Update website (#19)

* Updating website and various minor corrections

DESCRIPTION

@@ -2,22 +2,22 @@ Package: chefStats
 Title: Provide methods for different statistics
 Version: 0.1.1
 Authors@R:
- c(person(given = "MEWP (Matthew Phelps)",
+ c(person(given = "Matthew David Phelps",
  role = "aut",
  email = "mewp@novonordisk.com"),
- person(given = "NOSJ (Nicolai Skov Johnsen)",
+ person(given = "Nicolai Skov Johnsen",
  role = "aut",
  email = "nosj@novonordisk.com"),
- person(given = "HSPU (Henrik Sparre Spiegelhauer)",
+ person(given = "Henrik Sparre Spiegelhauer",
  role = "aut",
  email = "hspu@novonordisk.com"), 
  person(given = "ABIU (Anders Bilgrau)",
  role = "aut",
  email = "abiu@novonordisk.com"),
- person(given = "SCQY (scqy)",
+ person(given = "Simon Clancy",
  role = "aut",
  email = "scqy@novonordisk.com"),
- person(given = "CINO (Christian Haargaard Olsen)",
+ person(given = "Christian Haargaard Olsen",
  role = c("aut", "cre"),
  email = "cino@novonordisk.com"),
  person(given = "Novo Nordisk A/S",
@@ -28,7 +28,8 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-Suggests: 
+Suggests:
+ testr,
  covr,
  pkgdown,
  testthat,
@@ -48,10 +49,12 @@ Imports:
  cli,
  usethis
 Remotes:
- hta-pharma/chef
+ hta-pharma/chef,
+ matthew-phelps/testr
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 Config/testthat/parallel: true
 URL: 
  https://hta-pharma.github.io/chefStats/,
+ https://github.com/hta-pharma/chefStats,
  https://app.codecov.io/github/hta-pharma/chefStats

NAMESPACE

@@ -13,8 +13,8 @@ export(mean_value)
 export(n_event)
 export(n_event_)
 export(n_event_100y)
-export(n_sub_)
 export(n_subj)
+export(n_subj_)
 export(n_subj_event)
 export(n_subj_event_)
 export(obs_time_by_trt)

R/building_blocks.R

@@ -11,7 +11,7 @@
 #' @return An integer
 #' @export
 #' 
-n_sub_ <-
+n_subj_ <-
  function(dat,
  cell_index,
  subjectid_var) {
@@ -72,7 +72,7 @@ p_subj_event_ <-
  cell_index,
  intersect_index,
  subjectid_var) {
- n_sub <- n_sub_(dat, cell_index = cell_index,subjectid_var = subjectid_var)
+ n_sub <- n_subj_(dat, cell_index = cell_index,subjectid_var = subjectid_var)
 
  # If there are no subjects, no need for further calculations
  if (n_sub == 0) {

R/by_strata_by_trt.R

@@ -18,7 +18,7 @@ n_subj <- function(dat,
  subjectid_var,
  ...) {
  stat <-
- n_sub_(dat = dat,
+ n_subj_(dat = dat,
  cell_index = cell_index,
  subjectid_var = subjectid_var)
 
@@ -176,15 +176,14 @@ p_subj_event <-
 #' @param ... Optional parameters.
 #' @return a data.table containing all statistical outputs
 #' @export
-#'
 count_set <- function(dat,
  event_index,
  cell_index,
  subjectid_var,
  ...) {
  intersect_index <- intersect(event_index, cell_index)
  n_subjects <-
- n_sub_(dat = dat,
+ n_subj_(dat = dat,
  cell_index = cell_index,
  subjectid_var = subjectid_var)
  n_events <- n_event_(dat = dat, intersect_index = intersect_index)

