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# classes: .coxph, .aareg, .survreg, .riskRegression, .survfit
#################### .survfit ------
#' @export
model_parameters.survfit <- function(model,
keep = NULL,
drop = NULL,
verbose = TRUE,
...) {
s <- summary(model)
# extract all elements with same length, which occur most in that list
# that is the data we need
uniqv <- unique(lengths(s))
tab <- tabulate(match(lengths(s), uniqv))
idx <- which.max(tab)
most_len <- uniqv[idx]
# convert list into data frame, only for elements of same length
params <- as.data.frame(s[lengths(s) == most_len])
# keep specific columns
keep_columns <- intersect(
c("time", "n.risk", "n.event", "surv", "std.err", "strata", "lower", "upper"),
colnames(params)
)
params <- params[keep_columns]
# rename
params <- datawizard::data_rename(
params,
select = c(
Time = "time", `N Risk` = "n.risk", `N Event` = "n.event", Survival = "surv",
SE = "std.err", Group = "strata", CI_low = "lower", CI_high = "upper"
)
)
# fix labels
params$Group <- gsub("x=", "", params$Group, fixed = TRUE)
# These are integers, need to be character to display without decimals
params$Time <- as.character(params$Time)
params[["N Risk"]] <- as.character(params[["N Risk"]])
params[["N Event"]] <- as.character(params[["N Event"]])
attr(params, "ci") <- s$conf.int
class(params) <- c("parameters_model", "see_parameters_model", class(params))
params
}
#################### .coxph ------
#' @export
standard_error.coxph <- function(model, method = NULL, ...) {
robust <- !is.null(method) && method == "robust"
if (isTRUE(robust)) {
return(standard_error(model, ...))
}
params <- insight::get_parameters(model)
cs <- stats::coef(summary(model))
se <- cs[, 3]
# check
if (length(se) > nrow(params)) {
se <- se[match(params$Parameter, .remove_backticks_from_string(rownames(cs)))]
}
.data_frame(
Parameter = params$Parameter,
SE = as.vector(se)
)
}
#' @export
p_value.coxph <- function(model, ...) {
params <- insight::get_parameters(model)
stats <- insight::get_statistic(model)
params <- merge(params, stats, sort = FALSE)
statistic <- attributes(stats)$statistic
# convert in case of z
if (identical(statistic, "z-statistic")) {
params$Statistic <- params$Statistic^2
}
.data_frame(
Parameter = params$Parameter,
p = as.vector(1 - stats::pchisq(params$Statistic, df = 1))
)
}
#################### .aareg ------
#' @export
standard_error.aareg <- function(model, ...) {
s <- summary(model)
se <- s$table[, "se(coef)"]
.data_frame(
Parameter = .remove_backticks_from_string(names(se)),
SE = as.vector(se)
)
}
#' @export
p_value.aareg <- function(model, ...) {
s <- summary(model)
p <- s$table[, "p"]
.data_frame(
Parameter = .remove_backticks_from_string(names(p)),
p = as.vector(p)
)
}
#################### .survreg ------
#' @export
standard_error.survreg <- function(model, method = NULL, ...) {
robust <- !is.null(method) && method == "robust"
if (.check_vcov_args(robust, ...)) {
return(standard_error.default(model, ...))
}
s <- summary(model)
se <- s$table[, 2]
.data_frame(
Parameter = .remove_backticks_from_string(names(se)),
SE = as.vector(se)
)
}
#' @export
p_value.survreg <- function(model, method = NULL, ...) {
robust <- !is.null(method) && method == "robust"
if (.check_vcov_args(robust, ...)) {
return(p_value.default(model, ...))
}
s <- summary(model)
p <- s$table[, "p"]
.data_frame(
Parameter = .remove_backticks_from_string(names(p)),
p = as.vector(p)
)
}
#################### .riskRegression ------
#' @export
standard_error.riskRegression <- function(model, ...) {
junk <- utils::capture.output(cs <- stats::coef(model))
.data_frame(
Parameter = .remove_backticks_from_string(as.vector(cs[, 1])),
SE = as.numeric(cs[, "StandardError"])
)
}
#' @export
p_value.riskRegression <- function(model, ...) {
junk <- utils::capture.output(cs <- stats::coef(model))
.data_frame(
Parameter = .remove_backticks_from_string(as.vector(cs[, 1])),
p = as.numeric(cs[, "Pvalue"])
)
}
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