diff --git a/R/add-expression-col.R b/R/add-expression-col.R index 7a0648c7..c18c8c43 100644 --- a/R/add-expression-col.R +++ b/R/add-expression-col.R @@ -4,8 +4,8 @@ #' @description #' #' Creates an expression from a data frame containing statistical details. -#' Ideally, this data frame would come from having run `tidy_model_parameters` -#' function on your model object. +#' Ideally, this data frame would come from having run `tidy_model_parameters()` +#' on your model object. #' #' This function is currently **not** stable and should not be used outside of #' this package context. diff --git a/R/centrality-description.R b/R/centrality-description.R index 0f3e3a2a..ca676d00 100644 --- a/R/centrality-description.R +++ b/R/centrality-description.R @@ -7,7 +7,7 @@ #' grouping variable in `x` by a set of indices (e.g., measures of centrality, #' dispersion, range, skewness, kurtosis, etc.). It additionally returns an #' expression containing a specified centrality measure. The function internally -#' relies on `datawizard::describe_distribution()` function. +#' relies on [`datawizard::describe_distribution()`] function. #' #' @description #' Parametric, non-parametric, robust, and Bayesian measures of centrality. diff --git a/R/contingency-table.R b/R/contingency-table.R index 0f6763b4..b1649ab8 100644 --- a/R/contingency-table.R +++ b/R/contingency-table.R @@ -25,10 +25,12 @@ #' represents a single observation. #' @param paired Logical indicating whether data came from a within-subjects or #' repeated measures design study (Default: `FALSE`). -#' @param sampling.plan Character describing the sampling plan. Possible options -#' are `"indepMulti"` (independent multinomial; default), `"poisson"`, -#' `"jointMulti"` (joint multinomial), `"hypergeom"` (hypergeometric). For -#' more, see `?BayesFactor::contingencyTableBF()`. +#' @param sampling.plan Character describing the sampling plan. Possible options: +#' - `"indepMulti"` (independent multinomial; default) +#' - `"poisson"` +#' - `"jointMulti"` (joint multinomial) +#' - `"hypergeom"` (hypergeometric). +#' For more, see [`BayesFactor::contingencyTableBF()`]. #' @param fixed.margin For the independent multinomial sampling plan, which #' margin is fixed (`"rows"` or `"cols"`). Defaults to `"rows"`. #' @param prior.concentration Specifies the prior concentration parameter, set diff --git a/R/data.R b/R/data.R index 98d1cbda..b975b8b8 100644 --- a/R/data.R +++ b/R/data.R @@ -1,6 +1,6 @@ #' @title Movie information and user ratings from IMDB.com (wide format). #' @name movies_wide -#' @details Modified dataset from `ggplot2movies` package. +#' @details Modified dataset from `{ggplot2movies}` package. #' #' The internet movie database, , is a website devoted #' to collecting movie data supplied by studios and fans. It claims to be the @@ -34,7 +34,7 @@ #' @title Movie information and user ratings from IMDB.com (long format). #' @name movies_long -#' @details Modified dataset from `ggplot2movies` package. +#' @details Modified dataset from `{ggplot2movies}` package. #' #' The internet movie database, , is a website devoted #' to collecting movie data supplied by studios and fans. It claims to be the @@ -72,7 +72,7 @@ #' petal length and width, respectively, for 50 flowers from each of 3 species #' of iris. The species are Iris setosa, versicolor, and virginica. #' -#' This is a modified dataset from `datasets` package. +#' This is a modified dataset from `{datasets}` package. #' #' @format A data frame with 600 rows and 5 variables #' diff --git a/R/helpers-easystats.R b/R/helpers-easystats.R index 0452a3ca..605e2eb8 100644 --- a/R/helpers-easystats.R +++ b/R/helpers-easystats.R @@ -46,7 +46,7 @@ tidy_model_parameters <- function(model, ...) { #' @name tidy_model_effectsize -#' @title Convert `effectsize` package output to `tidyverse` conventions +#' @title Convert `{effectsize}` package output to `{tidyverse}` conventions #' #' @param data A data frame returned by `{effectsize}` functions. #' @param ... Currently ignored. diff --git a/R/long-to-wide-converter.R b/R/long-to-wide-converter.R