rename package

Author: nbenn

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: sepsr
+Package: ricu
 Title: Tools for working with publicly available intensive care unit (ICU) datasets
 Description: What the package does (one paragraph).
 Version: 0.0.0.9000

LICENSE.md

@@ -1,7 +1,7 @@
 GNU General Public License
 ==========================
 
-_Version 3, 29 June 2007_  
+_Version 3, 29 June 2007_
 _Copyright © 2007 Free Software Foundation, Inc. &lt;<http://fsf.org/>&gt;_
 
 Everyone is permitted to copy and distribute verbatim copies of this license
@@ -573,7 +573,7 @@ Also add information on how to contact you by electronic and paper mail.
 If the program does terminal interaction, make it output a short notice like this
 when it starts in an interactive mode:
 
-    sepsr Copyright (C) 2019 Drago Plecko; Nicolas Bennett
+    ricu Copyright (C) 2019 Drago Plecko; Nicolas Bennett
     This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type 'show c' for details.

R/data-import.R

@@ -1,7 +1,7 @@
 
 #' Data import utilities
 #'
-#' In order to speed up data access operations, `sepsr` does not directly use
+#' In order to speed up data access operations, `ricu` does not directly use
 #' the PhysioNet provided CSV files, but converts all data to [fst::fst()]
 #' format, which allows for random row and column access. Large tables are
 #' split into chunks in order to keep memory requirements under control.

R/utils.R

@@ -8,14 +8,14 @@
 #'
 #' | **Platform** | **Location**                          |
 #' | ------------ | ------------------------------------- |
-#' | Linux        | `~/.local/share/sepsr`                |
-#' | macOS        | `~/Library/Application Support/sepsr` |
-#' | Windows      | `%LOCALAPPDATA%/sepsr`                |
+#' | Linux        | `~/.local/share/ricu`                |
+#' | macOS        | `~/Library/Application Support/ricu` |
+#' | Windows      | `%LOCALAPPDATA%/ricu`                |
 #'
 #' If the default storage directory does not exists, it will only be created
 #' upon user consent (requiring an interactive session).
 #'
-#' The environment variable `SEPSR_DATA_PATH` can be used to overwrite the
+#' The environment variable `RICU_DATA_PATH` can be used to overwrite the
 #' default location. If desired, this variable can be set in an R startup file
 #' to make it apply to all R sessions. For example, it could be set within:
 #'
@@ -31,7 +31,7 @@
 #' @rdname file_utils
 #'
 #' @examples
-#' Sys.setenv(SEPSR_DATA_PATH = tempdir())
+#' Sys.setenv(RICU_DATA_PATH = tempdir())
 #' identical(data_dir(), tempdir())
 #'
 #' dir.exists(file.path(tempdir(), "some_subdir"))
@@ -61,7 +61,7 @@ default_data_path <- function() {
     Sys.getenv("XDG_DATA_HOME", "~/.local/share")
   )
 
-  root <- file.path(root, "sepsr")
+  root <- file.path(root, "ricu")
 
   if (!dir.exists(root)) {
     message("Attempting to set up data directory at\n  ", root,
@@ -103,7 +103,7 @@ ensure_dir <- function(paths) {
 
 data_dir_path <- function() {
 
-  env_var <- Sys.getenv("SEPSR_DATA_PATH", unset = NA_character_)
+  env_var <- Sys.getenv("RICU_DATA_PATH", unset = NA_character_)
 
   if (is.na(env_var)) default_data_path()
   else                ensure_dir(env_var)
@@ -115,14 +115,14 @@ default_config_path <- function() {
 
 config_dir_path <- function() {
 
-  env_var <- Sys.getenv("SEPSR_CONFIG_PATH", unset = NA_character_)
+  env_var <- Sys.getenv("RICU_CONFIG_PATH", unset = NA_character_)
 
   if (is.na(env_var)) default_config_path()
   else                ensure_dir(env_var)
 }
 
