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

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Nov 6, 2024
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Reduce methods appearing in docs, to make docs clearer #961

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2136e71
Don't show "usage" for all classes (make docs clearer)
strengejacke Nov 6, 2024
476f7e2
docs
strengejacke Nov 6, 2024
629a568
docs
strengejacke Nov 6, 2024
cb260d8
docs
strengejacke Nov 6, 2024
260d2e5
docs
strengejacke Nov 6, 2024
7d65eb8
Merge branch 'main' into reduce_methods_docs
strengejacke Nov 6, 2024
07fbcc5
docs
strengejacke Nov 6, 2024
3c5b699
typo
strengejacke Nov 6, 2024
cd73d6d
docs
strengejacke Nov 6, 2024
b21b653
find_param
strengejacke Nov 6, 2024
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32 changes: 16 additions & 16 deletions R/find_parameter_zi.R
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Expand Up @@ -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_")],
Expand All @@ -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),
Expand All @@ -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."))
Expand Down
16 changes: 4 additions & 12 deletions R/find_parameters.R
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Expand Up @@ -259,13 +259,9 @@

# 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(
Expand Down Expand Up @@ -807,13 +803,9 @@


## For questions or problems with this ask Fernando Miguez (femiguez@iastate.edu)
#' @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)
Expand All @@ -830,7 +822,7 @@

# helper ----------------------------

.filter_parameters <- function(l, effects, component = "all", flatten, recursive = TRUE) {

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file=R/find_parameters.R,line=825,col=63,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
if (isTRUE(recursive)) {
# recursively remove back-ticks from all list-elements parameters
l <- rapply(l, text_remove_backticks, how = "list")
Expand Down
21 changes: 12 additions & 9 deletions R/find_parameters_bayesian.R
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Expand Up @@ -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"))),
Expand All @@ -71,16 +74,16 @@
#' @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"
Expand Down Expand Up @@ -429,7 +432,7 @@
#' @export
find_parameters.stanreg <- function(x,
effects = c("all", "fixed", "random"),
component = c("location", "all", "conditional", "smooth_terms", "sigma", "distributional", "auxiliary"),

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file=R/find_parameters_bayesian.R,line=435,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 140 characters.
flatten = FALSE,
parameters = NULL,
...) {
Expand Down Expand Up @@ -488,7 +491,7 @@
#' @export
find_parameters.stanmvreg <- function(x,
effects = c("all", "fixed", "random"),
component = c("location", "all", "conditional", "smooth_terms", "sigma", "distributional", "auxiliary"),

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file=R/find_parameters_bayesian.R,line=494,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 142 characters.
flatten = FALSE,
parameters = NULL,
...) {
Expand Down
36 changes: 10 additions & 26 deletions R/find_parameters_gam.R
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Expand Up @@ -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)

Expand All @@ -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])

Expand All @@ -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)],
Expand All @@ -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)

Expand All @@ -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
Expand Down Expand Up @@ -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(
Expand All @@ -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])

Expand Down
30 changes: 15 additions & 15 deletions R/find_parameters_mfx.R
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Expand Up @@ -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])

Expand All @@ -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])

Expand All @@ -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])

Expand Down
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