Remove serodata from pre-loaded datasets of the package (#107)

* remove serodata .Rdata and .Rd files * remove R/serodata.R * doc: update functions documentation replacing for in examples * doc: update serofoi logo * doc: update README and vignettes This commit changes the removed preloaded dataset `serodata` for the identical `chagas2012`. * fix: minor correction to test_modelling
epiverse-trace · Aug 22, 2023 · 7462065 · 7462065
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diff --git a/R/model_comparison.R b/R/model_comparison.R
@@ -6,10 +6,10 @@
 #' @return rhats table
 #' @examples
 #' \dontrun{
-#' data("serodata")
-#' data_test <- prepare_serodata(serodata = serodata)
-#' model_constant <- run_seromodel(serodata = data_test, 
-#'                                 foi_model = "constant", 
+#' data(chagas2012)
+#' data_test <- prepare_serodata(serodata = chagas2012)
+#' model_constant <- run_seromodel(serodata = data_test,
+#'                                 foi_model = "constant",
 #'                                 n_iters = 1500)
 #' get_table_rhats(model_object = model_constant)
 #' }

diff --git a/R/modelling.R b/R/modelling.R
@@ -43,9 +43,9 @@
 #' @return \code{seromodel_object}. An object containing relevant information about the implementation of the model. For further details refer to \link{fit_seromodel}.
 #' @examples
 #' \dontrun{
-#' serodata <- prepare_serodata(serodata)
-#' run_seromodel (serodata,
-#'            foi_model = "constant")
+#' serodata <- prepare_serodata(chagas2012)
+#' run_seromodel (chagas2012,
+#'                foi_model = "constant")
 #' }
 #' @export
 run_seromodel <- function(serodata,
@@ -114,8 +114,8 @@ run_seromodel <- function(serodata,
 
 #' @examples
 #' \dontrun{
-#' data("serodata")
-#' serodata <- prepare_serodata(serodata)
+#' data(chagas2012)
+#' serodata <- prepare_serodata(chagas2012)
 #' seromodel_fit <- fit_seromodel(serodata = serodata,
 #'                                foi_model = "constant")
 #' }
@@ -255,8 +255,8 @@ fit_seromodel <- function(serodata,
 #' @return \code{exposure_ages}. An atomic vector with the numeration of the exposition years in serodata
 #' @examples
 #' \dontrun{
-#' data("serodata")
-#' serodata <- prepare_serodata(serodata = serodata, alpha = 0.05)
+#' data(chagas2012)
+#' serodata <- prepare_serodata(serodata = chagas2012, alpha = 0.05)
 #' exposure_ages <- get_exposure_ages(serodata)
 #' }
 #' @export
@@ -271,8 +271,8 @@ get_exposure_ages <- function(serodata) {
 #' @return \code{exposure_output}. An atomic matrix containing the expositions for each entry of \code{serodata} by year.
 #' @examples
 #' \dontrun{
-#' data("serodata")
-#' serodata <- prepare_serodata(serodata = serodata)
+#' data(chagas2012)
+#' serodata <- prepare_serodata(serodata = chagas2012)
 #' exposure_matrix <- get_exposure_matrix(serodata = serodata)
 #' }
 #' @export
@@ -313,8 +313,8 @@ get_exposure_matrix <- function(serodata) {
 #' }
 #' @examples
 #' \dontrun{
-#' data("serodata")
-#' serodata <- prepare_serodata(serodata)
+#' data(chagas2012)
+#' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- run_seromodel(serodata = serodata,
 #'                                   foi_model = "constant")
 #' extract_seromodel_summary(seromodel_object)
@@ -366,7 +366,8 @@ extract_seromodel_summary <- function(seromodel_object) {
 #' @return \code{prev_final}. The expanded prevalence data. This is used for plotting purposes in the \code{visualization} module.
 #' @examples
 #' \dontrun{
-#' serodata <- prepare_serodata(serodata)
+#' data(chagas2012)
+#' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- run_seromodel(serodata = serodata,
 #'                           foi_model = "constant")
 #' foi <- rstan::extract(seromodel_object$fit, "foi")[[1]]

