations to run
-    nburn = 100, # Number of unrecorded samples before sampling begins
-    nmc = 1000,
-    niter = 2000, # Number of iterations
-    strat = "strat"
-  ) # Variable to be stratified
-}
-}
-\author{
-Sam Schildhauer
-}

From eb4e282c2f32fd4a93b8b8cb4d7b9f0e9a213fb9 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 9 Jul 2025 17:34:54 -0700
Subject: [PATCH 20/53] Updating wordlist

---
 inst/WORDLIST | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/inst/WORDLIST b/inst/WORDLIST
index 12b8fafc..ba6d083d 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -1,6 +1,8 @@
+Biomarker
 CMD
 CodeFactor
 Codecov
+Hyperpriors
 JAGs
 Lifecycle
 Postprocess
@@ -9,6 +11,8 @@ Traceplots
 behaviour
 biomarker
 biomarkers
+bmatrix
+cdot
 dobson
 dotplots
 geoms
@@ -16,21 +20,27 @@ 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

From 141ba3c7aebfc6fa4b9a9fc5d1dd1b7b61db507d Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 9 Jul 2025 17:46:37 -0700
Subject: [PATCH 21/53] Updating lint

---
 R/print.sr_model.R | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 00780c98..a5dff189 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -14,17 +14,14 @@
 #' print(nepal_sees_jags_output)
 print.sr_model <- function(data) {
   data_group <- data |>
-    dplyr::group_by(Stratification, Iso_type, Parameter) |>
-    dplyr::summarise(mean_val = mean(value)) |>
-    pivot_wider(Parameter, mean_val) |>
-    dplyr::arrange(Iso_type)
+    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")) {
-    data_group <- data_group[,2:7]
+  if (unique(data$Stratification == "None")) {
+    data_group <- data_group[, 2:7]
   } 
   data_group
 }
-    
-  
-  
-  
\ No newline at end of file

From f95a88aa4b0323d8a901e055ff01b55862321926 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 9 Jul 2025 20:29:47 -0700
Subject: [PATCH 22/53] Fixing no lint.

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index a5dff189..33a3fed2 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -12,7 +12,7 @@
 #' @export
 #' @examples
 #' print(nepal_sees_jags_output)
-print.sr_model <- function(data) {
+print.sr_model <- function(data) { # nolint
   data_group <- data |>
     dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |>
     dplyr::summarise(mean_val = mean(.data$value)) |>

From 4dcd890514bcf6fec80a3a040595c778a6f6d30a Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Sun, 13 Jul 2025 19:32:41 -0700
Subject: [PATCH 23/53] Updating test lint

---
 tests/testthat/test-print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
index 3f0d0e11..1a523b39 100644
--- a/tests/testthat/test-print.sr_model.R
+++ b/tests/testthat/test-print.sr_model.R
@@ -3,7 +3,7 @@ test_that(
   code = {
     withr::local_seed(1)
     results <- print(nepal_sees_jags_output) |>
-          ssdtools:::expect_snapshot_data("default-print-runmod-object")
+      ssdtools:::expect_snapshot_data("default-print-runmod-object")
         
   }
 )

From ee0a73c934f0266f10feea147e79761aaac9a71c Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Sun, 13 Jul 2025 19:36:59 -0700
Subject: [PATCH 24/53] Changing review recommended test code

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 33a3fed2..86aee141 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -17,7 +17,7 @@ print.sr_model <- function(data) { # nolint
     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) |>
+                       values_from = mean_val) |>
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified
   if (unique(data$Stratification == "None")) {

From 0dbc9a2e811a37566f1050b08cf9e29fba32dfcd Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Sun, 13 Jul 2025 19:38:03 -0700
Subject: [PATCH 25/53] Updating test code based on review recommendations

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 86aee141..675acad5 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -16,7 +16,7 @@ print.sr_model <- function(data) { # nolint
   data_group <- data |>
     dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |>
     dplyr::summarise(mean_val = mean(.data$value)) |>
-    tidyr::pivot_wider(names_from = .data$Parameter, 
+    tidyr::pivot_wider(names_from = Parameter, 
                        values_from = mean_val) |>
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified

From a22ed27c47ec4093deaf5b157bb0997d1ea95844 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Sun, 13 Jul 2025 20:13:05 -0700
Subject: [PATCH 26/53] Adding .data$ back in to code

---
 R/print.sr_model.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 675acad5..33a3fed2 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -16,8 +16,8 @@ print.sr_model <- function(data) { # nolint
   data_group <- data |>
     dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |>
     dplyr::summarise(mean_val = mean(.data$value)) |>
-    tidyr::pivot_wider(names_from = Parameter, 
-                       values_from = mean_val) |>
+    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")) {

