Removed r-cmd-check warnings

DESCRIPTION

@@ -59,7 +59,8 @@ Imports:
     RcppParallel,
     purrr,
     cowplot,
-    jsonlite
+    jsonlite,
+    qtl
 Suggests: 
     knitr,
     rmarkdown

R/chagas2012.R

@@ -1,3 +1,4 @@
+# TODO Check if we really need to have the package `qtl` installed. Otherwise remove all entries of the form `see \code{\link[qtl]...`
 #' Seroprevalence data on serofoi
 #'
 #' Data from a serological surveys

R/modelling.R

@@ -1,3 +1,6 @@
+  # TODO Complete @param documentation
+
+
 #' Function that runs the specified stan model for the Force-of-Infection and estimates de seroprevalence based on the result of the fit
 #'
 #' This function runs the specified model for the Force-of-Infection \code{foi_model} using the data froma seroprevalence survey
@@ -36,6 +39,7 @@
 #' For further details refer to the \code{control} parameter in \link[rstan]{sampling} or \href{https://mc-stan.org/rstanarm/reference/adapt_delta.html}{here}.
 #' @param m_treed Maximum tree depth for the binary tree used in the NUTS stan sampler. For further details refer to the \code{control} parameter in \link[rstan]{sampling}.
 #' @param decades Number of decades covered by the survey data.
+#' @param print_summary TBD
 #' @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{
@@ -385,14 +389,15 @@ extract_seromodel_summary <- function(seromodel_object) {
   return(model_summary)
 }
 
-
+# TODO Complete @param documentation
 #' Function that generates an object containing the confidence interval based on a
 #' Force-of-Infection fitting
 #'
 #' This function computes the corresponding binomial confidence intervals for the obtained prevalence based on a fitting
 #' of the Force-of-Infection \code{foi} for plotting an analysis purposes.
-#' @param serodata A data frame containing the data from a seroprevalence survey. For further details refer to \link{run_seromodel}.
 #' @param foi Object containing the information of the force of infection. It is obtained from \code{rstan::extract(seromodel_object$fit, "foi", inc_warmup = FALSE)[[1]]}.
+#' @param serodata A data frame containing the data from a seroprevalence survey. For further details refer to \link{run_seromodel}.
+#' @param bin_data TBD
 #' @return \code{prev_final}. The expanded prevalence data. This is used for plotting purposes in the \code{visualization} module.
 #' @examples
 #' \dontrun{

R/seroprevalence_data.R

@@ -1,3 +1,6 @@
+# TODO Complete @param documentation
+
+
 #' Function that prepares the data from a serological survey for modelling
 #'
 #' This function adds the necessary additional variables to the given dataset \code{serodata} corresponding to a serological survey.
@@ -14,7 +17,8 @@
 #' \code{test} \tab The type of test taken \cr \tab \cr
 #' \code{antibody} \tab antibody \cr \tab \cr
 #' }
-#' @param alpha probability of a type I error. For further details refer to \link{Hmisc::binconf}.
+#' @param alpha probability of a type I error. For further details refer to \link[Hmisc]{binconf}.
+#' @param add_age_mean_f TBD
 #' @return serodata with additional columns necessary for the analysis. These columns are:
 #' \tabular{ll}{
 #' \code{age_mean_f} \tab Floor value of the average between age_min and age_max \cr \tab \cr

R/visualisation.R

@@ -119,13 +119,17 @@ plot_seroprev_fitted <- function(seromodel_object,
   return(prev_plot)
 }
 
+# TODO Complete @param documentation
+
 #' Function that generates a Force-of-Infection plot corresponding to the specified fitted serological model
 #'
 #' This function generates a Force-of-Infection plot from the results obtained by fitting a serological model.
 #' This includes the corresponding binomial confidence interval. 
 #' The x axis corresponds to the decades covered by the survey the y axis to the Force-of-Infection.
 #' @param seromodel_object Object containing the results of fitting a model by means of \link{run_seromodel}.
 #' @param size_text Text size use in the theme of the graph returned by the function.
+#' @param max_lambda TBD
+#' @param foi_sim TBD
 #' @return A ggplot2 object containing the Force-of-infection-vs-time including the corresponding confidence interval.
 #' @examples
 #' \dontrun{
@@ -278,12 +282,15 @@ plot_rhats <- function(seromodel_object,
   return(rhats_plot)
 }
 
+# TODO Complete @param documentation
 
 #' Function that generates a vertical arrange of plots showing a summary of a model, the estimated seroprevalence,
 #' the Force-of-Infection fit and the R-hat estimates plots.
 #'
 #' @param seromodel_object Object containing the results of fitting a model by means of \link{run_seromodel}.
 #' @param size_text Text size use in the theme of the graph returned by the function.
+#' @param max_lambda TBD
+#' @param foi_sim TBD
 #' @return A ggplot object with a vertical arrange containing the seropositivity, force of infection, and convergence plots.
 #' @examples
 #' \dontrun{
@@ -362,12 +369,13 @@ plot_seromodel <- function(seromodel_object,
   return(plot_arrange)
 }
 
-
+# TODO Improve documentation of @return. 
+# TODO Give more details about the generated plot
 #' Function that generates a plot for a given table
 #'
 #' @param info the information that will be contained in the table
 #' @param size_text Text size of the graph returned by the function
-#' @return p, a variable that will be used in the \link{visualisation} module
+#' @return p the plot for the given table
 #' @examples
 #' \dontrun{
 #'  data_test <- prepare_serodata(serodata)