Improve check

Author: c-marc

.Rbuildignore

@@ -1,2 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^dev_history\.R$
+^README\.Rmd$

DESCRIPTION

@@ -8,8 +8,7 @@ Authors@R:
            email = "[email protected]",
            comment = c(ORCID = "YOUR-ORCID-ID"))
 Description: What the package does (one paragraph).
-License: `use_mit_license()`, `use_gpl3_license()` or friends to
-    pick a license
+License: file LICENCE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
@@ -20,3 +19,12 @@ Suggests:
 VignetteBuilder: knitr
 URL: https://github.com/c-marc/predictr
 BugReports: https://github.com/c-marc/predictr/issues
+Imports: 
+    ggplot2,
+    dplyr,
+    magrittr,
+    zeallot,
+    tidyr,
+    tibble,
+    bslib,
+    scales

R/estimate.R

@@ -4,6 +4,10 @@
 #' @param TPF True Positive Fraction
 #'
 #' @return a list with positive and negative likelihood ratios
+#' @export
+#' 
+#' @examples
+#' getLRatios(.4, .6)
 getLRatios <- function(FPF, TPF){
   list(
     negative = (1-TPF) / (1-FPF),
@@ -17,6 +21,11 @@ getLRatios <- function(FPF, TPF){
 #' @param TPF True Positive Fraction
 #'
 #' @return a value
+#' @export
+#' @importFrom stats qlogis plogis
+#' 
+#' @examples
+#' getOR(.4, .6)
 getOR <- function(FPF, TPF){
   logOR <- qlogis(TPF) - qlogis(FPF)
   exp(logOR)
@@ -28,10 +37,12 @@ getOR <- function(FPF, TPF){
 #' @param TPF True Positive Fraction
 #'
 #' @return a tibble with of FPF and TPF values
+#' @export
+#' @importFrom stats qlogis plogis
 getIsoOR <- function(FPF, TPF) {
   OR <- getOR(FPF, TPF)
   x <- seq(0, 1, length.out = 101)
-  tibble(FPF = x) %>%
+  tibble::tibble(FPF = x) %>%
     mutate(TPF = ifelse(FPF %in% c(0, 1),
       FPF,
       plogis(qlogis(x) + log(OR))
@@ -44,26 +55,41 @@ getIsoOR <- function(FPF, TPF) {
 #' @param TPF True Positive Fraction
 #'
 #' @return a tibble with intercept and slope for each LR
+#' @export
 getIsoLR <- function(FPF, TPF){
   lRatios <- getLRatios(FPF, TPF)
-  tribble(
+  tibble::tribble(
     ~type, ~intercept, ~slope,
     "positive", 0, lRatios$positive,
     "negative", 1 - lRatios$negative, lRatios$negative
   )
 }
 
 
+#' Get predictive values
+#'
+#' @param FPF False Positive Fraction
+#' @param TPF True Positive Fraction
+#' @param prior a vector of prior probabilities. If NULL, will compute over (0,1)
+#'
+#' @return a tibble with:
+#' - prior
+#' - type: "negative" or "positive" 
+#' - posterior: posterior probabilities
+#' @export
+#' @importFrom dplyr inner_join mutate
+#' @examples
+#' getPredValues(.4, .6, .5)
 getPredValues <- function(FPF, TPF, prior = NULL) {
   # get LR as a list and transform in a tidy format
   lRatios <- getLRatios(FPF, TPF) %>%
-    as_tibble() %>%
-    pivot_longer(c(positive, negative), names_to = "type")
+    tibble::as_tibble() %>%
+    tidyr::pivot_longer(c(positive, negative), names_to = "type")
 
   # if prior unspecified, compute over ]0-1[
   if (is.null(prior)) prior <- seq(0, 1, length.out = 101)
 
-  dat <- expand_grid(
+  dat <- tidyr::expand_grid(
     prior = prior,
     type = c("positive", "negative")
   )
@@ -76,10 +102,30 @@ getPredValues <- function(FPF, TPF, prior = NULL) {
 }
 
 
+#' Prettify proportions
+#'
+#' @param prop A proportion
+#' @param digits passed to round()
+#'
+#' @return A pretty string
+#' @export
+#'
+#' @examples
+#' prettyProp(.501)
 prettyProp <- function(prop, digits = 0){
   paste0(round(100*prop, digits), "%")
 }
 
+#' Prettify ratios
+#'
+#' @param ratio A ratio
+#' @param digits passed to signif() 
+#'
+#' @return A pretty string
+#' @export
+#'
+#' @examples
+#' prettyRatio(1/2.41)
 prettyRatio <- function(ratio, digits = 2){
   if(ratio >= 1){
     paste0(signif(ratio, digits), " : 1")

vignettes/draft.Rmd

@@ -15,17 +15,19 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup}
-library(tidyverse)
 library(predictr)
+library(dplyr)
+library(ggplot2)
 ```
 
 # estimate.R
 
 ```{r}
 FPF <- .2
 TPF <- .85
-getLRatio(TPF, FPF)
+getLRatios(FPF, TPF)
 ```
+
 ```{r}
 ggplot()+
   geom_point(aes(x = FPF, y = TPF)) +
@@ -35,8 +37,9 @@ ggplot()+
   coord_cartesian(xlim = c(0,1), ylim = c(0,1), expand = F) + 
   theme_bw()
 ```
+
 ```{r}
-getPValues(TPF, FPF) %>%
+getPredValues(FPF, TPF) %>%
   ggplot(aes(x = prior, y = posterior, group = type)) +
   geom_line() +
   theme_bw()