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added option to select which global pValue to show #46

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added option to select which global pValue to show #46

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3ec866d
changed logrank to likelihood in show_global_p
gernophil Aug 26, 2023
945eb64
minor change
gernophil Sep 2, 2023
a0dbda9
changed global to Wald test
gernophil Oct 13, 2023
829f112
added selection for global p
gernophil Nov 18, 2023
59906bf
added selection for global p
gernophil Nov 18, 2023
06af3ae
test
gernophil Nov 18, 2023
6fda8fb
test
gernophil Nov 18, 2023
4fcb411
test
gernophil Nov 18, 2023
d15699e
simplified code
gernophil Nov 18, 2023
1299e14
added some documentation
gernophil Nov 18, 2023
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13 changes: 11 additions & 2 deletions R/default_forest_panels.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,16 @@
#' @return `list` ready to be passed to `forest_model`
#' @export
#'
default_forest_panels <- function(model = NULL, factor_separate_line = FALSE, measure = NULL, trans_char = "I") {
default_forest_panels <- function(model = NULL, factor_separate_line = FALSE, measure = NULL, trans_char = "I", which_global_p = "logtest") {
if (which_global_p != "logtest") {
if (which_global_p == "waldtest") {
global_p_text <- "(Wald test)"
} else if (which_global_p == "sctest") {
global_p_text <- "(Score (logrank))"
}
} else {
global_p_text <- "(Likelihood ratio test)"
}
if (is.list(model) && inherits(model[[1]], "rma")) {
model <- model[[1]]
}
Expand Down Expand Up @@ -70,7 +79,7 @@ default_forest_panels <- function(model = NULL, factor_separate_line = FALSE, me
forest_panel(width = 0.03, item = "vline", hjust = 0.5),
forest_panel(
width = 0.12,
display = if_else(reference, if_else(is_na(p.value), "Reference", "Reference; Variable logrank:"),
display = if_else(reference, if_else(is_na(p.value), "Reference", paste0("Reference | Global p ", global_p_text, ":")),
sprintf("%0.2f (%0.2f, %0.2f)", trans(estimate), trans(conf.low), trans(conf.high))
),
display_na = NA
Expand Down
28 changes: 24 additions & 4 deletions R/forest_model.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,10 @@
#' - 'none', don't show.
#' - 'bottom', show global p value in the bottom.
#' - 'aside', show global p value along with 'Reference', this is useful when you plot a list of models.
#' @param which_global_p Select which global p value to show, only works for Cox model.
#' - 'logtest', Likelihood ratio test.
#' - 'waldtest', Wald test.
#' - 'sctest', Score (logrank).
#' @param n_logical_true_only whether to only count TRUE values in n for logical
#' covariates
#'
Expand Down Expand Up @@ -127,7 +131,7 @@
#'
#' print(forest_model(glm(outcome ~ ., binomial(), data_for_logistic)))
forest_model <- function(model,
panels = default_forest_panels(model, factor_separate_line = factor_separate_line),
panels = default_forest_panels(model, factor_separate_line = factor_separate_line, which_global_p = which_global_p),
covariates = NULL, exponentiate = NULL, funcs = NULL,
factor_separate_line = FALSE,
format_options = forest_model_format_options(),
Expand All @@ -136,8 +140,10 @@ forest_model <- function(model,
recalculate_width = TRUE, recalculate_height = TRUE,
model_list = NULL, merge_models = FALSE, exclude_infinite_cis = TRUE,
show_global_p = c("none", "bottom", "aside"),
which_global_p = c("logtest", "waldtest", "sctest"),
n_logical_true_only = FALSE) {
show_global_p <- match.arg(show_global_p)
which_global_p <- match.arg(which_global_p)
mapping <- aes(estimate, xmin = conf.low, xmax = conf.high)
if (!is.null(model_list)) {
if (!is.list(model_list)) {
Expand All @@ -161,7 +167,7 @@ forest_model <- function(model,
(inherits(model_list[[1]], "glm") && model_list[[1]]$family$link == "logit")
}
if (missing(panels)) {
panels <- default_forest_panels(model_list[[1]], factor_separate_line = factor_separate_line)
panels <- default_forest_panels(model_list[[1]], factor_separate_line = factor_separate_line, which_global_p = which_global_p)
}
} else {
if (is.null(exponentiate)) {
Expand Down Expand Up @@ -286,9 +292,23 @@ forest_model <- function(model,

if (show_global_p != "none") {
if (inherits(model, "coxph")) {
p_val <- as.numeric(summary(model)$sctest[3])
p_val_logtest <- as.numeric(summary(model)$logtest[3])
p_val_waldtest <- as.numeric(summary(model)$waldtest[3])
p_val_sctest <- as.numeric(summary(model)$sctest[3])
if (which_global_p != "logtest") {
if (which_global_p == "waldtest") {
p_val <- p_val_waldtest
global_p_text <- "(Wald test)"
} else if (which_global_p == "sctest") {
p_val <- p_val_sctest
global_p_text <- "(Score (logrank))"
}
} else {
p_val <- p_val_logtest
global_p_text <- "(Likelihood ratio test)"
}
if (show_global_p == "bottom") {
label <- paste("Global p", format.pval(p_val, digits = 1, eps = 1e-3))
label <- paste(" Global p ", global_p_text, ":", format.pval(p_val, digits = 1, eps = 1e-3))
forest_terms <- forest_terms %>%
dplyr::add_row(term_label = "Global p", variable = label)
} else if (show_global_p == "aside") {
Expand Down
6 changes: 6 additions & 0 deletions man/forest_model.Rd
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