#' Calculate confidence intervals
#'
#' Given 2 column matrix or data frame, returns 3 column data.frame
#' with coefficient estimate plus lower and upper borders of the
#' 95% confidence intervals.
#'
#' @param ftab A table with two columns, containing coefficients in the first
#' column and standard-errors in the second column.
#' @importFrom tibble as_tibble
calc_ci <- function(ftab) {
colnames(ftab) <- c("coef", "se")
rnames <- rownames(ftab)
ftab <- as_tibble(ftab)
ftab$variable <- rnames
ftab$lower <- ftab$coef - 2*ftab$se
ftab$upper <- ftab$coef + 2*ftab$se
ftab$se <- NULL
ftab[, c("variable", "coef", "lower", "upper")]
}
#' Extract fixed coefficient table from model object
#'
#' Given a model object, returns data frame with columns \code{variable},
#' \code{coef} (coefficient), \code{lower} (lower 95\% CI) and
#' \code{upper} (upper 95% CI).
#'
#' @param x A model object.
#' @param ... Currently not used.
#' @export
tidy_fixed <- function(x, ...) {
UseMethod("tidy_fixed", x)
}
#' @inheritParams tidy_fixed
#' @param intercept Should intercept also be returned?
#' @rdname tidy_fixed
#' @export
tidy_fixed.gam <- function(x, intercept=FALSE, ...) {
ftab <- summary(x)[["p.table"]][, 1:2]
if(!intercept) {
ftab <- ftab[!grepl("Intercept", rownames(ftab)), ]
}
calc_ci(ftab)
}
#' @inheritParams tidy_fixed
#' @importFrom tibble as_tibble
#' @rdname tidy_fixed
#' @export
tidy_fixed.coxph <- function(x, ...) {
ftab <- summary(x)[["coefficients"]][, c(1, 3)]
calc_ci(ftab)
}
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