index d50edac9..2f9bd7c4 100644 --- a/R/long-to-wide-converter.R +++ b/R/long-to-wide-converter.R @@ -17,7 +17,7 @@ #' internal identifier. So if your data is **not** sorted, the results *can* #' be inaccurate when there are more than two levels in `x` and there are #' `NA`s present. The data is expected to be sorted by user in -#' subject-1,subject-2, ..., pattern. +#' subject-1, subject-2, ..., pattern. #' @param y The response (or outcome or dependent) variable from `data`. #' @param subject.id Relevant in case of a repeated measures or within-subjects #' design (`paired = TRUE`, i.e.), it specifies the subject or repeated diff --git a/R/meta-analysis.R b/R/meta-analysis.R index 71939a0c..8822fcf3 100644 --- a/R/meta-analysis.R +++ b/R/meta-analysis.R @@ -7,10 +7,9 @@ #' @param data A data frame. It **must** contain columns named `estimate` (effect #' sizes or outcomes) and `std.error` (corresponding standard errors). These #' two columns will be used: -#' - as `yi` and `sei` arguments in `metafor::rma()` (for **parametric** test) -#' or `metaplus::metaplus()` (for **robust** test) -#' - as `y` and `SE` arguments in `metaBMA::meta_random()` (for **Bayesian** -#' test). +#' - as `yi` and `sei` arguments in [`metafor::rma()`] (for **parametric** test) +#' - as `yi` and `sei` arguments in [`metaplus::metaplus()`] (for **robust** test) +#' - as `y` and `SE` arguments in [`metaBMA::meta_random()`] (for **Bayesian** test) #' @inheritParams one_sample_test #' @inheritParams metaplus::metaplus #' @inheritParams oneway_anova diff --git a/R/oneway-anova.R b/R/oneway-anova.R index 3cc7b7b8..ffbdbd0e 100644 --- a/R/oneway-anova.R +++ b/R/oneway-anova.R @@ -34,8 +34,8 @@ #' width to use in calculating Bayes factors and posterior estimates. In #' addition to numeric arguments, several named values are also recognized: #' `"medium"`, `"wide"`, and `"ultrawide"`, corresponding to *r* scale values -#' of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value -#' corresponds to scale for fixed effects. +#' of `1/2`, `sqrt(2)/2`, and `1`, respectively. In case of an ANOVA, this +#' value corresponds to scale for fixed effects. #' @inheritParams two_sample_test #' @inheritParams add_expression_col #' @param ... Additional arguments (currently ignored). diff --git a/R/tidy-model-expressions.R b/R/tidy-model-expressions.R index 99008214..9a83ab3c 100644 --- a/R/tidy-model-expressions.R +++ b/R/tidy-model-expressions.R @@ -3,7 +3,7 @@ #' #' @param ... Currently ignored. #' @param data A tidy data frame from regression model object (see -#' `statsExpressions::tidy_model_parameters()`). +#' [`statsExpressions::tidy_model_parameters()`]). #' @param statistic Which statistic is to be displayed (either `"t"` or `"f"`or #' `"z"` or `"chi"`) in the expression. #' @inheritParams oneway_anova @@ -13,11 +13,6 @@ #' `p.value`) are missing, for these rows, a `NULL` is returned instead of an #' expression with empty strings. #' -#' @note -#' -#' This is an **experimental** function and may change in the future. Please do -#' not use it yet in your workflow. -#' #' @autoglobal #' #' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true") @@ -46,9 +41,8 @@ tidy_model_expressions <- function( statistic <- substring(tolower(statistic), 1L, 1L) # if any of the necessary numeric columns are missing, there shouldn't be an - # expression corresponding to that row - # - # convert the necessary columns to character type for expression + # expression corresponding to that row; convert the necessary columns to + # character type for expression df_expr <- data %>% filter(if_all( .cols = matches("estimate|statistic|std.error|p.value"), @@ -95,8 +89,7 @@ tidy_model_expressions <- function( # nolint end # Replace `NA` with `NULL` to show nothing instead of an empty string ("") - left_join(data, select(df_expr, term, expression), by = "term") %>% - .glue_to_expression() + left_join(data, select(df_expr, term, expression), by = "term") %>% .glue_to_expression() } diff --git a/man/add_expression_col.Rd b/man/add_expression_col.Rd index efcce499..c2bdad96 100644 --- a/man/add_expression_col.Rd +++ b/man/add_expression_col.Rd @@ -63,8 +63,8 @@ for the parameters (default: \code{0L}).