From 29ec557dcc461c794fd95eefc5f47047b7f19ebe Mon Sep 17 00:00:00 2001
From: Samuel Schildhauer <165851188+sschildhauer@users.noreply.github.com>
Date: Tue, 15 Jul 2025 18:18:44 -0700
Subject: [PATCH 27/53] Update NEWS.md

Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index a51dca5d..3d2dedea 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,7 +4,7 @@
 
 ## New features
 
-* Creating default print.sr_model function for sr_model class (#)
+* Creating default print.sr_model function for sr_model class (#114)
 * Replacing old data object with new run_mod output (#102)
 * Adding class assignment to run_mod output (#76)
 * Making prep_priors modifiable (#78)

From 9de64b06cfe30434bac93abe35ec3001e8688418 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 16 Jul 2025 20:29:10 -0700
Subject: [PATCH 28/53] Updating parameter inputs to refelct x, ...

---
 R/print.sr_model.R    | 7 ++++---
 man/print.sr_model.Rd | 6 ++++--
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 33a3fed2..d71fcbe3 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -4,7 +4,8 @@
 #'  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 data An `sr_model` output object from the
+#' @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
@@ -12,8 +13,8 @@
 #' @export
 #' @examples
 #' print(nepal_sees_jags_output)
-print.sr_model <- function(data) { # nolint
-  data_group <- data |>
+print.sr_model <- function(x, ...) { # nolint
+  data_group <- 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, 
diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd
index eb91c2a4..7f4d0fee 100644
--- a/man/print.sr_model.Rd
+++ b/man/print.sr_model.Rd
@@ -5,10 +5,12 @@
 \title{Default print for \code{\link[=run_mod]{run_mod()}} output object of class
 \code{sr_model}}
 \usage{
-\method{print}{sr_model}(data)
+\method{print}{sr_model}(x, ...)
 }
 \arguments{
-\item{data}{An \code{sr_model} output object from the
+\item{x}{An \code{sr_model} output object from \code{\link[=run_mod]{run_mod()}}.}
+
+\item{...}{Additional arguments affecting the summary produced.
 \code{\link[=run_mod]{run_mod()}} function.}
 }
 \value{

From b1d15c48a72dbfe2760052edbec12f976b9d9341 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 16 Jul 2025 20:32:13 -0700
Subject: [PATCH 29/53] Fixing column call for taking out Stratification

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index d71fcbe3..da8abbbf 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -22,7 +22,7 @@ print.sr_model <- function(x, ...) { # nolint
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified
   if (unique(data$Stratification == "None")) {
-    data_group <- data_group[, 2:7]
+    data_group <- data_group |> select(-c(Stratification))
   } 
   data_group
 }

From 0dcac1899160dd16f9bfcca60c3271d77d596fb2 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 16 Jul 2025 20:33:09 -0700
Subject: [PATCH 30/53] Fixing column Stratification exclusion

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index da8abbbf..5c4b4c6f 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -22,7 +22,7 @@ print.sr_model <- function(x, ...) { # nolint
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified
   if (unique(data$Stratification == "None")) {
-    data_group <- data_group |> select(-c(Stratification))
+    data_group <- data_group |> select(-all_of(Stratification))
   } 
   data_group
 }

From 86e9965108ecc6ca870d3c86b459b3028ed3d191 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 16 Jul 2025 20:36:01 -0700
Subject: [PATCH 31/53] Changing object call in function to "x"

---
 R/print.sr_model.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 5c4b4c6f..46bf5d26 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -14,7 +14,7 @@
 #' @examples
 #' print(nepal_sees_jags_output)
 print.sr_model <- function(x, ...) { # nolint
-  data_group <- x |>
+  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$Parameter, 
@@ -22,7 +22,7 @@ print.sr_model <- function(x, ...) { # nolint
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified
   if (unique(data$Stratification == "None")) {
-    data_group <- data_group |> select(-all_of(Stratification))
+    x <- x |> select(-all_of(Stratification))
   } 
-  data_group
+  invisible(x)
 }

From d97e4b2e750d3913cc7593464704b05fdae3dc9f Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 16 Jul 2025 20:46:07 -0700
Subject: [PATCH 32/53] Updating test for default print

---
 tests/testthat/test-print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
index 1a523b39..440b820b 100644
--- a/tests/testthat/test-print.sr_model.R
+++ b/tests/testthat/test-print.sr_model.R
@@ -3,7 +3,7 @@ test_that(
   code = {
     withr::local_seed(1)
     results <- print(nepal_sees_jags_output) |>
-      ssdtools:::expect_snapshot_data("default-print-runmod-object")
+      ssdtools:::expect_snapshot("default-print-runmod-object")
         