diff --git a/R/serodata.R b/R/serodata.R
diff --git a/R/seroprevalence_data.R b/R/seroprevalence_data.R
@@ -30,8 +30,8 @@
 #' }
 #' @examples
 #'\dontrun{
-#' data("serodata")
-#' data_test <- prepare_serodata(serodata)
+#' data(chagas2012)
+#' serodata <- prepare_serodata(chagas2012)
 #' }
 #' @export
 prepare_serodata <- function(serodata = serodata,
@@ -91,7 +91,8 @@ prepare_serodata <- function(serodata = serodata,
 #' @return data set with the binomial confidence intervals
 #' @examples
 #'\dontrun{
-#' prepare_bin_data (serodata)
+#' data(chagas2012)
+#' prepare_bin_data(chagas2012)
 #' }
 #' @export
 prepare_bin_data <- function(serodata) {

diff --git a/R/visualisation.R b/R/visualisation.R
@@ -17,9 +17,10 @@
 #' @return A ggplot object containing the seropositivity-vs-age graph of the raw data of a given seroprevalence survey with its corresponging binomial confidence interval.
 #' @examples
 #' \dontrun{
-#'  data_test <- prepare_serodata(serodata)
+#'  data(chagas2012)
+#'  serodata <- prepare_serodata(chagas2012)
 #'  seromodel_object <- run_seromodel(
-#'  serodata = data_test,
+#'  serodata = serodata,
 #'  foi_model = "constant",
 #'  n_iters = 1000
 #')
@@ -52,9 +53,9 @@ plot_seroprev <- function(serodata,
 #' @return A ggplot object containing the seropositivity-vs-age graph including the data, the fitted model and their corresponding confindence intervals.
 #' @examples
 #' \dontrun{
-#' data("serodata")
-#' data_test <- prepare_serodata(serodata)
-#' seromodel_object <- run_seromodel(serodata = data_test,
+#' data(chagas2012)
+#' serodata <- prepare_serodata(chagas2012)
+#' seromodel_object <- run_seromodel(serodata = serodata,
 #'                                   foi_model = "constant",
 #'                                   n_iters = 1000)
 #' plot_seroprev_fitted(seromodel_object, size_text = 15)
@@ -133,12 +134,13 @@ plot_seroprev_fitted <- function(seromodel_object,
 #' @return A ggplot2 object containing the Force-of-infection-vs-time including the corresponding confidence interval.
 #' @examples
 #' \dontrun{
-#'    data_test <- prepare_serodata(serodata)
-#'    seromodel_object <- run_seromodel(
-#'    serodata = data_test,
+#'  data(chagas2012)
+#'  serodata <- prepare_serodata(chagas2012)
+#'  seromodel_object <- run_seromodel(
+#'    serodata = serodata,
 #'    foi_model = "constant",
 #'    n_iters = 1000
-#' )
+#'  )
 #' plot_foi(seromodel_object, size_text = 15)
 #' }
 #' @export
@@ -228,14 +230,14 @@ plot_foi <- function(seromodel_object,
 #' @return The rhats-convergence plot of the selected model.
 #' @examples
 #' \dontrun{
-#' data("serodata")
-#' data_test <- prepare_serodata(serodata)
+#' data(chagas2012)
+#' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- run_seromodel(
-#'  serodata = data_test,
+#'  serodata = serodata,
 #'  foi_model = "constant",
 #'  n_iters = 1000
-#')
-#' plot_rhats(seromodel_object, 
+#'  )
+#' plot_rhats(seromodel_object,
 #'            size_text = 15)
 #' }
 #' @export
@@ -294,12 +296,13 @@ plot_rhats <- function(seromodel_object,
 #' @return A ggplot object with a vertical arrange containing the seropositivity, force of infection, and convergence plots.
 #' @examples
 #' \dontrun{
-#' data_test <- prepare_serodata(serodata)
-#' seromodel_object <- run_seromodel(
-#'  serodata = data_test,
-#'  foi_model = "constant",
-#'  n_iters = 1000
-#')
+#'  data(chagas2012)
+#'  serodata <- prepare_serodata(chagas2012)
+#'  seromodel_object <- run_seromodel(
+#'    serodata = serodata,
+#'    foi_model = "constant",
+#'    n_iters = 1000
+#'  )
 #' plot_seromodel(seromodel_object, size_text = 15)
 #' }
 #' @export
@@ -378,12 +381,12 @@ plot_seromodel <- function(seromodel_object,
 #' @return p the plot for the given table
 #' @examples
 #' \dontrun{
-#'  data_test <- prepare_serodata(serodata)
+#'  serodata <- prepare_serodata(chagas2012)
 #'  seromodel_object <- run_seromodel(
-#'  serodata = data_test,
-#'  foi_model = "constant",
-#'  n_iters = 1000
-#')
+#'    serodata = serodata,
+#'    foi_model = "constant",
+#'    n_iters = 1000
+#'  )
 #' info = t(seromodel_object$model_summary)
 #' plot_info_table (info, size_text = 15)
 #' }

diff --git a/README.Rmd b/README.Rmd
@@ -15,7 +15,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-## *serofoi*: force-of-infection from population based serosurveys with age-disagregated data <img src="man/figures/serofoi-logo.png" align="right" width="130"/>
+## *serofoi*: force-of-infection from population based serosurveys with age-disagregated data <img src="man/figures/logo.svg" align="right" width="130"/>
 
