Reduce methods appearing in docs, to make docs clearer (#961)

* Don't show "usage" for all classes (make docs clearer) * docs * docs * docs * docs * docs * typo * docs * find_param
easystats · Nov 6, 2024 · 05b9c3c · 05b9c3c
1 parent 911cb38
commit 05b9c3c
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Showing 30 changed files with 417 additions and 515 deletions.
diff --git a/R/find_parameter_zi.R b/R/find_parameter_zi.R
@@ -15,18 +15,17 @@
 #' - `conditional`, the "fixed effects" part from the model.
 #' - `zero_inflated`, the "fixed effects" part from the zero-inflation
 #'   component of the model.
+#' - Special models are `mhurdle`, which also can have the components
+#'   `infrequent_purchase`, `ip`, and `auxiliary`.
 #'
 #' @examples
 #' data(mtcars)
 #' m <- lm(mpg ~ wt + cyl + vs, data = mtcars)
 #' find_parameters(m)
 #' @export
-find_parameters.zeroinfl <- function(x,
-                                     component = c("all", "conditional", "zi", "zero_inflated"),
-                                     flatten = FALSE,
-                                     ...) {
+find_parameters.zeroinfl <- function(x, component = "all", flatten = FALSE, ...) {
   cf <- names(stats::coef(x))
-  component <- match.arg(component)
+  component <- validate_argument(component, c("all", "conditional", "zi", "zero_inflated"))
 
   l <- compact_list(list(
     conditional = cf[startsWith(cf, "count_")],
@@ -50,12 +49,9 @@ find_parameters.zerotrunc <- find_parameters.zeroinfl
 
 
 #' @export
-find_parameters.zcpglm <- function(x,
-                                   component = c("all", "conditional", "zi", "zero_inflated"),
-                                   flatten = FALSE,
-                                   ...) {
+find_parameters.zcpglm <- function(x, component = "all", flatten = FALSE, ...) {
   cf <- stats::coef(x)
-  component <- match.arg(component)
+  component <- validate_argument(component, c("all", "conditional", "zi", "zero_inflated"))
 
   l <- compact_list(list(
     conditional = names(cf$tweedie),
@@ -72,15 +68,19 @@ find_parameters.zcpglm <- function(x,
 }
 
 
-#' @rdname find_parameters.zeroinfl
 #' @export
-find_parameters.mhurdle <- function(x,
-                                    component = c("all", "conditional", "zi", "zero_inflated", "infrequent_purchase", "ip", "auxiliary"),
-                                    flatten = FALSE,
-                                    ...) {
-  component <- match.arg(component)
+find_parameters.mhurdle <- function(x, component = "all", flatten = FALSE, ...) {
+  component <- validate_argument(
+    component,
+    c("all", "conditional", "zi", "zero_inflated", "infrequent_purchase", "ip", "auxiliary", "distributional")
+  )
   cf <- stats::coef(x)
 
+  # handle alias
+  if (component == "distributional") {
+    component <- "auxiliary"
+  }
+
   cond_pars <- which(startsWith(names(cf), "h2."))
   zi_pars <- which(startsWith(names(cf), "h1."))
   ip_pars <- which(startsWith(names(cf), "h3."))

diff --git a/R/find_parameters.R b/R/find_parameters.R
@@ -259,13 +259,9 @@ find_parameters.lavaan <- function(x, flatten = FALSE, ...) {
 
 # Panel models ----------------------------------------
 
-#' @rdname find_parameters
 #' @export
-find_parameters.pgmm <- function(x,
-                                 component = c("conditional", "all"),
-                                 flatten = FALSE,
-                                 ...) {
-  component <- match.arg(component)
+find_parameters.pgmm <- function(x, component = "conditional", flatten = FALSE, ...) {
+  component <- validate_argument(component, c("conditional", "all"))
   s <- summary(x, robust = FALSE)
 
   l <- list(
@@ -807,13 +803,9 @@ find_parameters.mira <- function(x, flatten = FALSE, ...) {
 
