Added whichSetOfN() and some cleaning and updating.

.Rbuildignore

@@ -16,3 +16,4 @@
 ^CODE_OF_CONDUCT.md$
 ^CONTRIBUTING.md$
 ^docs$
+^doc$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CECPfuns
 Type: Package
 Title: Package of Utility Functions for Psychological Therapies, Mental Health and Well-being Work (Created by Chris Evans and Clara Paz)
-Version: 0.0.0.9041
+Version: 0.0.0.9042
 Maintainer: Chris Evans <chris@psyctc.org>
 Description: This should evolve into a repository of all the functions that I (CE)
   and Clara Paz (CP) have created (so far only CE!) and tested enough to
@@ -26,8 +26,8 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: no
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
-RdMacros: mathjaxr 
+RoxygenNote: 7.3.2
+RdMacros: mathjaxr
 Imports:
     mathjaxr,
     ggplot2,

NAMESPACE

@@ -32,6 +32,7 @@ export(plotBinconf)
 export(plotCIPearson)
 export(plotCIProportion)
 export(plotQuantileCIsfromDat)
+export(whichSetOfN)
 importFrom(clipr,clipr_available)
 importFrom(clipr,read_clip)
 importFrom(clipr,write_clip)
@@ -73,6 +74,7 @@ importFrom(ggplot2,theme_update)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
 importFrom(magrittr,"%>%")
+importFrom(mathjaxr,preview_rd)
 importFrom(methods,is)
 importFrom(readr,read_csv)
 importFrom(rlang,":=")

R/correctAttenuation.R

@@ -0,0 +1,28 @@
+#' Function to check if something is a vector, ignoring attributes
+#'
+#' @param x object to test
+#' @noRd
+#' @return logical: TRUE if x is a vector even if it has attributes
+#'
+#' @importFrom methods is
+#'
+#' @examples
+#' \dontrun{
+#' tmpLetters <- letters
+#' is.vector(tmpLetters)
+#' comment(tmpLetters) <- "Attached comment"
+#' is.vector(tmpLetters) # FALSE because tmpLetters is no longer a simple vector
+#' checkIsVector(tmpLetters) # TRUE
+#' }
+#'
+#' @author Chris Evans
+#' @section History/development log:
+#' Started 12.iv.21
+#'
+checkIsVector <- function(x) {
+  ### alternative to base::is.vector() where you aren't worried about a vector having additional attributes
+  ### if it does base::is.vector() will return FALSE
+  methods::is(x, "vector") && !is.list(x)
+  ### this will return FALSE if x is a list, you may occasionally want to treat a list of length 1 as a vector
+  ### use checkIsOneDim() for that
+}

R/getCIPearson.R

@@ -33,7 +33,7 @@
 #' observed correlation really was perfect there is no way given the data to compute a
 #' sensible lower bound (for observed R = 1.0, upper bound for observed R = -1).  Returning
 #' c(1, 1) for perfect positive correlation and c(-1, -1) for perfect negative correlation
-#' is the only sensible option and is in line with cor.test{stats}.
+#' is the only sensible option and is in line with stats::cor.test().
 
 #' @examples
 #' \dontrun{

R/getCSC.R

@@ -27,6 +27,7 @@
 #' method c is this.
 #'
 #' \loadmathjax{}
+#'
 #' \mjdeqn{\frac{SD_{HS}*M_{notHS} + SD_{notHS}*M_{HS}}{SD_{HS}+SD_{notHS}}}{}
 #'
 #' (with SD for Standard Deviation (doh!) and M for Mean)
@@ -36,6 +37,7 @@
 #'
 #' @export
 #'
+#' @importFrom mathjaxr preview_rd
 #' @importFrom stats qnorm
 #' @importFrom tibble as_tibble
 #' @importFrom magrittr %>%

R/whichSetofN.R

@@ -0,0 +1,60 @@
+#' Function that takes an index number and gives which sequential set of N it is in
+#' @description
+#' Finds the sequential number of sets of data when reading fixed size multirow blocks of rows.
+#' @param x object to test
+#' @param n size of set
+#'
+#' @return integer: the number of the set, 1,2,3 ...
+#'
+#' @family utility functions
+#'
+#' @section Background:
+#' I am quite often importing data with a multirow nested structure so I may have data from participants
+#' with different ID values and with different occasions per participant and then some fixed number of
+#' rows of data per person per occasion. For one set of data I might have say four rows of medication
+#' data per participant per occasion per actual medication prescribed.  I use whichSetOfN(row_number(), 4)
+#' to tell me the sequential number of the prescription this row (found by row_number() inside a group_by()).
+#'
+#' @export
+#'
+#' @examples
+#' whichSetOfN(1:7, 3)
+#' ### shows that 1:3 belong to set 1, 4:6 to set 2 and 7 to set 3
+#'
+#'
+#' @author Chris Evans
+#' @section History/development log:
+#' Started 12.x.24
+#'
+whichSetOfN <- function(x, n){
+  ### sanity checking
+  if (x[1] <= 0) {
+    stop("Index number, x, must be 1 or higher")
+  }
+  if (abs(x[1] - round(x[1])) > .05) {
+    warning(paste0("The x value you input: ",
+                   x[1],
+                   " is not an integer, is this really what you want?"))
+  }
+  if (n <= 2) {
+    stop("Set size must be 2 or higher")
+  }
+  if (abs(n - round(n)) > .0000005) {
+    stop(paste0("The n value you input: ",
+                   x,
+                   " is not an integer. I don't believe you meant that, the set size must be an integer."))
+  }
+
+  ### OK do the work
+  if (x == 1){
+    return(1)
+  }
+  tmpX <- 1 + (x %/% n)
+  if (x[1] %% n == 0) {
+    return(tmpX - 1)
+  } else {
+    return(tmpX)
+  }
+}
+
+whichSetOfN <- Vectorize(whichSetOfN, vectorize.args = "x")

tests/testthat/whichSetOfN.R

@@ -0,0 +1,22 @@
+testthat::test_that("sanity checks work", {
+  testthat::expect_error(whichSetOfN(0, 3))
+  testthat::expect_error(whichSetOfN(-1:3, 3))
+    testthat::expect_error(whichSetOfN(3, -3))
+  testthat::expect_error(whichSetOfN(3, 0))
+  testthat::expect_error(whichSetOfN(3, 1))
+  testthat::expect_error(whichSetOfN(3, 2.1))
+})
+
+## test warnings
+testthat::test_that("sanity checks work", {
+  testthat::expect_warning(whichSetOfN(.5, 10))
+  testthat::expect_warning(whichSetOfN(0.2, 3))
+})
+
+### test of outputs
+testthat::test_that("Output correct", {
+  set.seed(12345)
+  testthat::expect_equal(whichSetOfN(1:30, 9),
+                         c(1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3,
+                           3, 3, 3, 3, 3, 3, 3, 4, 4, 4))
+})