rm empty first lines

nbenn · nbenn · commit 88c61e9366dc · 2023-09-04T11:31:35.000+02:00
diff --git a/R/assertions.R b/R/assertions.R
@@ -1,4 +1,3 @@
-
 #' @importFrom assertthat see_if on_failure<- validate_that
 #' @importFrom assertthat is.string is.flag is.dir is.count is.scalar
 #' @importFrom assertthat has_name has_attr are_equal is.number
diff --git a/R/callback-cncpt.R b/R/callback-cncpt.R
@@ -1,4 +1,3 @@
-
 collect_dots <- function(concepts, interval, ..., merge_dat = FALSE) {
 
   assert_that(is.character(concepts))
diff --git a/R/callback-itm.R b/R/callback-itm.R
@@ -1,4 +1,3 @@
-
 vent_flag <- function(x, val_var, ...) {
   x <- x[as.logical(get(val_var)), ]
   set(x, j = c(index_var(x), val_var),
diff --git a/R/callback-scores.R b/R/callback-scores.R
@@ -1,4 +1,3 @@
-
 #' SIRS score label
 #'
 #' The SIRS (Systemic Inflammatory Response Syndrome) score is a commonly used
diff --git a/R/callback-sep3.R b/R/callback-sep3.R
@@ -1,4 +1,3 @@
-
 #' Sepsis 3 label
 #'
 #' The sepsis 3 label consists of a suspected infection combined with an acute
diff --git a/R/callback-sofa.R b/R/callback-sofa.R
@@ -1,4 +1,3 @@
-
 #' SOFA score label
 #'
 #' The SOFA (Sequential Organ Failure Assessment) score is a commonly used
diff --git a/R/concept-load.R b/R/concept-load.R
@@ -1,4 +1,3 @@
-
 #' Load concept data
 #'
 #' Concept objects are used in `ricu` as a way to specify how a clinical
diff --git a/R/concept-utils.R b/R/concept-utils.R
@@ -1,4 +1,3 @@
-
 #' Data items
 #'
 #' Item objects are used in `ricu` as a way to specify how individual data
diff --git a/R/config-class.R b/R/config-class.R
@@ -1,4 +1,3 @@
-
 #' Internal utilities for working with data source configurations
 #'
 #' Data source configuration objects store information on data sources used
diff --git a/R/config-utils.R b/R/config-utils.R
@@ -1,4 +1,3 @@
-
 #' @param x Object to coerce/query
 #'
 #' @rdname src_cfg
diff --git a/R/data-env.R b/R/data-env.R
@@ -1,4 +1,3 @@
-
 #' ICU datasets
 #'
 #' The [Laboratory for Computational Physiology
diff --git a/R/data-load.R b/R/data-load.R
@@ -1,4 +1,3 @@
-
 #' Low level functions for loading data
 #'
 #' Data loading involves a cascade of S3 generic functions, which can
diff --git a/R/data-utils.R b/R/data-utils.R
@@ -1,4 +1,3 @@
-
 #' Data loading utilities
 #'
 #' Two important tools for smoothing out differences among used datasets are
diff --git a/R/ricu.R b/R/ricu.R
@@ -1,4 +1,3 @@
-
 #' @keywords internal
 #' @importFrom data.table setattr setcolorder set setnames setorderv
 #' @importFrom data.table setDT setDF fifelse rbindlist data.table
diff --git a/R/setup-attach.R b/R/setup-attach.R
@@ -1,4 +1,3 @@
-
 #' Data attach utilities
 #'
 #' Making a dataset available to `ricu` consists of 3 steps: downloading
diff --git a/R/setup-download.R b/R/setup-download.R
@@ -1,4 +1,3 @@
-
 #' Data download utilities
 #'
 #' Making a dataset available to `ricu` consists of 3 steps: downloading
diff --git a/R/setup-import.R b/R/setup-import.R
@@ -1,4 +1,3 @@
-
 #' Data import utilities
 #'
 #' Making a dataset available to `ricu` consists of 3 steps: downloading
diff --git a/R/tbl-base.R b/R/tbl-base.R
@@ -1,4 +1,3 @@
-
 #' @export
 `[.id_tbl` <- function(x, ...) wrap_ptype(as_ptype(x), NextMethod())
 