   }
 )

From 42b181013acd8ce2c63ff31bbeb8f8d709453c0c Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 16 Jul 2025 20:59:15 -0700
Subject: [PATCH 33/53] Increment version number to 0.0.0.9036

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index eac0b2cf..a5726c00 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: serodynamics
 Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9035
+Version: 0.0.0.9036
 Authors@R: c(
     person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

From 5c9fe1c125f97c996fb400b1b254476c2a9229f8 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Wed, 16 Jul 2025 21:10:23 -0700
Subject: [PATCH 34/53] Updating visible binding

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 46bf5d26..356501c6 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -22,7 +22,7 @@ print.sr_model <- function(x, ...) { # nolint
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified
   if (unique(data$Stratification == "None")) {
-    x <- x |> select(-all_of(Stratification))
+    x <- x |> select(-all_of(.data$Stratification))
   } 
   invisible(x)
 }

From 1252e18ec751ff8b89d7e3e8058a45589be44a25 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Thu, 31 Jul 2025 16:12:25 +0700
Subject: [PATCH 35/53] Merged origin/main into default_print

---
 NEWS.md                     |  1 +
 R/ab.R                      | 11 +++++------
 tests/testthat/_snaps/ab.md |  6 +++---
 tests/testthat/test-ab.R    |  6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 5b444e15..b854db07 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -47,6 +47,7 @@ None yet
 
 ## Developer-facing changes
 
+* vectorized `ab()` function (#116)
 * Added `lintr::undesirable_function_linter()` to `.lintr.R` (#81)
 * Reformatted `.lintr` as R file (following 
 https://github.com/r-lib/lintr/issues/2844#issuecomment-2776725389) (#81)
diff --git a/R/ab.R b/R/ab.R
index 10d2d585..652995c1 100644
--- a/R/ab.R
+++ b/R/ab.R
@@ -1,10 +1,9 @@
 ab <- function(t, y0, y1, t1, alpha, shape) {
   beta <- bt(y0, y1, t1)
-  yt <- 0
-  if (t <= t1) {
-    yt <- y0 * exp(beta * t)
-  } else {
-    yt <- (y1^(1 - shape) - (1 - shape) * alpha * (t - t1))^(1 / (1 - shape))
-  }
+  yt <- ifelse(
+    t <= t1,
+    y0 * exp(beta * t),
+    (y1^(1 - shape) - (1 - shape) * alpha * (t - t1))^(1 / (1 - shape))
+  )
   return(yt)
 }
diff --git a/tests/testthat/_snaps/ab.md b/tests/testthat/_snaps/ab.md
index 70d5f3c2..cdacb76b 100644
--- a/tests/testthat/_snaps/ab.md
+++ b/tests/testthat/_snaps/ab.md
@@ -1,8 +1,8 @@
 # results are consistent
 
     Code
-      do.call(dplyr::mutate(dplyr::select(params, -c(antigen_iso, iter), shape = r),
-      t = 10), what = ab)
+      do.call(dplyr::mutate(dplyr::rename(dplyr::select(params, -c(antigen_iso, iter)),
+      shape = r), t = 10), what = ab)
     Output
-      [1] 63.09329
+      [1]  63.09329 157.74561
 
diff --git a/tests/testthat/test-ab.R b/tests/testthat/test-ab.R
index f9407dae..51f388f2 100644
--- a/tests/testthat/test-ab.R
+++ b/tests/testthat/test-ab.R
@@ -1,11 +1,11 @@
 test_that("results are consistent", {
   params <- 
     serocalculator::typhoid_curves_nostrat_100 |> 
-    head(1)
+    head(2)
   
   params |> 
-    dplyr::select(-c(antigen_iso, iter), 
-                          shape = r) |> 
+    dplyr::select(-c(antigen_iso, iter)) |> 
+    dplyr::rename(shape = r) |> 
     dplyr::mutate(t = 10) |> 
     do.call(what = ab) |> 
     expect_snapshot()

From 9a6931eb04c65cfbc3bc8f7539c53a340207b832 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Thu, 31 Jul 2025 22:00:15 +0700
Subject: [PATCH 36/53] Updating output description and documentation

