diff --git a/R/model_comparison.R b/R/model_comparison.R
index 3c6dd0ff..c2bb29c9 100644
--- 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
index 8558f109..1da29f19 100644
--- 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
deleted file mode 100644
index 1404ed4f..00000000
--- a/R/serodata.R
+++ /dev/null
@@ -1,15 +0,0 @@
-#' Seroprevalence data on serofoi
-#'
-#' Data from a serological surveys
-#'
-#' @docType data
-#'
-#' @usage serodata
-#'
-#' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
-#'
-#' @keywords datasets
-#'
-#' @examples
-#' serodata
-"serodata"
\ No newline at end of file
diff --git a/R/seroprevalence_data.R b/R/seroprevalence_data.R
index f4168cfe..8c466f26 100644
--- 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
index 26f7fd81..775b06eb 100644
--- 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
index e15802fb..65fc44b1 100644
--- 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 
+## *serofoi*: force-of-infection from population based serosurveys with age-disagregated data 
@@ -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
index 5eef2793..0b6a0862 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
-## *serofoi*: force-of-infection from population based serosurveys with age-disagregated data
+## *serofoi*: force-of-infection from population based serosurveys with age-disagregated data
@@ -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
deleted file mode 100644
index f9570b14..00000000
Binary files a/data/serodata.RData and /dev/null differ
diff --git a/man/extract_seromodel_summary.Rd b/man/extract_seromodel_summary.Rd
index cd037799..106b1ca7 100644
--- a/man/extract_seromodel_summary.Rd
+++ b/man/extract_seromodel_summary.Rd
@@ -35,8 +35,8 @@ corresponding standar deviation.
}
\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)
diff --git a/man/figures/logo.svg b/man/figures/logo.svg
index e6d58887..3ee0a32c 100644
--- a/man/figures/logo.svg
+++ b/man/figures/logo.svg
@@ -1,577 +1,40877 @@
-
-
-
-
diff --git a/man/fit_seromodel.Rd b/man/fit_seromodel.Rd
index 67908578..30770ff1 100644
--- a/man/fit_seromodel.Rd
+++ b/man/fit_seromodel.Rd
@@ -64,8 +64,8 @@ object needs to be compiled by rstan.
}
\examples{
\dontrun{
-data("serodata")
-serodata <- prepare_serodata(serodata)
+data(chagas2012)
+serodata <- prepare_serodata(chagas2012)
seromodel_fit <- fit_seromodel(serodata = serodata,
foi_model = "constant")
}
diff --git a/man/get_exposure_ages.Rd b/man/get_exposure_ages.Rd
index aec51f06..3a1e2ca1 100644
--- a/man/get_exposure_ages.Rd
+++ b/man/get_exposure_ages.Rd
@@ -18,8 +18,8 @@ The exposition years to the disease for each individual corresponds to the time
}
\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)
}
}
diff --git a/man/get_exposure_matrix.Rd b/man/get_exposure_matrix.Rd
index 8b4f1abf..b92816f5 100644
--- a/man/get_exposure_matrix.Rd
+++ b/man/get_exposure_matrix.Rd
@@ -17,8 +17,8 @@ Function that generates the exposure matrix corresponding to a serological surve
}
\examples{
\dontrun{
-data("serodata")
-serodata <- prepare_serodata(serodata = serodata)
+data(chagas2012)
+serodata <- prepare_serodata(serodata = chagas2012)
exposure_matrix <- get_exposure_matrix(serodata = serodata)
}
}
diff --git a/man/get_prev_expanded.Rd b/man/get_prev_expanded.Rd
index a95f4899..2138efa4 100644
--- a/man/get_prev_expanded.Rd
+++ b/man/get_prev_expanded.Rd
@@ -23,7 +23,8 @@ of the Force-of-Infection \code{foi} for plotting an analysis purposes.
}
\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/man/get_table_rhats.Rd b/man/get_table_rhats.Rd
index 4aac86a0..7fb2f4b8 100644
--- a/man/get_table_rhats.Rd
+++ b/man/get_table_rhats.Rd
@@ -18,10 +18,10 @@ This method relies in the function \link[bayesplot]{rhat} to extract the R-hat e
}
\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/man/plot_foi.Rd b/man/plot_foi.Rd
index 6e376c70..f9f3a061 100644
--- a/man/plot_foi.Rd
+++ b/man/plot_foi.Rd
@@ -25,12 +25,13 @@ The x axis corresponds to the decades covered by the survey the y axis to the Fo
}
\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)
}
}
diff --git a/man/plot_info_table.Rd b/man/plot_info_table.Rd
index 72ddc003..1ec2cd73 100644
--- a/man/plot_info_table.Rd
+++ b/man/plot_info_table.Rd
@@ -19,12 +19,12 @@ Function that generates a plot for a 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/man/plot_rhats.Rd b/man/plot_rhats.Rd
index 02b73f00..b1d42253 100644
--- a/man/plot_rhats.Rd
+++ b/man/plot_rhats.Rd
@@ -21,14 +21,14 @@ All rhats must be smaller than 1 to ensure convergence (for further details chec
}
\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)
}
}
diff --git a/man/plot_seromodel.Rd b/man/plot_seromodel.Rd
index 6a36f736..2a2964bd 100644
--- a/man/plot_seromodel.Rd
+++ b/man/plot_seromodel.Rd
@@ -30,12 +30,13 @@ the Force-of-Infection fit and the R-hat estimates 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)
}
}
diff --git a/man/plot_seroprev.Rd b/man/plot_seroprev.Rd
index 8948decb..f61698e8 100644
--- a/man/plot_seroprev.Rd
+++ b/man/plot_seroprev.Rd
@@ -31,9 +31,10 @@ Function that generates the sero-positivity plot from a raw serological survey d
}
\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
)
diff --git a/man/plot_seroprev_fitted.Rd b/man/plot_seroprev_fitted.Rd
index 18740584..a7663518 100644
--- a/man/plot_seroprev_fitted.Rd
+++ b/man/plot_seroprev_fitted.Rd
@@ -21,9 +21,9 @@ corresponding confidence interval.
