Add CI of Response Rate and Odds Ratio (#9)

* add s_propci function for proportion calculation with DescTools

* Add s_odds_ratio for odds ratio calculation and tests

* add print method for prop_ci and or_ci classes

DESCRIPTION

@@ -1,26 +1,31 @@
 Package: stabiot
 Type: Package
-Title: Common Statistical Analysis for Clinical Trials in Biotech
+Title: Common Statistical Analysis for Clinical Trials
 Version: 0.0.0.9000
 Authors@R: c(
     person("Kai", "Gu", , "gukai1212@163.com", role = c("aut", "cre", "cph"))
   )
 Maintainer: Kai Gu <gukai1212@163.com>
-Description: Providing common statistical analysis for oversighting process in 
-    clinical trials of biotech, making the outputs can be compared with SAS results.
+Description: Provides common statistical analysis for oversighting process in 
+    clinical trials of biotech, makes the outputs can be compared with SAS results.
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 Depends: 
     R (>= 3.6)
 Imports:
     checkmate,
+    DescTools,
     dplyr,
     emmeans,
     lifecycle,
     magrittr,
+    purrr,
+    rlang,
     stats,
-    tibble
+    survival,
+    tibble,
+    tidyr
 Suggests: 
     knitr,
     mmrm,

NAMESPACE

@@ -1,12 +1,29 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,or_ci)
+S3method(print,prop_ci)
 S3method(print,s_lsmeans)
 export("%>%")
+export(h_prep_prop)
 export(rrPostProb)
 export(s_get_lsmeans)
+export(s_odds_ratio)
+export(s_propci)
 import(checkmate)
+importFrom(dplyr,add_count)
+importFrom(dplyr,count)
+importFrom(dplyr,group_by)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
+importFrom(rlang,":=")
+importFrom(rlang,.data)
+importFrom(rlang,sym)
+importFrom(stats,as.formula)
+importFrom(stats,coef)
 importFrom(stats,confint)
 importFrom(stats,pbeta)
 importFrom(stats,rbinom)
+importFrom(stats,setNames)
+importFrom(survival,Surv)
+importFrom(survival,coxph)
+importFrom(survival,strata)

R/package.R

@@ -6,7 +6,10 @@
 
 #' @import checkmate
 #' @importFrom lifecycle deprecated
-#' @importFrom stats pbeta rbinom confint
+#' @importFrom stats pbeta rbinom confint as.formula setNames coef
+#' @importFrom dplyr count add_count group_by
+#' @importFrom rlang sym := .data
+#' @importFrom survival coxph Surv strata
 NULL
 
 .onLoad <- function(libname, pkgname) {

R/pkg-methods.R

@@ -33,3 +33,44 @@ print.s_lsmeans <- function(x, ...) {
 
   invisible(x)
 }
+
+#' @describeIn prop_odds_ratio prints proportion and confidence interval.
+#' @exportS3Method
+#' @keywords internal
+print.prop_ci <- function(x, ...) {
+  cat(sprintf("Proportion and %s confidence interval:", x$params$method))
+  cat("\n")
+  print(x$prop_est)
+
+  if (!is.null(x$params$by.level)) {
+    cat(sprintf("\nProportion Difference and %s confidence interval:", x$params$diff.method))
+    cat("\n")
+    print(x$prop_diff)
+  }
+
+  invisible(x)
+}
+
+#' @describeIn prop_odds_ratio prints odds ratio and confidence interval.
+#' @exportS3Method
+#' @keywords internal
+print.or_ci <- function(x, ...) {
+  comp <- paste0(rev(x$params$by.level), collapse = "/")
+  cat(sprintf("Common Odds Ratio (%s) and %s confidence interval:", comp, x$params$or.method))
+  cat("\n")
+  print(x$or)
+
+  if (!is.null(x$params$strata)) {
+    cat(sprintf(
+      "\nStratified Odds Ratio (%s) using %s", comp,
+      ifelse(x$params$strata.method == "CMH",
+        "Cochran-Mantel-Haenszel Chi-Squared Test:",
+        "Conditional logistic regression:"
+      )
+    ))
+    cat("\n")
+    print(x$strata_or)
+  }
+
+  invisible(x)
+}