---
 R/print.sr_model.R    | 7 ++++++-
 man/print.sr_model.Rd | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 356501c6..861e43c6 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -7,13 +7,17 @@
 #' @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
+#' @returns A data summary 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
+  
+  cat("An sr_model with the following mean values:")
+  cat("\n")
+  cat("\n")
   x <- x |>
     dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |>
     dplyr::summarise(mean_val = mean(.data$value)) |>
@@ -24,5 +28,6 @@ print.sr_model <- function(x, ...) { # nolint
   if (unique(data$Stratification == "None")) {
     x <- x |> select(-all_of(.data$Stratification))
   } 
+  print(data.frame(x))
   invisible(x)
 }
diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd
index 7f4d0fee..49fc5db4 100644
--- a/man/print.sr_model.Rd
+++ b/man/print.sr_model.Rd
@@ -14,7 +14,7 @@
 \code{\link[=run_mod]{run_mod()}} function.}
 }
 \value{
-A \link[dplyr:grouped_df]{dplyr::grouped_df} that
+A data summary that
 contains the mean posterior distribution for antibody kinetic curve
 parameters by \code{Iso_type} and \code{Stratification} (if specified).
 }

From 6dda0ca8f74cd2e7238d3caf73381047a821c2ee Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Thu, 31 Jul 2025 22:12:30 +0700
Subject: [PATCH 37/53] Increment version number to 0.0.0.9037

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a5726c00..44d2af08 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: serodynamics
 Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9036
+Version: 0.0.0.9037
 Authors@R: c(
     person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

From 26c78000fd23d35b884f078c4625a8e7393701c6 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Thu, 31 Jul 2025 22:27:30 +0700
Subject: [PATCH 38/53] Updating test and snapshot

---
 tests/testthat/_snaps/print.sr_model.md | 27 +++++++++++++++++++++++++
 tests/testthat/test-print.sr_model.R    |  5 +----
 2 files changed, 28 insertions(+), 4 deletions(-)
 create mode 100644 tests/testthat/_snaps/print.sr_model.md

diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
new file mode 100644
index 00000000..a235ba65
--- /dev/null
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -0,0 +1,27 @@
+# results are consistent with printed output for sr_model class
+
+    Code
+      print(nepal_sees_jags_output)
+    Output
+      An sr_model with the following mean values:
+      
+    Condition
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Parameter"` instead of `.data$Parameter`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"mean_val"` instead of `.data$mean_val`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Parameter"` instead of `.data$Parameter`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"mean_val"` instead of `.data$mean_val`
+    Output
+        Stratification Iso_type       alpha    shape       t1       y0        y1
+      1      paratyphi HlyE_IgA 0.002286716 1.664825 3.850284 2.550720 1024.2988
+      2          typhi HlyE_IgA 0.002905432 1.612991 7.306797 2.967301 1031.8956
+      3      paratyphi HlyE_IgG 0.002568724 1.360532 4.779399 1.721313  833.1053
+      4          typhi HlyE_IgG 0.001536668 1.408457 8.728905 2.314505  338.5723
+
diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
index 440b820b..50966cd5 100644
--- a/tests/testthat/test-print.sr_model.R
+++ b/tests/testthat/test-print.sr_model.R
@@ -1,9 +1,6 @@
 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")
-        
+      expect_snapshot(print(nepal_sees_jags_output))
   }
 )

From 27b1c52b3872b226a07d63461a9f0f68b3bf7283 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 1 Aug 2025 11:47:49 +0700
Subject: [PATCH 39/53] Fixing lint in test

---
 tests/testthat/test-print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
index 50966cd5..d0b248c6 100644
--- a/tests/testthat/test-print.sr_model.R
+++ b/tests/testthat/test-print.sr_model.R
@@ -1,6 +1,6 @@
 test_that(
   desc = "results are consistent with printed output for sr_model class",
   code = {
-      expect_snapshot(print(nepal_sees_jags_output))
+    expect_snapshot(print(nepal_sees_jags_output))
   }
 )

From e6b54c1c57dcc402d6bdd16f4df8e78c56506f15 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 1 Aug 2025 11:49:09 +0700
Subject: [PATCH 40/53] Fixing for closure

---
 R/print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 861e43c6..3d18e6b0 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -25,7 +25,7 @@ print.sr_model <- function(x, ...) { # nolint
                        values_from = .data$mean_val) |>
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified
-  if (unique(data$Stratification == "None")) {
+  if (unique(.data$Stratification == "None")) {
     x <- x |> select(-all_of(.data$Stratification))
   } 
   print(data.frame(x))

From 1657ff1ad6c00ecae7e5fbcec0ccb82901fbf046 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 1 Aug 2025 11:59:46 +0700
Subject: [PATCH 41/53] Fixing data call in if statement

---
 R/print.sr_model.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 3d18e6b0..90edf098 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -25,8 +25,8 @@ print.sr_model <- function(x, ...) { # nolint
                        values_from = .data$mean_val) |>
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified
-  if (unique(.data$Stratification == "None")) {
-    x <- x |> select(-all_of(.data$Stratification))
+  if (unique(x$Stratification == "None")) {
+    x <- x |> select(-c(.data$Stratification))
   } 
   print(data.frame(x))
   invisible(x)

From 571bf165e8f31de981d793903280b96b026fe265 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 1 Aug 2025 13:38:56 +0700
Subject: [PATCH 42/53] Updating snap.