 
 ## For questions or problems with this ask Fernando Miguez ([email protected])
-#' @rdname find_parameters
 #' @export
-find_parameters.nls <- function(x,
-                                component = c("all", "conditional", "nonlinear"),
-                                flatten = FALSE,
-                                ...) {
-  component <- match.arg(component)
+find_parameters.nls <- function(x, component = "all", flatten = FALSE, ...) {
+  component <- validate_argument(component, c("all", "conditional", "nonlinear"))
   f <- find_formula(x)
   elements <- .get_elements(effects = "fixed", component = component)
   f <- .prepare_predictors(x, f, elements)

diff --git a/R/find_parameters_bayesian.R b/R/find_parameters_bayesian.R
@@ -37,16 +37,19 @@
 #' - `mix`, mixture parameters (**brms** only)
 #' - `shiftprop`, shifted proportion parameters (**brms** only)
 #'
+#' Models of class **BGGM** additionally can return the elements `correlation`
+#' and `intercept`.
+#'
+#' Models of class **BFBayesFactor** additionally can return the element
+#' `extra`.
+#'
 #' @examples
 #' data(mtcars)
 #' m <- lm(mpg ~ wt + cyl + vs, data = mtcars)
 #' find_parameters(m)
 #' @export
-find_parameters.BGGM <- function(x,
-                                 component = c("correlation", "conditional", "intercept", "all"),
-                                 flatten = FALSE,
-                                 ...) {
-  component <- match.arg(component)
+find_parameters.BGGM <- function(x, component = "correlation", flatten = FALSE, ...) {
+  component <- validate_argument(component, c("correlation", "conditional", "intercept", "all"))
   l <- switch(component,
     correlation = list(correlation = colnames(get_parameters(x, component = "correlation"))),
     conditional = list(conditional = colnames(get_parameters(x, component = "conditional"))),
@@ -71,16 +74,16 @@ find_parameters.BGGM <- function(x,
 #' @rdname find_parameters.BGGM
 #' @export
 find_parameters.BFBayesFactor <- function(x,
-                                          effects = c("all", "fixed", "random"),
-                                          component = c("all", "extra"),
+                                          effects = "all",
+                                          component = "all",
                                           flatten = FALSE,
                                           ...) {
   conditional <- NULL
   random <- NULL
   extra <- NULL
 
-  effects <- match.arg(effects)
-  component <- match.arg(component)
+  effects <- validate_argument(effects, c("all", "fixed", "random"))
+  component <- validate_argument(component, c("all", "extra"))
 
   if (.classify_BFBayesFactor(x) == "correlation") {
     conditional <- "rho"

diff --git a/R/find_parameters_gam.R b/R/find_parameters_gam.R
@@ -38,12 +38,8 @@ find_parameters.gamlss <- function(x, flatten = FALSE, ...) {
 }
 
 
-#' @rdname find_parameters.gamlss
 #' @export
-find_parameters.gam <- function(x,
-                                component = c("all", "conditional", "smooth_terms", "location"),
-                                flatten = FALSE,
-                                ...) {
+find_parameters.gam <- function(x, component = "all", flatten = FALSE, ...) {
   pars <- list(conditional = names(stats::coef(x)))
   pars$conditional <- text_remove_backticks(pars$conditional)
 
@@ -54,7 +50,7 @@ find_parameters.gam <- function(x,
 
   pars <- compact_list(pars)
 
-  component <- match.arg(component)
+  component <- validate_argument(component, c("all", "conditional", "smooth_terms", "location"))
   elements <- .get_elements(effects = "all", component = component)
   pars <- compact_list(pars[elements])
 
@@ -70,12 +66,9 @@ find_parameters.scam <- find_parameters.gam
 
 
 #' @export
-find_parameters.Gam <- function(x,
-                                component = c("all", "conditional", "smooth_terms", "location"),
-                                flatten = FALSE,
-                                ...) {
+find_parameters.Gam <- function(x, component = "all", flatten = FALSE, ...) {
   pars <- names(stats::coef(x))
-  component <- match.arg(component)
+  component <- validate_argument(component, c("all", "conditional", "smooth_terms", "location"))
 
   l <- compact_list(list(
     conditional = pars[.grep_non_smoothers(pars)],
@@ -96,13 +89,10 @@ find_parameters.vgam <- find_parameters.Gam
 
 
 #' @export
-find_parameters.gamm <- function(x,
-                                 component = c("all", "conditional", "smooth_terms", "location"),
-                                 flatten = FALSE,
-                                 ...) {
+find_parameters.gamm <- function(x, component = "all", flatten = FALSE, ...) {
   x <- x$gam
   class(x) <- c(class(x), c("glm", "lm"))
-  component <- match.arg(component)
+  component <- validate_argument(component, c("all", "conditional", "smooth_terms", "location"))
 
   l <- find_parameters.gam(x, component = component)
 