R/use_chefStats.R

@@ -18,9 +18,10 @@ use_chefStats <-
  "stat_across_strata_across_trt"
  ),
  file_name = NULL) {
+ check_use_chefStats_inputs(fn_name)
  type <- match.arg(fn_type)
  fn_path <-
- normalizePath(file.path("R", paste0(fn_name, ".R")), mustWork = FALSE)
+ file.path("R", paste0(fn_name, ".R"))
  switch(
  type,
  stat_by_strata_by_trt = usethis::use_template(
@@ -48,3 +49,43 @@ use_chefStats <-
  )
 
  }
+
+error_no_dir <- function(dir){
+ if (!dir.exists(dir)) {
+ stop(paste0("Directory ", dir, " does not exist"))
+ } 
+}
+
+extract_function_names <- function(dir) {
+ x <- list.files(dir, full.names = TRUE, pattern = "*.[Rr]")
+ fn_names_ls <- lapply(x, function(i) {
+ lang_objs <- Filter(is.language, parse(i))
+ fun_entries <-
+ Filter(function(x) {
+ grepl(", function", toString(x))
+ }, lang_objs)
+ sapply(fun_entries, function(fun_entry_i) {
+ trimws(strsplit(toString(fun_entry_i), ",")[[1]][2])
+ })
+ })
+ unlist(fn_names_ls)
+}
+error_function_already_exists <- function(new_fn_name, existing_fn_names){
+ fn_exists <- any(new_fn_name == existing_fn_names)
+ if (!fn_exists) {
+ return(invisible(TRUE))
+ }
+ msg <- paste0(
+ "The function name `",
+ new_fn_name,
+ "` already exists. Please choose another name"
+ )
+ stop(msg,call. = FALSE)
+}
+
+check_use_chefStats_inputs <- function(new_fn_name, dir = "R/"){
+ error_no_dir(dir)
+ existing_fn_names <- extract_function_names(dir)
+ error_function_already_exists(new_fn_name, existing_fn_names)
+ return(invisible(TRUE))
+}

README.Rmd

@@ -3,18 +3,30 @@ output: github_document
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
+# chefStats <a href="https://hta-pharma.github.io/chefStats/"><img src="man/figures/logo.png" align="right" height="138" alt="chefStats website" /></a>
 
-# A library of statistical methods for chef-style AMNOG analyses <a href="https://hta-pharma.github.io/chefStats/"><img src="man/figures/logo.png" align="right" height="138" alt="chefStats website" /></a>
+A library of statistical methods for chef-style AMNOG analyses
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
+# Aim
 
 The {chefStats} package aims to provide a library of fast, validated methods for use in AMNOG analysis created by the chef package.
 
-As the functions found in chefStats are designed to be used with chef, it may be unwieldy to use these functions independently. 
+As the functions found in chefStats are designed to be used with [chef](https://hta-pharma.github.io/chef) in the context of the [ramnog](https://hta-pharma.github.io/ramnog) framework, it may be unwieldy to use these functions independently. 
+
+
+# Installation
+
+The package is available to install from GitHub:
+
+```{r, eval=FALSE}
+remotes::install_github("hta-pharma/chefStats")
+```
+
+
+# How to contribute
 
+For information on how to contribute, please refer to [ramnog contributing documentation](https://hta-pharma.github.io/ramnog/articles/dev_contribute).
 
-# Developer Documentation
+# More information
 
-Please refer to {ramnog} for general [developer documentation](https://hta-pharma.github.io/ramnog/articles/#:~:text=Debugging-,Development,-Git%20Workflow).
+These site focuses on the functions of chefStats. For more context on how these functions should be utilized to produce an AMNOG-like analysis, please see the [ramnog](https://hta-pharma.github.io/ramnog) documentation.

