79 add binary endpoints to wrapper anchored function (#112)

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Isaac Gravestock <83659704+gravesti@users.noreply.github.com>
Co-authored-by: Isaac Gravestock <isaac.gravestock@roche.com>

.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
 }