diff --git a/R/tbl-class.R b/R/tbl-class.R
@@ -1,4 +1,3 @@
-
 #' Tabular ICU data classes
 #'
 #' In order to simplify handling or tabular ICU data, `ricu` provides
diff --git a/R/tbl-utils.R b/R/tbl-utils.R
@@ -1,4 +1,3 @@
-
 #' ICU class meta data utilities
 #'
 #' The two data classes `id_tbl` and `ts_tbl`, used by `ricu` to represent ICU
diff --git a/R/utils-cli.R b/R/utils-cli.R
@@ -1,4 +1,3 @@
-
 is_interactive <- function() {
   !isTRUE(getOption('knitr.in.progress')) && interactive()
 }
diff --git a/R/utils-export.R b/R/utils-export.R
@@ -1,4 +1,3 @@
-
 #' Read and write utilities
 #'
 #' Support for reading from and writing to pipe separated values (`.psv`)
diff --git a/R/utils-file.R b/R/utils-file.R
@@ -1,4 +1,3 @@
-
 #' File system utilities
 #'
 #' Determine the location where to place data meant to persist between
diff --git a/R/utils-misc.R b/R/utils-misc.R
@@ -1,4 +1,3 @@
-
 agg_or_na <- function(agg_fun) {
   function(x) {
     if (all(is.na(x))) return(x[1L])
diff --git a/R/utils-ts.R b/R/utils-ts.R
@@ -1,4 +1,3 @@
-
 #' Time series utility functions
 #'
 #' ICU data as handled by `ricu` is mostly comprised of time series data and as
diff --git a/R/zzz.R b/R/zzz.R
@@ -1,4 +1,3 @@
-
 .onLoad <- function(libname, pkgname) { # nocov start
 
   fix_base_fun <- function(fun, fix) {
diff --git a/README.md b/README.md
@@ -1,4 +1,3 @@
-
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # [ricu](https://eth-mds.github.io/ricu/)
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,4 +1,3 @@
-
 title: ICU data with R
 
 url: https://eth-mds.github.io/ricu
diff --git a/man/change_id.Rd b/man/change_id.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,4 +1,3 @@
-
 library(testthat)
 library(ricu)
 
diff --git a/tests/testthat/helpers.R b/tests/testthat/helpers.R
@@ -1,4 +1,3 @@
-
 expect_all_identical <- function(object, expected = object[[1L]], ...,
                                  info = NULL, label = NULL,
                                  expected_label = NULL) {
diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R
@@ -1,4 +1,3 @@
-
 test_that("assertions", {
 
   expect_true(is_dt(data.table::data.table(a = 1, b = 2)))
diff --git a/tests/testthat/test-callback.R b/tests/testthat/test-callback.R
@@ -1,4 +1,3 @@
-
 test_that("aumc callbacks", {
 
   skip_if_not_installed("mockthat")
diff --git a/tests/testthat/test-concept.R b/tests/testthat/test-concept.R
@@ -1,4 +1,3 @@
-
 test_that("load hirid items", {
 
   skip_if_not_installed("mockthat")
diff --git a/tests/testthat/test-config.R b/tests/testthat/test-config.R
@@ -1,4 +1,3 @@
-
 skip_if_srcs_missing(c("mimic_demo", "eicu_demo"))
 
 test_that("config classes", {
diff --git a/tests/testthat/test-data-env.R b/tests/testthat/test-data-env.R
@@ -1,4 +1,3 @@
-
 skip_if_srcs_missing(c("mimic_demo", "eicu_demo"))
 
 test_that("demo envs", {
diff --git a/tests/testthat/test-data-tbl.R b/tests/testthat/test-data-tbl.R
@@ -1,4 +1,3 @@
-
 skip_if_srcs_missing(c("mimic_demo", "eicu_demo"))
 
 test_that("load_src()", {
diff --git a/tests/testthat/test-data-utils.R b/tests/testthat/test-data-utils.R
@@ -1,4 +1,3 @@
-
 skip_if_srcs_missing(c("mimic_demo", "eicu_demo"))
 
 test_that("stay windows", {
diff --git a/tests/testthat/test-helpers.R b/tests/testthat/test-helpers.R
@@ -1,4 +1,3 @@
-
 test_that("expect_all_identical", {
 
   expect_success(expect_all_identical("foo", "foo"))
diff --git a/tests/testthat/test-scores.R b/tests/testthat/test-scores.R
@@ -1,4 +1,3 @@
-
 skip_if_srcs_missing(c("mimic_demo", "eicu_demo"))
 
 so_mi <- load_concepts("sofa", "mimic_demo", verbose = FALSE)
diff --git a/tests/testthat/test-setup-attach.R b/tests/testthat/test-setup-attach.R
@@ -1,4 +1,3 @@
-
 test_that("auto attach env var", {
 