} } \description{ Creates an expression from a data frame containing statistical details. -Ideally, this data frame would come from having run \code{tidy_model_parameters} -function on your model object. +Ideally, this data frame would come from having run \code{tidy_model_parameters()} +on your model object. This function is currently \strong{not} stable and should not be used outside of this package context. diff --git a/man/centrality_description.Rd b/man/centrality_description.Rd index ac9ebfdb..8fdb2902 100644 --- a/man/centrality_description.Rd +++ b/man/centrality_description.Rd @@ -60,7 +60,7 @@ This function describes a distribution for \code{y} variable for each level of t grouping variable in \code{x} by a set of indices (e.g., measures of centrality, dispersion, range, skewness, kurtosis, etc.). It additionally returns an expression containing a specified centrality measure. The function internally -relies on \code{datawizard::describe_distribution()} function. +relies on \code{\link[datawizard:describe_distribution]{datawizard::describe_distribution()}} function. } \section{Centrality measures}{ diff --git a/man/contingency_table.Rd b/man/contingency_table.Rd index d9cc0f04..7dd5786a 100644 --- a/man/contingency_table.Rd +++ b/man/contingency_table.Rd @@ -72,10 +72,14 @@ significant figures (see also \code{\link[=signif]{signif()}}).} confidence/credible intervals, \code{0.95}). If \code{NULL}, no confidence intervals will be computed.} -\item{sampling.plan}{Character describing the sampling plan. Possible options -are \code{"indepMulti"} (independent multinomial; default), \code{"poisson"}, -\code{"jointMulti"} (joint multinomial), \code{"hypergeom"} (hypergeometric). For -more, see \code{?BayesFactor::contingencyTableBF()}.} +\item{sampling.plan}{Character describing the sampling plan. Possible options: +\itemize{ +\item \code{"indepMulti"} (independent multinomial; default) +\item \code{"poisson"} +\item \code{"jointMulti"} (joint multinomial) +\item \code{"hypergeom"} (hypergeometric). +For more, see \code{\link[BayesFactor:contingencyTableBF]{BayesFactor::contingencyTableBF()}}. +}} \item{fixed.margin}{For the independent multinomial sampling plan, which margin is fixed (\code{"rows"} or \code{"cols"}). Defaults to \code{"rows"}.} diff --git a/man/corr_test.Rd b/man/corr_test.Rd index b68cf50e..7a15ca1a 100644 --- a/man/corr_test.Rd +++ b/man/corr_test.Rd @@ -57,8 +57,8 @@ of an error, try reducing the value of \code{tr}, which is by default set to width to use in calculating Bayes factors and posterior estimates. In addition to numeric arguments, several named values are also recognized: \code{"medium"}, \code{"wide"}, and \code{"ultrawide"}, corresponding to \emph{r} scale values -of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value -corresponds to scale for fixed effects.} +of \code{1/2}, \code{sqrt(2)/2}, and \code{1}, respectively. In case of an ANOVA, this +value corresponds to scale for fixed effects.} \item{...}{Additional arguments (currently ignored).} } diff --git a/man/iris_long.Rd b/man/iris_long.Rd index d3f9b911..c98fa629 100644 --- a/man/iris_long.Rd +++ b/man/iris_long.Rd @@ -31,7 +31,7 @@ measurements in centimeters of the variables sepal length and width and petal length and width, respectively, for 50 flowers from each of 3 species of iris. The species are Iris setosa, versicolor, and virginica. -This is a modified dataset from \code{datasets} package. +This is a modified dataset from \code{{datasets}} package. } \examples{ dim(iris_long) diff --git a/man/long_to_wide_converter.Rd b/man/long_to_wide_converter.Rd index f07571b1..da93aea8 100644 --- a/man/long_to_wide_converter.Rd +++ b/man/long_to_wide_converter.Rd @@ -27,7 +27,7 @@ data has already been sorted by such an id by the user and creates an internal identifier. So if your data is \strong{not} sorted, the results \emph{can} be inaccurate when there are more than two levels in \code{x} and there are \code{NA}s present. The data is expected to be sorted by user in -subject-1,subject-2, ..., pattern.