}
\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)
diff --git a/man/prepare_bin_data.Rd b/man/prepare_bin_data.Rd
index a2d767a4..bcb324e8 100644
--- a/man/prepare_bin_data.Rd
+++ b/man/prepare_bin_data.Rd
@@ -38,6 +38,7 @@ of its corresponding seroprevalence grouped by age group.
}
\examples{
\dontrun{
-prepare_bin_data (serodata)
+data(chagas2012)
+prepare_bin_data(chagas2012)
}
}
diff --git a/man/prepare_serodata.Rd b/man/prepare_serodata.Rd
index 33b4a1de..273e7b32 100644
--- a/man/prepare_serodata.Rd
+++ b/man/prepare_serodata.Rd
@@ -41,7 +41,7 @@ This function adds the necessary additional variables to the given dataset \code
}
\examples{
\dontrun{
-data("serodata")
-data_test <- prepare_serodata(serodata)
+data(chagas2012)
+serodata <- prepare_serodata(chagas2012)
}
}
diff --git a/man/run_seromodel.Rd b/man/run_seromodel.Rd
index becb135a..a8432187 100644
--- a/man/run_seromodel.Rd
+++ b/man/run_seromodel.Rd
@@ -67,8 +67,8 @@ This function runs the specified model for the Force-of-Infection \code{foi_mode
}
\examples{
\dontrun{
-serodata <- prepare_serodata(serodata)
-run_seromodel (serodata,
- foi_model = "constant")
+serodata <- prepare_serodata(chagas2012)
+run_seromodel (chagas2012,
+ foi_model = "constant")
}
}
diff --git a/man/serodata.Rd b/man/serodata.Rd
deleted file mode 100644
index a0644814..00000000
--- a/man/serodata.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/serodata.R
-\docType{data}
-\name{serodata}
-\alias{serodata}
-\title{Seroprevalence data on serofoi}
-\format{
-An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
-}
-\usage{
-serodata
-}
-\description{
-Data from a serological surveys
-}
-\examples{
-serodata
-}
-\keyword{datasets}
diff --git a/tests/testthat/test_modelling.R b/tests/testthat/test_modelling.R
index 76494b19..edea5876 100644
--- a/tests/testthat/test_modelling.R
+++ b/tests/testthat/test_modelling.R
@@ -7,12 +7,11 @@ test_that("individual models", {
set.seed(1234) # For reproducibility
library(devtools)
- library(dplyr)
library(vdiffr)
#----- Read and prepare data
- data("serodata")
- data_test <- serodata %>% prepare_serodata(alpha = 0.05)
+ data(chagas2012)
+ serodata <- prepare_serodata(chagas2012, alpha = 0.05)
data_constant_path <- testthat::test_path("extdata", "prev_expanded_constant.RDS")
data_tv_normal_path <- testthat::test_path("extdata", "prev_expanded_tv_normal.RDS")
@@ -23,7 +22,7 @@ test_that("individual models", {
#----- Test for the constant model
model_name <- "constant"
- model_object <- run_seromodel(serodata = data_test,
+ model_object <- run_seromodel(serodata = serodata,
foi_model = model_name,
n_iters = 1000,
print_summary = FALSE)
@@ -37,7 +36,7 @@ test_that("individual models", {
#----- Test for the tv_normal model
model_name <- "tv_normal"
- model_object <- run_seromodel(serodata = data_test,
+ model_object <- run_seromodel(serodata = serodata,
foi_model = model_name,
n_iters = 1000)
@@ -49,7 +48,7 @@ test_that("individual models", {
#----- Test for the tv_normal_log model
model_name <- "tv_normal_log"
- model_object <- run_seromodel(serodata = data_test,
+ model_object <- run_seromodel(serodata = serodata,
foi_model = model_name,
n_iters = 1000)
diff --git a/vignettes/foi_models.Rmd b/vignettes/foi_models.Rmd
index 2c53d6a9..e8c9a2f1 100644
--- a/vignettes/foi_models.Rmd
+++ b/vignettes/foi_models.Rmd
@@ -18,8 +18,6 @@ knitr::opts_chunk$set(
```{r cleaning, include = FALSE, echo = TRUE}
library(serofoi)
-rownames(serodata) <- NULL
-
```
The current version of ***serofoi*** supports three different models for estimating the *Force-of-Infection (FoI)*, including constant and time-varying trajectories. For fitting the model to the sero-prevalence data we use a suit of bayesian models that include prior and upper prior distributions
diff --git a/vignettes/serofoi.Rmd b/vignettes/serofoi.Rmd
index 082e86ef..3fe42205 100644
--- a/vignettes/serofoi.Rmd
+++ b/vignettes/serofoi.Rmd
@@ -60,8 +60,8 @@ The integrated dataset `serodata_test` provides a minimal example of the input o
```{r model_constant, include = TRUE, echo = TRUE, results="hide", errors = FALSE, warning = FALSE, message = FALSE, fig.width=4, fig.asp=1.5, fig.align="center"}
library(serofoi)
# Loading and preparing data for modelling
-data("serodata")
-serodata_test <- prepare_serodata(serodata)
+data(chagas2012)
+serodata_test <- prepare_serodata(chagas2012)
# Model implementation
model_constant <- run_seromodel(serodata = serodata_test,
foi_model = "constant")