79 add binary endpoints to wrapper anchored function

.pre-commit-config.yaml

@@ -14,6 +14,7 @@ repos:
  - lubridate
  - DescTools
  - lmtest
+ - sandwich
  # codemeta must be above use-tidy-description when both are used
  # - id: codemeta-description-updated
  - id: use-tidy-description
@@ -50,6 +51,11 @@ repos:
  - id: parsable-R
  - id: no-browser-statement
  - id: deps-in-desc
+ exclude: >
+ (?x)^(
+ data-raw/.*|
+ (.*/|)\.Rprofile
+ )$
  - repo: https://github.com/pre-commit/mirrors-prettier
  rev: v4.0.0-alpha.8
  hooks:

DESCRIPTION

@@ -22,14 +22,14 @@ Imports:
  MASS,
  boot,
  stringr,
- lmtest
+ lmtest,
+ sandwich
 Suggests:
  knitr,
  testthat (>= 2.0),
  ggplot2,
  rmarkdown,
  dplyr,
- sandwich,
  survminer,
  flexsurv,
  tibble,

NAMESPACE

@@ -39,10 +39,14 @@ import(lubridate)
 import(stats)
 import(stringr)
 import(survival)
+importFrom(boot,boot)
+importFrom(boot,boot.ci)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,rgb)
 importFrom(lmtest,coefci)
 importFrom(lmtest,coeftest)
+importFrom(sandwich,vcovHC)
 importFrom(survival,Surv)
+importFrom(survival,coxph)
 importFrom(survival,survfit)
 importFrom(utils,stack)

R/bucher.R

@@ -135,9 +135,32 @@ find_SE_from_CI <- function(CI_lower = NULL, CI_upper = NULL,
 
 print.maicplus_bucher <- function(x, ci_digits = 2, pval_digits = 3,
  exponentiate = FALSE, ...) {
+ output <- reformat(x, ci_digits, pval_digits,
+ show_pval = TRUE, exponentiate
+ )
+ print(output)
+}
+
+#' Reformat `maicplus_bucher` alike object
+#'
+#' @param x a list, structured like a `maicplus_bucher` object
+#' @param ci_digits an integer, number of decimal places for point
+#' estimate and derived confidence limits
+#' @param pval_digits an integer, number of decimal places to display
+#' Z-test p-value
+#' @param show_pval a logical value, default is TRUE. If FALSE, p-value will not
+#' be output as the second element of the character vector
+#' @param exponentiate whether the treatment effect and confidence
+#' interval should be exponentiated. This applies to relative
+#' treatment effects. Default is set to false.
+
+
+reformat <- function(x, ci_digits = 2, pval_digits = 3,
+ show_pval = TRUE, exponentiate = FALSE) {
  transform_this <- function(x) {
  ifelse(exponentiate, exp(x), x)
  }
+
  a <- format(round(transform_this(x$est), ci_digits),
  nsmall = ci_digits
  )
@@ -156,7 +179,13 @@ print.maicplus_bucher <- function(x, ci_digits = 2, pval_digits = 3,
  format(disp_pval, nsmall = pval_digits)
  )
 
- output <- c(res, disp_pval)
- names(output) <- c("result", "pvalue")
- print(output)
+ if (show_pval) {
+ output <- c(res, disp_pval)
+ names(output) <- c("result", "pvalue")
+ } else {
+ output <- res
+ names(output) <- "result"
+ }
+
+ output
 }