---
 R/print.sr_model.R                      |  7 ++++---
 tests/testthat/_snaps/print.sr_model.md | 21 ++++++++++++++++-----
 2 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 90edf098..2fe15be5 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -19,8 +19,9 @@ print.sr_model <- function(x, ...) { # nolint
   cat("\n")
   cat("\n")
   x <- x |>
-    dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |>
-    dplyr::summarise(mean_val = mean(.data$value)) |>
+    dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, 
+                             .data$Parameter), 
+                     mean_val = mean(.data$value)) |>
     tidyr::pivot_wider(names_from = .data$Parameter, 
                        values_from = .data$mean_val) |>
     dplyr::arrange(.data$Iso_type)
@@ -28,6 +29,6 @@ print.sr_model <- function(x, ...) { # nolint
   if (unique(x$Stratification == "None")) {
     x <- x |> select(-c(.data$Stratification))
   } 
-  print(data.frame(x))
+  print(x)
   invisible(x)
 }
diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
index a235ba65..7da7bdd4 100644
--- a/tests/testthat/_snaps/print.sr_model.md
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -6,6 +6,15 @@
       An sr_model with the following mean values:
       
     Condition
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Stratification"` instead of `.data$Stratification`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Iso_type"` instead of `.data$Iso_type`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Parameter"` instead of `.data$Parameter`
       Warning:
       Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
       i Please use `"Parameter"` instead of `.data$Parameter`
@@ -19,9 +28,11 @@
       Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
       i Please use `"mean_val"` instead of `.data$mean_val`
     Output
-        Stratification Iso_type       alpha    shape       t1       y0        y1
-      1      paratyphi HlyE_IgA 0.002286716 1.664825 3.850284 2.550720 1024.2988
-      2          typhi HlyE_IgA 0.002905432 1.612991 7.306797 2.967301 1031.8956
-      3      paratyphi HlyE_IgG 0.002568724 1.360532 4.779399 1.721313  833.1053
-      4          typhi HlyE_IgG 0.001536668 1.408457 8.728905 2.314505  338.5723
+      # A tibble: 4 x 7
+        Stratification Iso_type   alpha shape    t1    y0    y1
+        <chr>          <chr>      <dbl> <dbl> <dbl> <dbl> <dbl>
+      1 typhi          HlyE_IgA 0.00291  1.61  7.31  2.97 1032.
+      2 paratyphi      HlyE_IgA 0.00229  1.66  3.85  2.55 1024.
+      3 typhi          HlyE_IgG 0.00154  1.41  8.73  2.31  339.
+      4 paratyphi      HlyE_IgG 0.00257  1.36  4.78  1.72  833.
 

From 95a91c9843bf911288e8595a145c97681c9c022e Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Sun, 3 Aug 2025 22:30:27 +0700
Subject: [PATCH 43/53] making output table a dataframe to get rid of tibble
 descriptors

---
 R/print.sr_model.R                      |  2 +-
 tests/testthat/_snaps/print.sr_model.md | 12 +++++-------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 2fe15be5..cb9e8cd9 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -29,6 +29,6 @@ print.sr_model <- function(x, ...) { # nolint
   if (unique(x$Stratification == "None")) {
     x <- x |> select(-c(.data$Stratification))
   } 
-  print(x)
+  print(as.data.frame(x))
   invisible(x)
 }
diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
index 7da7bdd4..db291607 100644
--- a/tests/testthat/_snaps/print.sr_model.md
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -28,11 +28,9 @@
       Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
       i Please use `"mean_val"` instead of `.data$mean_val`
     Output
-      # A tibble: 4 x 7
-        Stratification Iso_type   alpha shape    t1    y0    y1
-        <chr>          <chr>      <dbl> <dbl> <dbl> <dbl> <dbl>
-      1 typhi          HlyE_IgA 0.00291  1.61  7.31  2.97 1032.
-      2 paratyphi      HlyE_IgA 0.00229  1.66  3.85  2.55 1024.
-      3 typhi          HlyE_IgG 0.00154  1.41  8.73  2.31  339.
-      4 paratyphi      HlyE_IgG 0.00257  1.36  4.78  1.72  833.
+        Stratification Iso_type       alpha    shape       t1       y0        y1
+      1          typhi HlyE_IgA 0.002905432 1.612991 7.306797 2.967301 1031.8956
+      2      paratyphi HlyE_IgA 0.002286716 1.664825 3.850284 2.550720 1024.2988
+      3          typhi HlyE_IgG 0.001536668 1.408457 8.728905 2.314505  338.5723
+      4      paratyphi HlyE_IgG 0.002568724 1.360532 4.779399 1.721313  833.1053
 