@@ -115,11 +105,8 @@ find_parameters.gamm <- function(x,
 
 
 #' @export
-find_parameters.cgam <- function(x,
-                                 component = c("all", "conditional", "smooth_terms", "location"),
-                                 flatten = FALSE,
-                                 ...) {
-  component <- match.arg(component)
+find_parameters.cgam <- function(x, component = "all", flatten = FALSE, ...) {
+  component <- validate_argument(component, c("all", "conditional", "smooth_terms", "location"))
   sc <- summary(x)
 
   estimates <- sc$coefficients
@@ -164,10 +151,7 @@ find_parameters.selection <- find_parameters.SemiParBIV
 
 
 #' @export
-find_parameters.rqss <- function(x,
-                                 component = c("all", "conditional", "smooth_terms", "location"),
-                                 flatten = FALSE,
-                                 ...) {
+find_parameters.rqss <- function(x, component = "all", flatten = FALSE, ...) {
   sc <- summary(x)
 
   pars <- list(
@@ -178,7 +162,7 @@ find_parameters.rqss <- function(x,
   pars$conditional <- text_remove_backticks(pars$conditional)
   pars$smooth_terms <- text_remove_backticks(pars$smooth_terms)
 
-  component <- match.arg(component)
+  component <- validate_argument(component, c("all", "conditional", "smooth_terms", "location"))
   elements <- .get_elements(effects = "all", component)
   pars <- compact_list(pars[elements])
 

diff --git a/R/find_parameters_mfx.R b/R/find_parameters_mfx.R
@@ -35,17 +35,20 @@
 #' m <- lm(mpg ~ wt + cyl + vs, data = mtcars)
 #' find_parameters(m)
 #' @export
-find_parameters.betamfx <- function(x,
-                                    component = c("all", "conditional", "precision", "marginal", "location", "distributional", "auxiliary"),
-                                    flatten = FALSE,
-                                    ...) {
+find_parameters.betamfx <- function(x, component = "all", flatten = FALSE, ...) {
   pars <- list(
     marginal = text_remove_backticks(rownames(x$mfxest)),
     conditional = text_remove_backticks(names(x$fit$coefficients$mean)),
     precision = text_remove_backticks(names(x$fit$coefficients$precision))
   )
 
-  component <- match.arg(component)
+  component <- validate_argument(
+    component,
+    c(
+      "all", "conditional", "precision", "marginal", "location",
+      "distributional", "auxiliary"
+    )
+  )
   elements <- .get_elements(effects = "all", component = component)
   pars <- compact_list(pars[elements])
 
@@ -58,16 +61,16 @@ find_parameters.betamfx <- function(x,
 
 
 #' @export
-find_parameters.betaor <- function(x,
-                                   component = c("all", "conditional", "precision", "location", "distributional", "auxiliary"),
-                                   flatten = FALSE,
-                                   ...) {
+find_parameters.betaor <- function(x, component = "all", flatten = FALSE, ...) {
   pars <- list(
     conditional = text_remove_backticks(names(x$fit$coefficients$mean)),
     precision = text_remove_backticks(names(x$fit$coefficients$precision))
   )
 
-  component <- match.arg(component)
+  component <- validate_argument(
+    component,
+    c("all", "conditional", "precision", "location", "distributional", "auxiliary")
+  )
   elements <- .get_elements(effects = "all", component = component)
   pars <- compact_list(pars[elements])
 
@@ -81,14 +84,11 @@ find_parameters.betaor <- function(x,
 
 #' @rdname find_parameters.betamfx
 #' @export
-find_parameters.logitmfx <- function(x,
-                                     component = c("all", "conditional", "marginal", "location"),
-                                     flatten = FALSE,
-                                     ...) {
+find_parameters.logitmfx <- function(x, component = "all", flatten = FALSE, ...) {
   p <- text_remove_backticks(names(stats::coef(x$fit)))
   pars <- list(marginal = text_remove_backticks(rownames(x$mfxest)), conditional = p)
 
-  component <- match.arg(component)
+  component <- validate_argument(component, c("all", "conditional", "marginal", "location"))
   elements <- .get_elements(effects = "all", component = component)
   pars <- compact_list(pars[elements])