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@strengejacke
strengejacke committed Sep 22, 2023
1 parent c28ece3 commit bebd95b
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Showing 8 changed files with 98 additions and 94 deletions.
50 changes: 24 additions & 26 deletions R/find_variables.R
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Original file line number Diff line number Diff line change
Expand Up @@ -25,34 +25,32 @@
#' - `zero_inflated`, the names of the predictor variables from the *zero-inflated* part of the model
#' - `zero_inflated_random`, the names of the random effects (grouping factors)
#'
#' @examples
#' if (require("lme4")) {
#' data(cbpp)
#' data(sleepstudy)
#' # some data preparation...
#' cbpp$trials <- cbpp$size - cbpp$incidence
#' sleepstudy$mygrp <- sample(1:5, size = 180, replace = TRUE)
#' sleepstudy$mysubgrp <- NA
#' for (i in 1:5) {
#' filter_group <- sleepstudy$mygrp == i
#' sleepstudy$mysubgrp[filter_group] <-
#' sample(1:30, size = sum(filter_group), replace = TRUE)
#' }
#' @examplesIf require("lme4")
#' data(cbpp, package = "lme4")
#' data(sleepstudy, package = "lme4")
#' # some data preparation...
#' cbpp$trials <- cbpp$size - cbpp$incidence
#' sleepstudy$mygrp <- sample(1:5, size = 180, replace = TRUE)
#' sleepstudy$mysubgrp <- NA
#' for (i in 1:5) {
#' filter_group <- sleepstudy$mygrp == i
#' sleepstudy$mysubgrp[filter_group] <-
#' sample(1:30, size = sum(filter_group), replace = TRUE)
#' }
#'
#' m1 <- glmer(
#' cbind(incidence, size - incidence) ~ period + (1 | herd),
#' data = cbpp,
#' family = binomial
#' )
#' find_variables(m1)
#' m1 <- lme4::glmer(
#' cbind(incidence, size - incidence) ~ period + (1 | herd),
#' data = cbpp,
#' family = binomial
#' )
#' find_variables(m1)
#'
#' m2 <- lmer(
#' Reaction ~ Days + (1 | mygrp / mysubgrp) + (1 | Subject),
#' data = sleepstudy
#' )
#' find_variables(m2)
#' find_variables(m2, flatten = TRUE)
#' }
#' m2 <- lme4::lmer(
#' Reaction ~ Days + (1 | mygrp / mysubgrp) + (1 | Subject),
#' data = sleepstudy
#' )
#' find_variables(m2)
#' find_variables(m2, flatten = TRUE)
#' @export
find_variables <- function(x,
effects = "all",
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10 changes: 5 additions & 5 deletions R/format_bf.R
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Expand Up @@ -40,7 +40,7 @@ format_bf <- function(bf,
is_small <- logical(length(bf))
}

digits <- ifelse(is.na(bf), 0, ifelse(bf < 1, 3, 2))
digits <- ifelse(is.na(bf), 0, ifelse(bf < 1, 3, 2)) # nolint

text <- paste0(
"= ",
Expand All @@ -57,7 +57,7 @@ format_bf <- function(bf,
text[is_extreme]
)
text[is_extreme] <- ifelse(bf_orig[is_extreme] < 1 / 1000,
ifelse(is_small[is_extreme],
ifelse(is_small[is_extreme], # nolint
sprintf("= 1/%.2e", bf[is_extreme]),
sprintf("= %.2e", bf_orig[is_extreme])
),
Expand All @@ -69,16 +69,16 @@ format_bf <- function(bf,
text[is_extreme]
)
text[is_extreme] <- ifelse(bf_orig[is_extreme] < 1 / 1000,
ifelse(is_small[is_extreme], "< 1/1000", "< 0.001"),
ifelse(is_small[is_extreme], "< 1/1000", "< 0.001"), # nolint
text[is_extreme]
)
}
}

## Add stars
text <- ifelse(bf_orig > 30, paste0(text, "***"),
ifelse(bf_orig > 10, paste0(text, "**"),
ifelse(bf_orig > 3, paste0(text, "*"), text)
ifelse(bf_orig > 10, paste0(text, "**"), # nolint
ifelse(bf_orig > 3, paste0(text, "*"), text) # nolint
)
)