From 3915ec2a24fcf199c080847692776fdf3656ce5d Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Mon, 4 Aug 2025 15:50:31 +0700
Subject: [PATCH 44/53] Updating print test

---
 tests/testthat/_snaps/print.sr_model.md | 2 +-
 tests/testthat/test-print.sr_model.R    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
index db291607..bbc55ae3 100644
--- a/tests/testthat/_snaps/print.sr_model.md
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -1,7 +1,7 @@
 # results are consistent with printed output for sr_model class
 
     Code
-      print(nepal_sees_jags_output)
+      nepal_sees_jags_output
     Output
       An sr_model with the following mean values:
       
diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
index d0b248c6..a3f99df4 100644
--- a/tests/testthat/test-print.sr_model.R
+++ b/tests/testthat/test-print.sr_model.R
@@ -1,6 +1,6 @@
 test_that(
   desc = "results are consistent with printed output for sr_model class",
   code = {
-    expect_snapshot(print(nepal_sees_jags_output))
+    expect_snapshot(nepal_sees_jags_output)
   }
 )

From 4233b52596183e23806d4724598d56729119cece Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Mon, 4 Aug 2025 16:14:42 +0700
Subject: [PATCH 45/53] Updating snap

---
 tests/testthat/_snaps/print.sr_model.md | 2 +-
 tests/testthat/test-print.sr_model.R    | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
index bbc55ae3..13a362ad 100644
--- a/tests/testthat/_snaps/print.sr_model.md
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -1,7 +1,7 @@
 # results are consistent with printed output for sr_model class
 
     Code
-      nepal_sees_jags_output
+      suppressWarnings(nepal_sees_jags_output)
     Output
       An sr_model with the following mean values:
       
diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
index a3f99df4..820bd268 100644
--- a/tests/testthat/test-print.sr_model.R
+++ b/tests/testthat/test-print.sr_model.R
@@ -1,6 +1,8 @@
 test_that(
   desc = "results are consistent with printed output for sr_model class",
   code = {
-    expect_snapshot(nepal_sees_jags_output)
+    nepal_sees_jags_output |>
+      suppressWarnings() |>
+      expect_snapshot() 
   }
 )

From 37f451e33ccc6fe940814aa6d56e5e5e9c0d7fe4 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Thu, 7 Aug 2025 13:10:20 +0700
Subject: [PATCH 46/53] Making model output median value

---
 R/print.sr_model.R    | 10 +++++-----
 man/print.sr_model.Rd |  6 +++---
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index cb9e8cd9..980904be 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -1,9 +1,9 @@
 #' @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).
+#'  A default print method for class `sr_model` that includes the median
+#'  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.
@@ -15,13 +15,13 @@
 #' print(nepal_sees_jags_output)
 print.sr_model <- function(x, ...) { # nolint
   
-  cat("An sr_model with the following mean values:")
+  cat("An sr_model with the following median values:")
   cat("\n")
   cat("\n")
   x <- x |>
     dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, 
                              .data$Parameter), 
-                     mean_val = mean(.data$value)) |>
+                     median_val = stats::median(.data$value)) |>
     tidyr::pivot_wider(names_from = .data$Parameter, 
                        values_from = .data$mean_val) |>
     dplyr::arrange(.data$Iso_type)
diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd
index 49fc5db4..67be9223 100644
--- a/man/print.sr_model.Rd
+++ b/man/print.sr_model.Rd
@@ -19,9 +19,9 @@ contains the mean posterior distribution for antibody kinetic curve
 parameters by \code{Iso_type} and \code{Stratification} (if specified).
 }
 \description{
-A default print method for class \code{sr_model} that includes the mean posterior
-distribution for antibody kinetic curve parameters by \code{Iso_type} and
-\code{Stratification} (if specified).
+A default print method for class \code{sr_model} that includes the median
+posterior distribution for antibody kinetic curve parameters by \code{Iso_type}
+and \code{Stratification} (if specified).
 }
 \examples{
 print(nepal_sees_jags_output)

From 3f8c7066ef5f106ed3811a65a86eb7d6bcaa0f3d Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Thu, 7 Aug 2025 13:11:32 +0700
Subject: [PATCH 47/53] Updating test snap

