Add dontrun to examples taking too long to run

CITATION.cff

@@ -10,7 +10,7 @@ license: MIT
 title: 'serofoi: Bayesian Estimation of the Force of Infection from Serological Data'
 version: 1.0.2
 abstract: Estimating the force of infection from time varying, age varying, or constant
-  serocatalytic models from population based seroprevalence studies using a bayesian
+  serocatalytic models from population based seroprevalence studies using a Bayesian
   framework, including data simulation functions enabling the generation of serological
   surveys based on this models. This tool also provides a flexible prior specification
   syntax for the force of infection and the seroreversion rate, as well as methods
@@ -229,7 +229,7 @@ references:
   title: Matrix
   abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
   notes: Imports
-  url: https://Matrix.R-forge.R-project.org
+  url: https://R-forge.R-project.org/tracker/?atid=294&group_id=61
   repository: https://CRAN.R-project.org/package=Matrix
   authors:
   - family-names: Bates

DESCRIPTION

@@ -25,7 +25,7 @@ Authors@R: c(
     person("Pontificia Universidad Javeriana", role = "cph")
   )
 Description: Estimating the force of infection from time varying, age varying, or constant
-    serocatalytic models from population based seroprevalence studies using a bayesian framework,
+    serocatalytic models from population based seroprevalence studies using a Bayesian framework,
     including data simulation functions enabling the generation of serological surveys based on this
     models. This tool also provides a flexible prior specification syntax for the force of infection
     and the seroreversion rate, as well as methods to assess model convergence and comparison

R/fit_seromodel.R

@@ -103,6 +103,7 @@ set_foi_init <- function(
 #' @return stan_fit object with Force-of-Infection and seroreversion
 #' (when applicable) samples
 #' @examples
+#' \donttest{
 #' data(chagas2012)
 #' seromodel <- fit_seromodel(
 #'   serosurvey = chagas2012,
@@ -113,6 +114,7 @@ set_foi_init <- function(
 #'   ),
 #'   iter = 100
 #' )
+#' }
 #' @export
 fit_seromodel <- function(
   serosurvey,

R/plot_seromodel.R

@@ -308,6 +308,7 @@ plot_seroprev_estimates <- function(
 #' @param foi_max Max FoI value for plotting
 #' @return ggplot object with estimated FoI
 #' @examples
+#' \donttest{
 #' data(chagas2012)
 #' seromodel <- fit_seromodel(
 #'   serosurvey = chagas2012,
@@ -320,6 +321,7 @@ plot_seroprev_estimates <- function(
 #'   chains = 2
 #' )
 #' plot_foi_estimates(seromodel, chagas2012)
+#' }
 #' @export
 plot_foi_estimates <- function(
   seromodel,
@@ -443,6 +445,7 @@ plot_foi_estimates <- function(
 #' @return ggplot object showing the r-hats of the model to be compared with the
 #' convergence criteria (horizontal dashed line)
 #' @examples
+#' \donttest{
 #' data(chagas2012)
 #' seromodel <- fit_seromodel(
 #'   serosurvey = chagas2012,
@@ -455,6 +458,7 @@ plot_foi_estimates <- function(
 #'   chains = 2
 #' )
 #' plot_rhats(seromodel, chagas2012)
+#' }
 #' @export
 plot_rhats <- function(
   seromodel,
@@ -545,9 +549,11 @@ plot_rhats <- function(
 #' Only relevant when `seromodel@model_name == "constant"`)
 #' @return ggplot object with a summary of the specified model
 #' @examples
+#' \donttest{
 #' data(veev2012)
 #' seromodel <- fit_seromodel(veev2012, iter = 100)
 #' plot_summary(seromodel, veev2012)
+#' }
 #' @export
 plot_summary <- function(
   seromodel,
@@ -611,9 +617,11 @@ plot_summary <- function(
 #' @param seroreversion_digits Number of seroreversion rate digits
 #' @return seromodel summary plot
 #' @examples
+#' \donttest{
 #' data(veev2012)
 #' seromodel <- fit_seromodel(veev2012, iter = 100)
 #' plot_seromodel(seromodel, veev2012)
+#' }
 #' @export
 plot_seromodel <- function(
   seromodel,

README.Rmd

@@ -122,7 +122,7 @@ To report a bug please open an [issue](https://github.com/{{ gh_repo }}/issues/n
 
 ## Contribute
 
-Contributions to _{{ packagename }}_ are welcomed. Please follow the [package contributing guide](https://github.com/{{ gh_repo }}/blob/main/.github/CONTRIBUTING.md).
+Contributions to _{{ packagename }}_ are welcomed. Please follow the [package contributing guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md).
 
 ## Code of conduct
 

README.md

@@ -152,7 +152,7 @@ To report a bug please open an
 
 Contributions to *serofoi* are welcomed. Please follow the [package
 contributing
-guide](https://github.com/epiverse-trace/serofoi/blob/main/.github/CONTRIBUTING.md).
+guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md).
 
 ## Code of conduct
 

inst/WORDLIST

@@ -7,6 +7,7 @@ BMJ
 Bahia
 Bajaj
 Basáñez
+Bayesian
 Binom
 CMD
 Christl
@@ -43,6 +44,7 @@ Quevedo
 RStan
 Refactorization
 Serocatalytic
+Serological
 Seroreversion
 Serosurvey
 Serosurveys
@@ -98,9 +100,11 @@ rstan
 sd
 se
 serocatalytic
+serological
 seromodel
 seropositives
 seropositivities
+seroprevalence
 seroreversion
 serosurvey
 serosurveys

vignettes/serofoi.Rmd

@@ -47,7 +47,7 @@ Current version of ***serofoi*** includes the following assumptions on the under
 * There is no impact from migration processes in the sampled population, which means the model is not suited for a situation with high levels of migration. 
 * There are no differences in the mortality rate of infected versus susceptible individuals. This may be a limitation for situations with a high infection fatality rate, such as Ebola.
 
-## The bayesian statistical framework
+## The Bayesian statistical framework
 
 To assess how well the mathematical representation of the different FoI models describes the seroprevalence data, we implement a fitting process that relies on a Bayesian framework. The priors and upper priors for each model indicate the assumed trajectory of the FoI (either constant or time-varying). serofoi provides a set of Bayesian comparison methods for the user to choose between various possible FoI models (trajectories) that best fit the seroprevalence data. For details see [An Introduction To Force-of-Infection Models](https://epiverse-trace.github.io/serofoi/articles/foi_models.html).