README.md

@@ -1,15 +1,37 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# A library of statistical methods for chef-style AMNOG analyses <a href="https://hta-pharma.github.io/chefStats/"><img src="man/figures/logo.png" align="right" height="138" alt="chefStats website" /></a>
+# chefStats <a href="https://hta-pharma.github.io/chefStats/"><img src="man/figures/logo.png" align="right" height="138" alt="chefStats website" /></a>
+
+A library of statistical methods for chef-style AMNOG analyses
+
+# Aim
 
 The {chefStats} package aims to provide a library of fast, validated
 methods for use in AMNOG analysis created by the chef package.
 
-As the functions found in chefStats are designed to be used with chef,
-it may be unwieldy to use these functions independently.
+As the functions found in chefStats are designed to be used with
+[chef](https://hta-pharma.github.io/chef) in the context of the
+[ramnog](https://hta-pharma.github.io/ramnog) framework, it may be
+unwieldy to use these functions independently.
+
+# Installation
+
+The package is available to install from GitHub:
+
+``` r
+remotes::install_github("hta-pharma/chefStats")
+```
+
+# How to contribute
+
+For information on how to contribute, please refer to [ramnog
+contributing
+documentation](https://hta-pharma.github.io/ramnog/articles/dev_contribute).
 
-# Developer Documentation
+# More information
 
-Please refer to {ramnog} for general [developer
-documentation](https://hta-pharma.github.io/ramnog/articles/#:~:text=Debugging-,Development,-Git%20Workflow).
+These site focuses on the functions of chefStats. For more context on
+how these functions should be utilized to produce an AMNOG-like
+analysis, please see the [ramnog](https://hta-pharma.github.io/ramnog)
+documentation.

_pkgdown.yml

@@ -1,6 +1,13 @@
 url: https://hta-pharma.github.io/chefStats/
 template:
  bootstrap: 5
+ bootswatch: flatly
+
+navbar:
+ structure:
+ left: [intro, articles, reference, news]
+ right: [github]
+
 reference:
 - title: By strata and treatment level
  desc: |
@@ -11,6 +18,7 @@ reference:
  - n_subj_event
  - p_subj_event
  - count_set
+ - count_set
 - title: By strata, across treatment levels
  desc: |
  Function that operate by strata level but across treatment levels
@@ -31,7 +39,7 @@ reference:
  - barnard_test_
  - make_two_by_two_by_k_
  - make_two_by_two_
- - n_sub_
+ - n_subj_
  - n_event_
  - n_subj_event_
  - p_subj_event_

inst/templates/template-stat_by_strata_by_trt.R

@@ -15,11 +15,7 @@
 #' @export
 #'
 #' @examples
-{
- {
- fn_name
- }
-} <- function(dat,
+{{fn_name}} <- function(dat,
  event_index,
  cell_index,
  strata_var,

pkgdown/extra.css

@@ -1,31 +1,8 @@
-.navbar-inverse {
- background-color: #033572;
+.dropdown-header {
+ font-size: 1.2rem;
+ color: #494646;
+ font-weight: 700;
 }
-.navbar-inverse .navbar-brand {
- color: #BDB5AB;
-}
-.navbar-inverse .navbar-nav>li>a {
- color: #BDB5AB;
-}
-.navbar-inverse .navbar-nav>.active>a {
- background-color: #033572;
-}
-.navbar-inverse .navbar-nav>.active:hover>a {
- background-color: #0069B4;
-}
-.list-group-item.active {
- background-color: #033572;
- border-color: #033572;
-}
-item.active, .list-group-item.active:hover {
- background-color: #0069B4;
- border-color: #0069B4;
-}
-
-
-.center {
- display: block;
- margin-left: auto;
- margin-right: auto;
- width: 50%;
+.text-muted {
+ color: #8f9c9d !important;
 }

tests/testthat/test-use_chefStats.R

@@ -0,0 +1,6 @@
+test_that("use_chefStats errors when given function name that already exists", {
+ testr::create_local_project()
+ dump("n_subj", file = "R/test.R")
+ expect_error(use_chefStats(fn_name = "n_subj",fn_type = "stat_by_strata_by_trt"),regexp = "The function name")
+
+})