fix doco

R/civilytics-package.R

@@ -0,0 +1,10 @@
+#' @keywords internal
+#' @importFrom stats qbeta
+#' @importFrom stats qnorm
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL
+
+

R/prop_conf.R

@@ -6,17 +6,15 @@
 # https://andrewpwheeler.com/2020/11/30/confidence-intervals-around-proportions/
 #' Get a simple Clopper Pearson interval
 #'
-#' @param num
-#' @param den
-#' @param confint
+#' @param num number of successes
+#' @param den number of trials
+#' @param conf.level default 0.95, set the confidence interval to return
 #'
-#' @return
+#' @return three values forming the upper and lower bounds of the confidence region and the true value
 #' @export
-#'
-#' @examples
-clopper_pearson <- function(num, den, confint = 0.95) {
+clopper_pearson <- function(num, den, conf.level = 0.95) {
   # Same results as binom.test in base R
-  quant <- (1 - confint) / 2
+  quant <- (1 - conf.level) / 2
   low <- qbeta(quant, num, den-num+1)
   hi <- qbeta(1-quant, num+1, den-num)
   obs <- num/den
@@ -24,7 +22,6 @@ clopper_pearson <- function(num, den, confint = 0.95) {
 }
 
 
-# TODO consider making a vectorized version
 # z_gap_test_v <- Vectorize(z_gap_test,
 #                           SIMPLIFY = TRUE)# we only want to return a scalar
 
@@ -53,6 +50,17 @@ z_univariate <- function(unit_prop, global_prop, unit_denom) {
 
 }
 
+#' Calculate a Wald interval
+#'
+#' @param x the numerator, number of times the event occurs
+#' @param n the denominator, the number of trials
+#' @param conf.level default 0.95, set the confidence interval to return
+#'
+#' @return two values forming the upper and lower bounds of the confidence region
+#' @export
+#'
+#' @examples
+#' waldInterval(x = 20, n =40) #this will return 0.345 and 0.655
 waldInterval <- function(x, n, conf.level = 0.95){
   p <- x/n
   sd <- sqrt(p*((1-p)/n))
@@ -60,11 +68,18 @@ waldInterval <- function(x, n, conf.level = 0.95){
   ci <- p + z*sd
   names(ci) <- c('lwr', 'upr')
   return(ci)
-}#example
-#waldInterval(x = 20, n =40) #this will return 0.345 and 0.655
+}
 
+#' Calculate the Agresti-Coull interval
+#'
+#' @param num a number of successes
+#' @param den a number of trials
+#' @param conf.level default 0.95, set the confidence interval to return
+#'
+#' @return an interval
 agresti_coull_interval <- function(num, den, conf.level) {
   num <- num + 2
   den <- den + 4
+  return(num/den)
 
 }