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22 changes: 11 additions & 11 deletions R/format_p.R
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Original file line number Diff line number Diff line change
Expand Up @@ -68,10 +68,10 @@ format_p <- function(p,
digits <- 5
}
text <- ifelse(is.na(p), NA,
ifelse(p < 0.001, sprintf("= %.*e***", digits, p),
ifelse(p < 0.01, sprintf("= %.*e**", digits, p),
ifelse(p < 0.05, sprintf("= %.*e*", digits, p),
ifelse(p > 0.999, sprintf("= %.*e", digits, p),
ifelse(p < 0.001, sprintf("= %.*e***", digits, p), # nolint
ifelse(p < 0.01, sprintf("= %.*e**", digits, p), # nolint
ifelse(p < 0.05, sprintf("= %.*e*", digits, p), # nolint
ifelse(p > 0.999, sprintf("= %.*e", digits, p), # nolint
sprintf("= %.*e", digits, p)
)
)
Expand All @@ -80,10 +80,10 @@ format_p <- function(p,
)
} else if (digits <= 3) {
text <- ifelse(is.na(p), NA,
ifelse(p < 0.001, "< .001***",
ifelse(p < 0.01, paste0("= ", format_value(p, digits), "**"),
ifelse(p < 0.05, paste0("= ", format_value(p, digits), "*"),
ifelse(p > 0.999, "> .999",
ifelse(p < 0.001, "< .001***", # nolint
ifelse(p < 0.01, paste0("= ", format_value(p, digits), "**"), # nolint
ifelse(p < 0.05, paste0("= ", format_value(p, digits), "*"), # nolint
ifelse(p > 0.999, "> .999", # nolint
paste0("= ", format_value(p, digits))
)
)
Expand All @@ -92,9 +92,9 @@ format_p <- function(p,
)
} else {
text <- ifelse(is.na(p), NA,
ifelse(p < 0.001, paste0("= ", format_value(p, digits), "***"),
ifelse(p < 0.01, paste0("= ", format_value(p, digits), "**"),
ifelse(p < 0.05, paste0("= ", format_value(p, digits), "*"),
ifelse(p < 0.001, paste0("= ", format_value(p, digits), "***"), # nolint
ifelse(p < 0.01, paste0("= ", format_value(p, digits), "**"), # nolint
ifelse(p < 0.05, paste0("= ", format_value(p, digits), "*"), # nolint
paste0("= ", format_value(p, digits))
)
)
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6 changes: 3 additions & 3 deletions R/format_pd.R
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Expand Up @@ -11,9 +11,9 @@
#' @export
format_pd <- function(pd, stars = FALSE, stars_only = FALSE, name = "pd") {
text <- ifelse(pd >= 1, "= 100%***",
ifelse(pd > 0.999, paste0("= ", format_value(pd * 100), "%***"),
ifelse(pd > 0.99, paste0("= ", format_value(pd * 100), "%**"),
ifelse(pd > 0.97, paste0("= ", format_value(pd * 100), "%*"),
ifelse(pd > 0.999, paste0("= ", format_value(pd * 100), "%***"), # nolint
ifelse(pd > 0.99, paste0("= ", format_value(pd * 100), "%**"), # nolint
ifelse(pd > 0.97, paste0("= ", format_value(pd * 100), "%*"), # nolint
paste0("= ", format_value(pd * 100), "%")
)
)
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2 changes: 1 addition & 1 deletion R/format_rope.R
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Expand Up @@ -12,7 +12,7 @@
#' @export
format_rope <- function(rope_percentage, name = "in ROPE", digits = 2) {
text <- ifelse(rope_percentage == 0, "0%",
ifelse(rope_percentage == 1, "100%",
ifelse(rope_percentage == 1, "100%", # nolint
format_value(rope_percentage, digits = digits, as_percent = TRUE)
)
)
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26 changes: 14 additions & 12 deletions R/format_table.R
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Expand Up @@ -55,21 +55,23 @@
#'
#' @note `options(insight_use_symbols = TRUE)` override the `use_symbols` argument
#' and always displays symbols, if possible.
#' @examples
#' @examplesIf require("rstanarm", warn.conflicts = FALSE) && require("parameters", , warn.conflicts = FALSE)
#' format_table(head(iris), digits = 1)
#'
#' if (require("parameters")) {
#' x <- model_parameters(lm(Sepal.Length ~ Species * Sepal.Width, data = iris))
#' as.data.frame(format_table(x))
#' as.data.frame(format_table(x, p_digits = "scientific"))
#' }
#' m <- lm(Sepal.Length ~ Species * Sepal.Width, data = iris)
#' x <- parameters::model_parameters(m)
#' as.data.frame(format_table(x))
#' as.data.frame(format_table(x, p_digits = "scientific"))
#'
#' \donttest{
#' if (require("rstanarm", warn.conflicts = FALSE) &&
#' require("parameters", , warn.conflicts = FALSE)) {
#' model <- stan_glm(Sepal.Length ~ Species, data = iris, refresh = 0, seed = 123)
#' x <- model_parameters(model, ci = c(0.69, 0.89, 0.95))
#' as.data.frame(format_table(x))
#' }
#' model <- rstanarm::stan_glm(
#' Sepal.Length ~ Species,
#' data = iris,
#' refresh = 0,
#' seed = 123
#' )
#' x <- parameters::model_parameters(model, ci = c(0.69, 0.89, 0.95))
#' as.data.frame(format_table(x))
#' }
#' @return A data frame. Note that `format_table()` converts all columns
#' into character vectors!
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50 changes: 25 additions & 25 deletions man/find_variables.Rd
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26 changes: 15 additions & 11 deletions man/format_table.Rd
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