---
 R/print.sr_model.R                      |  2 +-
 tests/testthat/_snaps/print.sr_model.md | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index 980904be..c7eca62c 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -23,7 +23,7 @@ print.sr_model <- function(x, ...) { # nolint
                              .data$Parameter), 
                      median_val = stats::median(.data$value)) |>
     tidyr::pivot_wider(names_from = .data$Parameter, 
-                       values_from = .data$mean_val) |>
+                       values_from = .data$median_val) |>
     dplyr::arrange(.data$Iso_type)
   # Taking out stratification column if not specified
   if (unique(x$Stratification == "None")) {
diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
index 13a362ad..01b63ff3 100644
--- a/tests/testthat/_snaps/print.sr_model.md
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -3,7 +3,7 @@
     Code
       suppressWarnings(nepal_sees_jags_output)
     Output
-      An sr_model with the following mean values:
+      An sr_model with the following median values:
       
     Condition
       Warning:
@@ -20,17 +20,17 @@
       i Please use `"Parameter"` instead of `.data$Parameter`
       Warning:
       Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"mean_val"` instead of `.data$mean_val`
+      i Please use `"median_val"` instead of `.data$median_val`
       Warning:
       Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
       i Please use `"Parameter"` instead of `.data$Parameter`
       Warning:
       Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"mean_val"` instead of `.data$mean_val`
+      i Please use `"median_val"` instead of `.data$median_val`
     Output
-        Stratification Iso_type       alpha    shape       t1       y0        y1
-      1          typhi HlyE_IgA 0.002905432 1.612991 7.306797 2.967301 1031.8956
-      2      paratyphi HlyE_IgA 0.002286716 1.664825 3.850284 2.550720 1024.2988
-      3          typhi HlyE_IgG 0.001536668 1.408457 8.728905 2.314505  338.5723
-      4      paratyphi HlyE_IgG 0.002568724 1.360532 4.779399 1.721313  833.1053
+        Stratification Iso_type       alpha    shape       t1       y0      y1
+      1          typhi HlyE_IgA 0.001788800 1.538820 6.235540 2.405515 342.565
+      2      paratyphi HlyE_IgA 0.001272495 1.614535 3.700500 2.406050 153.787
+      3          typhi HlyE_IgG 0.001140990 1.346445 7.025800 2.073250 252.156
+      4      paratyphi HlyE_IgG 0.001742340 1.321350 4.370495 1.537045 288.325
 

From ff21aa331d984005c6e6ee786f3da8c94e370993 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 8 Aug 2025 14:26:49 +0700
Subject: [PATCH 48/53] Increment version number to 0.0.0.9038

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 44d2af08..65983bda 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: serodynamics
 Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9037
+Version: 0.0.0.9038
 Authors@R: c(
     person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

From 47ab5b07d3193e95fd77f58f148035f9edf8c204 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 8 Aug 2025 14:33:51 +0700
Subject: [PATCH 49/53] Redoing snap

---
 tests/testthat/_snaps/print.sr_model.md | 36 -------------------------
 1 file changed, 36 deletions(-)
 delete mode 100644 tests/testthat/_snaps/print.sr_model.md

diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
deleted file mode 100644
index 01b63ff3..00000000
--- a/tests/testthat/_snaps/print.sr_model.md
+++ /dev/null
@@ -1,36 +0,0 @@
-# results are consistent with printed output for sr_model class
-
-    Code
-      suppressWarnings(nepal_sees_jags_output)
-    Output
-      An sr_model with the following median values:
-      
-    Condition
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Stratification"` instead of `.data$Stratification`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Iso_type"` instead of `.data$Iso_type`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Parameter"` instead of `.data$Parameter`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Parameter"` instead of `.data$Parameter`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"median_val"` instead of `.data$median_val`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Parameter"` instead of `.data$Parameter`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"median_val"` instead of `.data$median_val`
-    Output
-        Stratification Iso_type       alpha    shape       t1       y0      y1
-      1          typhi HlyE_IgA 0.001788800 1.538820 6.235540 2.405515 342.565
-      2      paratyphi HlyE_IgA 0.001272495 1.614535 3.700500 2.406050 153.787
-      3          typhi HlyE_IgG 0.001140990 1.346445 7.025800 2.073250 252.156
-      4      paratyphi HlyE_IgG 0.001742340 1.321350 4.370495 1.537045 288.325
-

From 0c2a6bd403bd0a9f4145d51824dc5ab4cd0715b3 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 8 Aug 2025 14:35:15 +0700
Subject: [PATCH 50/53] Updating snap to suppress warnings

