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try to reduce warnings in examples and use examplesIf #616

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Sep 15, 2023
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try to reduce warnings in examples and use examplesIf #616

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6c95f67
try to reduce warnings in examples and use examplesIf
strengejacke Sep 15, 2023
9c0359c
fix
strengejacke Sep 15, 2023
4e063c0
suppressWarnings
strengejacke Sep 15, 2023
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4 changes: 2 additions & 2 deletions R/looic.R
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Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@
#' @return A list with four elements, the ELPD, LOOIC and their standard errors.
#'
#' @examplesIf require("rstanarm")
#' model <- rstanarm::stan_glm(
#' model <- suppressWarnings(rstanarm::stan_glm(
#' mpg ~ wt + cyl,
#' data = mtcars,
#' chains = 1,
#' iter = 500,
#' refresh = 0
#' )
#' ))
#' looic(model)
#' @export
looic <- function(model, verbose = TRUE) {
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10 changes: 5 additions & 5 deletions R/model_performance.bayesian.R
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Expand Up @@ -42,25 +42,25 @@
#'
#' @examplesIf require("rstanarm") && require("rstantools") && require("BayesFactor")
#' \dontrun{
#' model <- rstanarm::stan_glm(
#' model <- suppressWarnings(rstanarm::stan_glm(
#' mpg ~ wt + cyl,
#' data = mtcars,
#' chains = 1,
#' iter = 500,
#' refresh = 0
#' )
#' ))
#' model_performance(model)
#'
#' model <- stan_glmer(
#' model <- suppressWarnings(rstanarm::stan_glmer(
#' mpg ~ wt + cyl + (1 | gear),
#' data = mtcars,
#' chains = 1,
#' iter = 500,
#' refresh = 0
#' )
#' ))
#' model_performance(model)
#'
#' model <- generalTestBF(carb ~ am + mpg, mtcars)
#' model <- BayesFactor::generalTestBF(carb ~ am + mpg, mtcars)
#'
#' model_performance(model)
#' model_performance(model[3])
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4 changes: 2 additions & 2 deletions R/model_performance.rma.R
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Original file line number Diff line number Diff line change
Expand Up @@ -47,8 +47,8 @@
#' See the documentation for `?metafor::fitstats`.
#' }
#'
#' @examplesIf require("metafor")
#' data(dat.bcg, package = "metafor")
#' @examplesIf require("metafor") && require("metadat")
#' data(dat.bcg, package = "metadat")
#' dat <- metafor::escalc(
#' measure = "RR",
#' ai = tpos,
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18 changes: 14 additions & 4 deletions R/r2_bayes.R
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Expand Up @@ -43,13 +43,13 @@
#' ))
#' r2_bayes(model)
#'
#' model <- stan_lmer(
#' model <- suppressWarnings(stan_lmer(
#' Petal.Length ~ Petal.Width + (1 | Species),
#' data = iris,
#' chains = 1,
#' iter = 500,
#' refresh = 0
#' )
#' ))
#' r2_bayes(model)
#' }
#'
Expand All @@ -75,10 +75,20 @@
#'
#' \dontrun{
#' if (require("brms")) {
#' model <- brms::brm(mpg ~ wt + cyl, data = mtcars)
#' model <- suppressWarnings(brms::brm(
#' mpg ~ wt + cyl,
#' data = mtcars,
#' silent = 2,
#' refresh = 0
#' ))
#' r2_bayes(model)
#'
#' model <- brms::brm(Petal.Length ~ Petal.Width + (1 | Species), data = iris)
#' model <- suppressWarnings(brms::brm(
#' Petal.Length ~ Petal.Width + (1 | Species),
#' data = iris,
#' silent = 2,
#' refresh = 0
#' ))
#' r2_bayes(model)
#' }
#' }
Expand All @@ -104,7 +114,7 @@
mean(i)
}
}),
"SE" = rapply(r2_bayesian, function(i) {

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file=R/r2_bayes.R,line=117,col=7,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
if (robust) {
stats::mad(i)
} else {
Expand All @@ -112,9 +122,9 @@
}
}),
# "Estimates" = rapply(r2_bayesian, bayestestR::point_estimate, centrality = "all", dispersion = TRUE),
"CI" = rapply(r2_bayesian, bayestestR::hdi, ci = ci),

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file=R/r2_bayes.R,line=125,col=7,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"ci_method" = "HDI",

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file=R/r2_bayes.R,line=126,col=7,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"robust" = robust

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file=R/r2_bayes.R,line=127,col=7,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
)
} else {
structure(
Expand All @@ -126,7 +136,7 @@
mean(i)
}
}),
"SE" = lapply(r2_bayesian, function(i) {

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file=R/r2_bayes.R,line=139,col=7,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
if (robust) {
stats::mad(i)
} else {
Expand All @@ -134,9 +144,9 @@
}
}),
# "Estimates" = lapply(r2_bayesian, bayestestR::point_estimate, centrality = "all", dispersion = TRUE),
"CI" = lapply(r2_bayesian, bayestestR::hdi, ci = ci),

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file=R/r2_bayes.R,line=147,col=7,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"ci_method" = "HDI",

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file=R/r2_bayes.R,line=148,col=7,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"robust" = robust

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file=R/r2_bayes.R,line=149,col=7,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
)
}
}
Expand Down Expand Up @@ -168,13 +178,13 @@
res <- insight::find_response(model)
if (mi[[1]]$is_mixed) {
br2_mv <- list(
"R2_Bayes" = rstantools::bayes_R2(

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file=R/r2_bayes.R,line=181,col=13,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
model,
re.form = NULL,
re_formula = NULL,
summary = FALSE
),
"R2_Bayes_marginal" = rstantools::bayes_R2(

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file=R/r2_bayes.R,line=187,col=13,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
model,
re.form = NA,
re_formula = NA,
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4 changes: 2 additions & 2 deletions man/looic.Rd
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4 changes: 2 additions & 2 deletions man/model_performance.rma.Rd
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10 changes: 5 additions & 5 deletions man/model_performance.stanreg.Rd
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18 changes: 14 additions & 4 deletions man/r2_bayes.Rd
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