 #' For configuration files, the default location is `extdata/config` and the
-#' environment variable `SEPSR_CONFIG_PATH` can be used to overwrite the
+#' environment variable `RICU_CONFIG_PATH` can be used to overwrite the
 #' default location. Files are first searched for in the user-specified
 #' directory and if not found there, the default dir ist taken into account.
 #' Additionally, `get_config()` has a `dir` argument which takes highest
@@ -139,7 +139,7 @@ config_dir_path <- function() {
 #' identical(
 #'   cfg,
 #'   get_config("eicu-demo",
-#'              system.file("extdata", "config", package = "sepsr"))
+#'              system.file("extdata", "config", package = "ricu"))
 #' )
 #'
 #' @export

inst/testdata/data-download.R

@@ -6,7 +6,7 @@ trace(
   exit = function() { output <<- returnValue() }
 )
 
-sepsr:::download_pysionet_file(
+ricu:::download_pysionet_file(
   "https://physionet.org/files/mimiciii-demo/1.4/SHA256SUMS.txt"
 )
 
@@ -23,13 +23,13 @@ close(con)
 
 saveRDS(output, "SHA256SUMS.txt.rds")
 
-sepsr:::download_pysionet_file(
+ricu:::download_pysionet_file(
   "https://physionet.org/files/mimiciii-demo/1.4/patients.csv"
 )
 
 saveRDS(output, "patients.csv.rds")
 
-sepsr:::download_pysionet_file(
+ricu:::download_pysionet_file(
   "https://physionet.org/files/mimiciii-demo/1.4/services.csv"
 )
 

man/data_import.Rd

@@ -1,15 +1,15 @@
 library(testthat)
-library(sepsr)
+library(ricu)
 
 if (requireNamespace("xml2")) {
   test_check(
-    "sepsr",
+    "ricu",
     reporter = MultiReporter$new(
       reporters = list(JunitReporter$new(file = "test-results.xml"),
                        CheckReporter$new()
       )
     )
   )
 } else {
-  test_check("sepsr")
+  test_check("ricu")
 }

man/file_utils.Rd

@@ -23,15 +23,15 @@ test_that("credential management", {
 
   creds <- with_mock(
     `keyring::key_set_with_value` = function(...) invisible(NULL),
-    `sepsr:::read_line` = function(...) "bar",
+    `ricu:::read_line` = function(...) "bar",
     get_set_physionet_creds("foo")
   )
 
   expect_identical(creds, list(username = "foo", password = "bar"))
 
   creds <- with_mock(
-    `sepsr:::is_pkg_available` = function(...) FALSE,
-    `sepsr:::read_line` = function(x, ...) {
+    `ricu:::is_pkg_available` = function(...) FALSE,
+    `ricu:::read_line` = function(x, ...) {
       if (grepl("user", x)) "foo" else if (grepl("pass", x)) "bar" else "baz"
     },
     get_set_physionet_creds()
@@ -41,7 +41,7 @@ test_that("credential management", {
 
   expect_error(
     with_mock(
-      `sepsr:::is_pkg_available` = function(...) FALSE,
+      `ricu:::is_pkg_available` = function(...) FALSE,
       get_set_physionet_creds()
     )
   )
@@ -50,7 +50,7 @@ test_that("credential management", {
 curl_mock_fm <- function(url, handle) {
 
   file <- system.file("testdata", paste0(basename(url), ".rds"),
-                      package = "sepsr")
+                      package = "ricu")
 
   if (identical(file, "")) stop("file ", basename(url), "not found")
 

tests/testthat.R

@@ -1,5 +1,5 @@
 
-pa <- sepsr:::eicu_sofa_pa(data_env = "eicu_demo")
+pa <- eicu_sofa_pa(data_env = "eicu_demo")
 
 test_that("fetch sofa pa", {
   expect_is(pa, "data.table")