From 22cb2a680e7730ad6774555ffa182b0e027471b1 Mon Sep 17 00:00:00 2001 From: Daniel Date: Sat, 16 Mar 2024 22:05:11 +0100 Subject: [PATCH] docs --- R/check_zeroinflation.R | 11 +++++++---- R/simulate_residuals.R | 11 +++++++---- man/check_overdispersion.Rd | 11 +++++++---- man/check_residuals.Rd | 11 +++++++---- man/check_zeroinflation.Rd | 11 +++++++---- man/simulate_residuals.Rd | 11 +++++++---- 6 files changed, 42 insertions(+), 24 deletions(-) diff --git a/R/check_zeroinflation.R b/R/check_zeroinflation.R index 0c4f80c0a..63badc5d4 100644 --- a/R/check_zeroinflation.R +++ b/R/check_zeroinflation.R @@ -35,10 +35,13 @@ #' complex model, such as mixed models or models with zero-inflation, there are #' several important considerations. Arguments specified in `...` are passed to #' [`simulate_residuals()`], which relies on [`DHARMa::simulateResiduals()`] (and -#' therefore, arguments in `...` are passed further down to _DHARMa_). It is -#' recommended to read the 'Details' in `?DHARMa::simulateResiduals` closely to -#' understand the implications of the simulation process and which arguments -#' should be modified to get the most accurate results. +#' therefore, arguments in `...` are passed further down to _DHARMa_). The +#' defaults in DHARMa are set on the most conservative option that works for +#' all models. However, in many cases, the help advises to use different settings +#' in particular situations or for particular models. It is recommended to read +#' the 'Details' in `?DHARMa::simulateResiduals` closely to understand the +#' implications of the simulation process and which arguments should be modified +#' to get the most accurate results. #' #' @family functions to check model assumptions and and assess model quality #' diff --git a/R/simulate_residuals.R b/R/simulate_residuals.R index 65eda8553..0dee1e045 100644 --- a/R/simulate_residuals.R +++ b/R/simulate_residuals.R @@ -29,10 +29,13 @@ #' complex model, such as mixed models or models with zero-inflation, there are #' several important considerations. `simulate_residuals()` relies on #' [`DHARMa::simulateResiduals()`], and additional arguments specified in `...` -#' are passed further down to that function. It is recommended to read the -#' 'Details' in `?DHARMa::simulateResiduals` closely to understand the -#' implications of the simulation process and which arguments should be modified -#' to get the most accurate results. +#' are passed further down to that function. The defaults in DHARMa are set on +#' the most conservative option that works for all models. However, in many +#' cases, the help advises to use different settings in particular situations +#' or for particular models. It is recommended to read the 'Details' in +#' `?DHARMa::simulateResiduals` closely to understand the implications of the +#' simulation process and which arguments should be modified to get the most +#' accurate results. #' #' @references #' diff --git a/man/check_overdispersion.Rd b/man/check_overdispersion.Rd index 8c88d44c9..762ede07f 100644 --- a/man/check_overdispersion.Rd +++ b/man/check_overdispersion.Rd @@ -81,10 +81,13 @@ traditionally used Pearson residuals. However, when simulating from more complex model, such as mixed models or models with zero-inflation, there are several important considerations. Arguments specified in \code{...} are passed to \code{\link[=simulate_residuals]{simulate_residuals()}}, which relies on \code{\link[DHARMa:simulateResiduals]{DHARMa::simulateResiduals()}} (and -therefore, arguments in \code{...} are passed further down to \emph{DHARMa}). It is -recommended to read the 'Details' in \code{?DHARMa::simulateResiduals} closely to -understand the implications of the simulation process and which arguments -should be modified to get the most accurate results. +therefore, arguments in \code{...} are passed further down to \emph{DHARMa}). The +defaults in DHARMa are set on the most conservative option that works for +all models. However, in many cases, the help advises to use different settings +in particular situations or for particular models. It is recommended to read +the 'Details' in \code{?DHARMa::simulateResiduals} closely to understand the +implications of the simulation process and which arguments should be modified +to get the most accurate results. } \examples{ diff --git a/man/check_residuals.Rd b/man/check_residuals.Rd index d9579dd8a..cf4295d81 100644 --- a/man/check_residuals.Rd +++ b/man/check_residuals.Rd @@ -40,10 +40,13 @@ the traditionally used Pearson residuals. However, when simulating from more complex model, such as mixed models or models with zero-inflation, there are several important considerations. \code{simulate_residuals()} relies on \code{\link[DHARMa:simulateResiduals]{DHARMa::simulateResiduals()}}, and additional arguments specified in \code{...} -are passed further down to that function. It is recommended to read the -'Details' in \code{?DHARMa::simulateResiduals} closely to understand the -implications of the simulation process and which arguments should be modified -to get the most accurate results. +are passed further down to that function. The defaults in DHARMa are set on +the most conservative option that works for all models. However, in many +cases, the help advises to use different settings in particular situations +or for particular models. It is recommended to read the 'Details' in +\code{?DHARMa::simulateResiduals} closely to understand the implications of the +simulation process and which arguments should be modified to get the most +accurate results. } \examples{ diff --git a/man/check_zeroinflation.Rd b/man/check_zeroinflation.Rd index b41ab5ec5..9de6c1f5c 100644 --- a/man/check_zeroinflation.Rd +++ b/man/check_zeroinflation.Rd @@ -59,10 +59,13 @@ traditionally used Pearson residuals. However, when simulating from more complex model, such as mixed models or models with zero-inflation, there are several important considerations. Arguments specified in \code{...} are passed to \code{\link[=simulate_residuals]{simulate_residuals()}}, which relies on \code{\link[DHARMa:simulateResiduals]{DHARMa::simulateResiduals()}} (and -therefore, arguments in \code{...} are passed further down to \emph{DHARMa}). It is -recommended to read the 'Details' in \code{?DHARMa::simulateResiduals} closely to -understand the implications of the simulation process and which arguments -should be modified to get the most accurate results. +therefore, arguments in \code{...} are passed further down to \emph{DHARMa}). The +defaults in DHARMa are set on the most conservative option that works for +all models. However, in many cases, the help advises to use different settings +in particular situations or for particular models. It is recommended to read +the 'Details' in \code{?DHARMa::simulateResiduals} closely to understand the +implications of the simulation process and which arguments should be modified +to get the most accurate results. } \examples{ diff --git a/man/simulate_residuals.Rd b/man/simulate_residuals.Rd index 5ead325c3..cf8042697 100644 --- a/man/simulate_residuals.Rd +++ b/man/simulate_residuals.Rd @@ -39,10 +39,13 @@ the traditionally used Pearson residuals. However, when simulating from more complex model, such as mixed models or models with zero-inflation, there are several important considerations. \code{simulate_residuals()} relies on \code{\link[DHARMa:simulateResiduals]{DHARMa::simulateResiduals()}}, and additional arguments specified in \code{...} -are passed further down to that function. It is recommended to read the -'Details' in \code{?DHARMa::simulateResiduals} closely to understand the -implications of the simulation process and which arguments should be modified -to get the most accurate results. +are passed further down to that function. The defaults in DHARMa are set on +the most conservative option that works for all models. However, in many +cases, the help advises to use different settings in particular situations +or for particular models. It is recommended to read the 'Details' in +\code{?DHARMa::simulateResiduals} closely to understand the implications of the +simulation process and which arguments should be modified to get the most +accurate results. } \examples{