   srcs <- c("mimic_demo", "eicu_demo")
diff --git a/tests/testthat/test-setup-download.R b/tests/testthat/test-setup-download.R
@@ -1,4 +1,3 @@
-
 mock_fetch_memory <- function(url, handle, ...) {
 
   file <- system.file("testdata", paste0(basename(url), ".rds"),
diff --git a/tests/testthat/test-setup-import.R b/tests/testthat/test-setup-import.R
@@ -1,4 +1,3 @@
-
 skip_on_cran()
 
 tmp_cars <- withr::local_tempdir()
diff --git a/tests/testthat/test-tbl-base.R b/tests/testthat/test-tbl-base.R
@@ -1,4 +1,3 @@
-
 test_that("icu_tbl subsetting", {
 
   col <- runif(10)
diff --git a/tests/testthat/test-tbl-class.R b/tests/testthat/test-tbl-class.R
@@ -1,4 +1,3 @@
-
 test_that("id_tbl constructors", {
 
   tbl <- id_tbl(a = 1:10, b = rnorm(10))
diff --git a/tests/testthat/test-tbl-utils.R b/tests/testthat/test-tbl-utils.R
@@ -1,4 +1,3 @@
-
 test_that("rename_cols for id_tbl", {
 
   tbl <- id_tbl(a = 1:10, b = rnorm(10), c = rnorm(10))
diff --git a/tests/testthat/test-utils-cli.R b/tests/testthat/test-utils-cli.R
@@ -1,4 +1,3 @@
-
 test_that("cli progress", {
 
   skip_if_not_installed("mockthat")
diff --git a/tests/testthat/test-utils-export.R b/tests/testthat/test-utils-export.R
@@ -1,4 +1,3 @@
-
 skip_on_cran()
 
 test_that("psv export", {
diff --git a/tests/testthat/test-utils-file.R b/tests/testthat/test-utils-file.R
@@ -1,4 +1,3 @@
-
 test_that("data dir", {
 
   dir <- withr::with_envvar(
diff --git a/tests/testthat/test-utils-ts.R b/tests/testthat/test-utils-ts.R
@@ -1,4 +1,3 @@
-
 test_that("collapse/expand", {
 
   tbl <- ts_tbl(x = 1:5, y = hours(1:5), z = hours(2:6), val = rnorm(5),
diff --git a/vignettes/ricu.bib b/vignettes/ricu.bib
@@ -1,4 +1,3 @@
-
 @article{johnson2016,
   title = {MIMIC-III, A Freely Accessible Critical Care Database},
   author = {Johnson, Alistair EW and Pollard, Tom J and Shen, Lu and Li-wei, H Lehman and Feng, Mengling and Ghassemi, Mohammad and Moody, Benjamin and Szolovits, Peter and Celi, Leo Anthony and Mark, Roger G},

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`#' @importFrom assertthat see_if on_failure<- validate_that`
`3`	`2`	`#' @importFrom assertthat is.string is.flag is.dir is.count is.scalar`
`4`	`3`	`#' @importFrom assertthat has_name has_attr are_equal is.number`
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`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`collect_dots <- function(concepts, interval, ..., merge_dat = FALSE) {`
`3`	`2`
`4`	`3`	`assert_that(is.character(concepts))`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`vent_flag <- function(x, val_var, ...) {`
`3`	`2`	`x <- x[as.logical(get(val_var)), ]`
`4`	`3`	`set(x, j = c(index_var(x), val_var),`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`#' SIRS score label`
`3`	`2`	`#'`
`4`	`3`	`#' The SIRS (Systemic Inflammatory Response Syndrome) score is a commonly used`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`#' Sepsis 3 label`
`3`	`2`	`#'`
`4`	`3`	`#' The sepsis 3 label consists of a suspected infection combined with an acute`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`#' SOFA score label`
`3`	`2`	`#'`
`4`	`3`	`#' The SOFA (Sequential Organ Failure Assessment) score is a commonly used`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`#' Load concept data`
`3`	`2`	`#'`
`4`	`3`	#' Concept objects are used in `ricu` as a way to specify how a clinical
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`#' Data items`
`3`	`2`	`#'`
`4`	`3`	#' Item objects are used in `ricu` as a way to specify how individual data
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`#' Internal utilities for working with data source configurations`
`3`	`2`	`#'`
`4`	`3`	`#' Data source configuration objects store information on data sources used`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`#' @param x Object to coerce/query`
`3`	`2`	`#'`
`4`	`3`	`#' @rdname src_cfg`