DESCRIPTION

@@ -23,4 +23,4 @@ Encoding: UTF-8
 LazyData: true
 Suggests: 
     testthat
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(add_logo)
 export(add_logo_ga)
+export(clopper_pearson)
 export(countCleanr)
 export(countDots)
 export(countNA)
@@ -31,6 +32,7 @@ export(safe_ratio)
 export(simpleCap)
 export(star_subs)
 export(theme_civilytics)
+export(waldInterval)
 export(z_gap_test)
 export(z_univariate)
 import(ggplot2)
@@ -43,6 +45,8 @@ importFrom(grid,rasterGrob)
 importFrom(gridExtra,arrangeGrob)
 importFrom(jpeg,readJPEG)
 importFrom(png,readPNG)
+importFrom(stats,qbeta)
+importFrom(stats,qnorm)
 importFrom(stats,runif)
 importFrom(stringdist,stringsim)
 importFrom(stringr,str_count)

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)
 
 }

man/agresti_coull_interval.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prop_conf.R
+\name{agresti_coull_interval}
+\alias{agresti_coull_interval}
+\title{Calculate the Agresti-Coull interval}
+\usage{
+agresti_coull_interval(num, den, conf.level)
+}
+\arguments{
+\item{num}{a number of successes}
+
+\item{den}{a number of trials}
+
+\item{conf.level}{default 0.95, set the confidence interval to return}
+}
+\value{
+an interval
+}
+\description{
+Calculate the Agresti-Coull interval
+}

man/civilytics-package.Rd

@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/civilytics-package.R
+\docType{package}
+\name{civilytics-package}
+\alias{civilytics}
+\alias{civilytics-package}
+\title{civilytics: Utilities Functions for Civilytics}
+\description{
+House R functions for Civilytics Consulting LLC This package implements a variety of useful functions for creating and branding analyses produced by Civilytics Consulting LLC.
+}
+\keyword{internal}

man/clopper_pearson.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prop_conf.R
+\name{clopper_pearson}
+\alias{clopper_pearson}
+\title{Get a simple Clopper Pearson interval}
+\usage{
+clopper_pearson(num, den, conf.level = 0.95)
+}
+\arguments{
+\item{num}{number of successes}
+
+\item{den}{number of trials}
+
+\item{conf.level}{default 0.95, set the confidence interval to return}
+}
+\value{
+three values forming the upper and lower bounds of the confidence region and the true value
+}
+\description{
+Get a simple Clopper Pearson interval
+}

man/waldInterval.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prop_conf.R
+\name{waldInterval}
+\alias{waldInterval}
+\title{Calculate a Wald interval}
+\usage{
+waldInterval(x, n, conf.level = 0.95)
+}
+\arguments{
+\item{x}{the numerator, number of times the event occurs}
+
+\item{n}{the denominator, the number of trials}
+
+\item{conf.level}{default 0.95, set the confidence interval to return}
+}
+\value{
+two values forming the upper and lower bounds of the confidence region
+}
+\description{
+Calculate a Wald interval
+}
+\examples{
+waldInterval(x = 20, n =40) #this will return 0.345 and 0.655
+}

man/z_univariate.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
+% Please edit documentation in R/prop_conf.R
 \name{z_univariate}
 \alias{z_univariate}
 \title{Calculate a univariate z score by comparing to a population}