} +subject-1, subject-2, ..., pattern.} \item{y}{The response (or outcome or dependent) variable from \code{data}.} diff --git a/man/meta_analysis.Rd b/man/meta_analysis.Rd index deecd721..6108ec65 100644 --- a/man/meta_analysis.Rd +++ b/man/meta_analysis.Rd @@ -18,10 +18,9 @@ meta_analysis( sizes or outcomes) and \code{std.error} (corresponding standard errors). These two columns will be used: \itemize{ -\item as \code{yi} and \code{sei} arguments in \code{metafor::rma()} (for \strong{parametric} test) -or \code{metaplus::metaplus()} (for \strong{robust} test) -\item as \code{y} and \code{SE} arguments in \code{metaBMA::meta_random()} (for \strong{Bayesian} -test). +\item as \code{yi} and \code{sei} arguments in \code{\link[metafor:rma.uni]{metafor::rma()}} (for \strong{parametric} test) +\item as \code{yi} and \code{sei} arguments in \code{\link[metaplus:metaplus]{metaplus::metaplus()}} (for \strong{robust} test) +\item as \code{y} and \code{SE} arguments in \code{\link[metaBMA:meta_random]{metaBMA::meta_random()}} (for \strong{Bayesian} test) }} \item{type}{A character specifying the type of statistical approach: diff --git a/man/movies_long.Rd b/man/movies_long.Rd index 33d2f466..a531dfb2 100644 --- a/man/movies_long.Rd +++ b/man/movies_long.Rd @@ -28,7 +28,7 @@ movies_long Movie information and user ratings from IMDB.com (long format). } \details{ -Modified dataset from \code{ggplot2movies} package. +Modified dataset from \code{{ggplot2movies}} package. The internet movie database, \url{https://imdb.com/}, is a website devoted to collecting movie data supplied by studios and fans. It claims to be the diff --git a/man/movies_wide.Rd b/man/movies_wide.Rd index 43d4000d..c69b60a8 100644 --- a/man/movies_wide.Rd +++ b/man/movies_wide.Rd @@ -30,7 +30,7 @@ movies_wide Movie information and user ratings from IMDB.com (wide format). } \details{ -Modified dataset from \code{ggplot2movies} package. +Modified dataset from \code{{ggplot2movies}} package. The internet movie database, \url{https://imdb.com/}, is a website devoted to collecting movie data supplied by studios and fans. It claims to be the diff --git a/man/one_sample_test.Rd b/man/one_sample_test.Rd index 32e3647b..2c9cb291 100644 --- a/man/one_sample_test.Rd +++ b/man/one_sample_test.Rd @@ -63,8 +63,8 @@ of an error, try reducing the value of \code{tr}, which is by default set to width to use in calculating Bayes factors and posterior estimates. In addition to numeric arguments, several named values are also recognized: \code{"medium"}, \code{"wide"}, and \code{"ultrawide"}, corresponding to \emph{r} scale values -of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value -corresponds to scale for fixed effects.} +of \code{1/2}, \code{sqrt(2)/2}, and \code{1}, respectively. In case of an ANOVA, this +value corresponds to scale for fixed effects.} \item{effsize.type}{Type of effect size needed for \emph{parametric} tests. The argument can be \code{"d"} (for Cohen's \emph{d}) or \code{"g"} (for Hedge's \emph{g}).} diff --git a/man/oneway_anova.Rd b/man/oneway_anova.Rd index 2d62ba84..346e45b5 100644 --- a/man/oneway_anova.Rd +++ b/man/oneway_anova.Rd @@ -34,7 +34,7 @@ data has already been sorted by such an id by the user and creates an internal identifier. So if your data is \strong{not} sorted, the results \emph{can} be inaccurate when there are more than two levels in \code{x} and there are \code{NA}s present. The data is expected to be sorted by user in -subject-1,subject-2, ..., pattern.} +subject-1, subject-2, ..., pattern.} \item{y}{The response (or outcome or dependent) variable from \code{data}.} @@ -85,8 +85,8 @@ omega-squared).} width to use in calculating Bayes factors and posterior estimates. In addition to numeric arguments, several named values are also recognized: \code{"medium"}, \code{"wide"}, and \code{"ultrawide"}, corresponding to \emph{r} scale values -of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value -corresponds to scale for fixed effects.