---
 R/print.sr_model.R                      |  3 ++-
 tests/testthat/_snaps/print.sr_model.md | 36 +++++++++++++++++++++++++
 2 files changed, 38 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat/_snaps/print.sr_model.md

diff --git a/R/print.sr_model.R b/R/print.sr_model.R
index c7eca62c..a10f930b 100644
--- a/R/print.sr_model.R
+++ b/R/print.sr_model.R
@@ -24,7 +24,8 @@ print.sr_model <- function(x, ...) { # nolint
                      median_val = stats::median(.data$value)) |>
     tidyr::pivot_wider(names_from = .data$Parameter, 
                        values_from = .data$median_val) |>
-    dplyr::arrange(.data$Iso_type)
+    dplyr::arrange(.data$Iso_type) |>
+    suppressWarnings()
   # Taking out stratification column if not specified
   if (unique(x$Stratification == "None")) {
     x <- x |> select(-c(.data$Stratification))
diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
new file mode 100644
index 00000000..01b63ff3
--- /dev/null
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -0,0 +1,36 @@
+# results are consistent with printed output for sr_model class
+
+    Code
+      suppressWarnings(nepal_sees_jags_output)
+    Output
+      An sr_model with the following median values:
+      
+    Condition
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Stratification"` instead of `.data$Stratification`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Iso_type"` instead of `.data$Iso_type`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Parameter"` instead of `.data$Parameter`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Parameter"` instead of `.data$Parameter`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"median_val"` instead of `.data$median_val`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"Parameter"` instead of `.data$Parameter`
+      Warning:
+      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+      i Please use `"median_val"` instead of `.data$median_val`
+    Output
+        Stratification Iso_type       alpha    shape       t1       y0      y1
+      1          typhi HlyE_IgA 0.001788800 1.538820 6.235540 2.405515 342.565
+      2      paratyphi HlyE_IgA 0.001272495 1.614535 3.700500 2.406050 153.787
+      3          typhi HlyE_IgG 0.001140990 1.346445 7.025800 2.073250 252.156
+      4      paratyphi HlyE_IgG 0.001742340 1.321350 4.370495 1.537045 288.325
+

From 04c720002ca5cb39520e0ce06f51cdfa654d75bf Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 8 Aug 2025 14:35:27 +0700
Subject: [PATCH 51/53] Updating snap

---
 tests/testthat/_snaps/print.sr_model.md | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
index 01b63ff3..e796e1c9 100644
--- a/tests/testthat/_snaps/print.sr_model.md
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -5,29 +5,6 @@
     Output
       An sr_model with the following median values:
       
-    Condition
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Stratification"` instead of `.data$Stratification`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Iso_type"` instead of `.data$Iso_type`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Parameter"` instead of `.data$Parameter`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Parameter"` instead of `.data$Parameter`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"median_val"` instead of `.data$median_val`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"Parameter"` instead of `.data$Parameter`
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"median_val"` instead of `.data$median_val`
-    Output
         Stratification Iso_type       alpha    shape       t1       y0      y1
       1          typhi HlyE_IgA 0.001788800 1.538820 6.235540 2.405515 342.565
       2      paratyphi HlyE_IgA 0.001272495 1.614535 3.700500 2.406050 153.787

From 87dd5c7351870aa0b4bcf0f406ed819078bdfdb2 Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 8 Aug 2025 14:49:45 +0700
Subject: [PATCH 52/53] troubleshooting snap

---
 tests/testthat/_snaps/print.sr_model.md | 2 +-
 tests/testthat/test-print.sr_model.R    | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md
index e796e1c9..634ff26c 100644
--- a/tests/testthat/_snaps/print.sr_model.md
+++ b/tests/testthat/_snaps/print.sr_model.md
@@ -1,7 +1,7 @@
 # results are consistent with printed output for sr_model class
 
     Code
-      suppressWarnings(nepal_sees_jags_output)
+      nepal_sees_jags_output
     Output
       An sr_model with the following median values:
       
diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
index 820bd268..b835db0e 100644
--- a/tests/testthat/test-print.sr_model.R
+++ b/tests/testthat/test-print.sr_model.R
@@ -1,8 +1,6 @@
 test_that(
   desc = "results are consistent with printed output for sr_model class",
   code = {
-    nepal_sees_jags_output |>
-      suppressWarnings() |>
-      expect_snapshot() 
+      testthat::expect_snapshot(nepal_sees_jags_output) 
   }
 )

From 9f2fd61a1b038df496865eff79455458bd91e41d Mon Sep 17 00:00:00 2001
From: sschildhauer <sschildhauer@ucdavis.edu>
Date: Fri, 8 Aug 2025 15:14:49 +0700
Subject: [PATCH 53/53] Fixing lint

---
 tests/testthat/test-print.sr_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R
index b835db0e..c1715a0d 100644
--- a/tests/testthat/test-print.sr_model.R
+++ b/tests/testthat/test-print.sr_model.R
@@ -1,6 +1,6 @@
 test_that(
   desc = "results are consistent with printed output for sr_model class",
   code = {
-      testthat::expect_snapshot(nepal_sees_jags_output) 
+    testthat::expect_snapshot(nepal_sees_jags_output) 
   }
 )