 <!-- badges: start -->
 
@@ -47,22 +47,20 @@ remotes::install_github("epiverse-trace/serofoi")
 
 ```{r cleaning, include = FALSE, echo = TRUE}
 library(serofoi)
-rownames(serodata) <- NULL 
-
 ```
 
 ***serofoi*** provides a minimal serosurvey dataset, `serodata`, that can be used to test out the package.
 
 ```{r ex, include = TRUE}
-# Load example serodata data included with the package
-data("serodata")
-head(serodata, 5)
+# Load example dataset chagas2012 included with the package
+data(chagas2012)
+head(chagas2012, 5)
 ```
 
 The function `prepare_serodata` will prepare the entry data for the use of the modelling module; this function computes the sample size, the years of birth and the binomial confidence interval for each age group in the provided dataset. A visualisation of the prepared seroprevalence data can be obtained using the function plot_seroprev:
 
 ```{r data_test, include = TRUE, out.fig.height="30%", out.width="50%", fig.align="center", message=FALSE}
-serodata_test <- prepare_serodata(serodata)
+serodata_test <- prepare_serodata(chagas2012)
 plot_seroprev(serodata_test, size_text = 15)
 ```
 

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 
-## *serofoi*: force-of-infection from population based serosurveys with age-disagregated data <img src="man/figures/serofoi-logo.png" align="right" width="130"/>
+## *serofoi*: force-of-infection from population based serosurveys with age-disagregated data <img src="man/figures/logo.svg" align="right" width="130"/>
 
 <!-- badges: start -->
 
@@ -48,9 +48,9 @@ remotes::install_github("epiverse-trace/serofoi")
 can be used to test out the package.
 
 ``` r
-# Load example serodata data included with the package
-data("serodata")
-head(serodata, 5)
+# Load example dataset chagas2012 included with the package
+data(chagas2012)
+head(chagas2012, 5)
 #>       survey total counts age_min age_max tsur country  test         antibody
 #> 1 COL-035-93    34      0       1       1 2012     COL ELISA IgG anti-T.cruzi
 #> 2 COL-035-93    25      0       2       2 2012     COL ELISA IgG anti-T.cruzi
@@ -66,7 +66,7 @@ in the provided dataset. A visualisation of the prepared seroprevalence
 data can be obtained using the function plot_seroprev:
 
 ``` r
-serodata_test <- prepare_serodata(serodata)
+serodata_test <- prepare_serodata(chagas2012)
 plot_seroprev(serodata_test, size_text = 15)
 ```
 
@@ -97,10 +97,10 @@ More details on how to use ***serofoi*** can be found in the [online
 documentation](https://epiverse-trace.github.io/serofoi/) as package
 vignettes, under [**Get
 Started**](https://epiverse-trace.github.io/serofoi/articles/serofoi.html),
-[**FoI
+[**An Introduction to FoI
 Models**](https://epiverse-trace.github.io/serofoi/articles/foi_models.html)
-and [**Use
-Cases**](https://epiverse-trace.github.io/serofoi/articles/use_cases.html)
+and [**Real-life Use Cases for
+serofoi**](https://epiverse-trace.github.io/serofoi/articles/use_cases.html)
 
 ## Help
 

diff --git a/data/serodata.RData b/data/serodata.RData
diff --git a/man/extract_seromodel_summary.Rd b/man/extract_seromodel_summary.Rd
diff --git a/man/fit_seromodel.Rd b/man/fit_seromodel.Rd
diff --git a/man/get_exposure_ages.Rd b/man/get_exposure_ages.Rd
diff --git a/man/get_exposure_matrix.Rd b/man/get_exposure_matrix.Rd
diff --git a/man/get_prev_expanded.Rd b/man/get_prev_expanded.Rd
diff --git a/man/get_table_rhats.Rd b/man/get_table_rhats.Rd
diff --git a/man/plot_foi.Rd b/man/plot_foi.Rd