} +of \code{1/2}, \code{sqrt(2)/2}, and \code{1}, respectively. In case of an ANOVA, this +value corresponds to scale for fixed effects.} \item{tr}{Trim level for the mean when carrying out \code{robust} tests. In case of an error, try reducing the value of \code{tr}, which is by default set to diff --git a/man/pairwise_comparisons.Rd b/man/pairwise_comparisons.Rd index e2e8c580..fa0faed1 100644 --- a/man/pairwise_comparisons.Rd +++ b/man/pairwise_comparisons.Rd @@ -32,7 +32,7 @@ data has already been sorted by such an id by the user and creates an internal identifier. So if your data is \strong{not} sorted, the results \emph{can} be inaccurate when there are more than two levels in \code{x} and there are \code{NA}s present. The data is expected to be sorted by user in -subject-1,subject-2, ..., pattern.} +subject-1, subject-2, ..., pattern.} \item{y}{The response (or outcome or dependent) variable from \code{data}.} @@ -72,8 +72,8 @@ of an error, try reducing the value of \code{tr}, which is by default set to width to use in calculating Bayes factors and posterior estimates. In addition to numeric arguments, several named values are also recognized: \code{"medium"}, \code{"wide"}, and \code{"ultrawide"}, corresponding to \emph{r} scale values -of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value -corresponds to scale for fixed effects.} +of \code{1/2}, \code{sqrt(2)/2}, and \code{1}, respectively. In case of an ANOVA, this +value corresponds to scale for fixed effects.} \item{p.adjust.method}{Adjustment method for \emph{p}-values for multiple comparisons. Possible methods are: \code{"holm"} (default), \code{"hochberg"}, diff --git a/man/tidy_model_expressions.Rd b/man/tidy_model_expressions.Rd index b4f17d2e..bc4bbd3d 100644 --- a/man/tidy_model_expressions.Rd +++ b/man/tidy_model_expressions.Rd @@ -14,7 +14,7 @@ tidy_model_expressions( } \arguments{ \item{data}{A tidy data frame from regression model object (see -\code{statsExpressions::tidy_model_parameters()}).} +\code{\link[=tidy_model_parameters]{tidy_model_parameters()}}).} \item{statistic}{Which statistic is to be displayed (either \code{"t"} or \code{"f"}or \code{"z"} or \code{"chi"}) in the expression.} @@ -40,10 +40,6 @@ When any of the necessary numeric column values (\code{estimate}, \code{statisti \code{p.value}) are missing, for these rows, a \code{NULL} is returned instead of an expression with empty strings. } -\note{ -This is an \strong{experimental} function and may change in the future. Please do -not use it yet in your workflow. -} \section{Citation}{ Patil, I., (2021). statsExpressions: R Package for Tidy Dataframes and Expressions with Statistical Details. Journal of Open Source Software, 6(61), 3236, https://doi.org/10.21105/joss.03236 } diff --git a/man/two_sample_test.Rd b/man/two_sample_test.Rd index 8128230b..676438c6 100644 --- a/man/two_sample_test.Rd +++ b/man/two_sample_test.Rd @@ -35,7 +35,7 @@ data has already been sorted by such an id by the user and creates an internal identifier. So if your data is \strong{not} sorted, the results \emph{can} be inaccurate when there are more than two levels in \code{x} and there are \code{NA}s present. The data is expected to be sorted by user in -subject-1,subject-2, ..., pattern.} +subject-1, subject-2, ..., pattern.} \item{y}{The response (or outcome or dependent) variable from \code{data}.} @@ -90,8 +90,8 @@ argument can be \code{"d"} (for Cohen's \emph{d}) or \code{"g"} (for Hedge's \em width to use in calculating Bayes factors and posterior estimates. In addition to numeric arguments, several named values are also recognized: \code{"medium"}, \code{"wide"}, and \code{"ultrawide"}, corresponding to \emph{r} scale values -of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value -corresponds to scale for fixed effects.} +of \code{1/2}, \code{sqrt(2)/2}, and \code{1}, respectively. In case of an ANOVA, this +value corresponds to scale for fixed effects.} \item{tr}{Trim level for the mean when carrying out \code{robust} tests. In case of an error, try reducing the value of \code{tr}, which is by default set to