Merge pull request #28 from lshtm-gigs/dev

gigs 0.4.1

.github/workflows/update-citation-cff.yaml

@@ -0,0 +1,55 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# The action runs when:
+# - A new release is published
+# - The DESCRIPTION or inst/CITATION are modified
+# - Can be run manually
+# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+  release:
+    types: [published]
+  push:
+    branches: [master, main]
+    paths:
+      - DESCRIPTION
+      - inst/CITATION
+  workflow_dispatch:
+
+name: Update CITATION.cff
+
+jobs:
+  update-citation-cff:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::cffr
+            any::V8
+
+      - name: Update CITATION.cff
+        run: |
+
+          library(cffr)
+
+          # Customize with your own code
+          # See https://docs.ropensci.org/cffr/articles/cffr.html
+
+          # Create your CITATION.cff file
+          cff_write()
+
+        shell: Rscript {0}
+
+      - name: Commit results
+        run: |
+          git config --local user.name "github-actions[bot]"
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add CITATION.cff
+          git commit -m 'Update CITATION.cff' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
+
+
+

CITATION.cff

@@ -7,8 +7,8 @@ cff-version: 1.2.0
 message: 'To cite package "gigs" in publications use:'
 type: software
 license: GPL-3.0-or-later
-title: 'gigs: Assess Fetal, Newborn, and Child Growth'
-version: 0.4.0
+title: 'gigs: Assess Fetal, Newborn, and Child Growth with International Standards'
+version: 0.4.1
 abstract: Convert between anthropometric measures and z-scores/centiles in multiple
   growth standards, and classify fetal, newborn, and child growth accordingly. With
   a simple interface to growth standards from the World Health Organisation and International
@@ -21,14 +21,14 @@ authors:
   orcid: https://orcid.org/0009-0003-8214-4496
 preferred-citation:
   type: manual
-  title: 'gigs: Assess Growth in Infants and Newborns'
+  title: 'gigs: Assess Fetal, Newborn, and Child Growth with International Standards'
   authors:
   - family-names: Parker
     given-names: Simon
     email: [email protected]
     orcid: https://orcid.org/0009-0003-8214-4496
   year: '2023'
-  notes: 0.4.0
+  notes: 0.4.1
   url: https://github.com/lshtm-gigs/gigs/
 repository-code: https://github.com/lshtm-gigs/gigs
 url: https://github.com/lshtm-gigs/gigs/

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: gigs
-Title: Assess Fetal, Newborn, and Child Growth
-Version: 0.4.0
+Title: Assess Fetal, Newborn, and Child Growth with International Standards
+Version: 0.4.1
 Authors@R: c(
     person(given = "Simon", family = "Parker",
            email = "[email protected]",

NEWS.md

@@ -1,3 +1,8 @@
+# gigs 0.4.1
+
+* Changes to documentation to facilitate `autotest::autotest_package()` pass.
+* Minor changes to vignettes for new patched version.
+
 # gigs 0.4.0
 
 * **BREAKING CHANGES:**

R/classification.R

@@ -16,28 +16,27 @@
 #'   behaviour can be customised using the functions in [gigs_options].
 #' @param severe A single logical value specifying whether to categorise SGA
 #'   values are below the third centile as `"SGA(<3)"`. Default = `FALSE`.
-#' @return Factor the same length as the longest input vector, with
-#'   size-for-gestational age classification(s). If `severe = FALSE`, levels are
-#'   `c("SGA", "AGA",  "LGA")`. If `severe = TRUE`, levels are `c("SGA(<3)",
-#'   "SGA", "AGA",  "LGA")`.
+#' @returns An object of class factor with the same length as the longest input
+#'   vector, containing size-for-GA classifications. If `severe = FALSE`, levels
+#'   are `c("SGA", "AGA", "LGA")`. If `severe = TRUE`, levels are `c("SGA(<3)",
+#'   "SGA", "AGA", "LGA")`.
 #' @note Input vectors are recycled by [vctrs::vec_recycle_common()], and must
 #'   adhere to the [vctrs] recycling rules.
 #' @seealso [ig_nbs_wfga_value2centile()], which this function calls to get
 #'   centiles for each observation.
 #' @examples
-#' # Without severe flag, does not differentiate between
-#' # p < 0.03 and p < 0.10
+#' # By default, does not differentiate between p < 0.03 and p < 0.10
 #' classify_sfga(
-#'   weight_kg = c(2.2, 3.4, 4.2),
-#'   gest_days = 267,
-#'   sex = "M"
+#'   weight_kg = c(2.2, 3.3, 4.2),
+#'   gest_days = 267:269,
+#'   sex = c("M", "F", "M")
 #' )
 #'
 #' # With severe = TRUE, highlights p < 0.03
 #' classify_sfga(
-#'   weight_kg = c(2.2, 3.4, 4.2),
-#'   gest_days = 267,
-#'   sex = "M",
+#'   weight_kg = c(2.2, 3.3, 4.2),
+#'   gest_days = 267:269,
+#'   sex = c("M", "F", "M"),
 #'   severe = TRUE
 #' )
 #' @references
@@ -77,8 +76,9 @@ classify_sfga <- function(weight_kg, gest_days, sex, severe = FALSE) {
 #' newborns according to their SVN type, for use in downstream analyses.
 #'
 #' @inherit classify_sfga params note
-#' @return Factor with small vulnerable newborn classification(s), with levels
-#'   `c("Preterm SGA", "Preterm AGA", "Preterm LGA", "Term SGA", "Term AGA",
+#' @returns An object of class factor with the same length as the longest input
+#'   vector, containing small vulnerable newborn classifications. Its levels
+#'   are `c("Preterm SGA", "Preterm AGA", "Preterm LGA", "Term SGA", "Term AGA",
 #'   "Term LGA")`.
 #' @examples
 #' classify_svn(
@@ -132,10 +132,11 @@ classify_svn <- function(weight_kg, gest_days, sex) {
 #' @param gest_days Numeric vector with gestational age(s) at birth in days.
 #' @param outliers A single `TRUE` or `FALSE` value specifying whether
 #'   implausible z-score value thresholds should be applied. Default = `FALSE`.
-#' @return Factor of stunting classification(s) with same length as longest
-#'   input vector. Levels are `c("stunting_severe", "stunting", "not_stunting")`
-#'   if `outliers = FALSE`, else `c("stunting_severe", "stunting",
-#'   "not_stunting", "outlier")`.
+#' @returns An object of class factor with the same length as the longest input
+#'   vector, containing stunting classifications. Its levels are
+#'   `c("stunting_severe", "stunting", "not_stunting")` if `outliers = FALSE`
+#'   (the default), else `c("stunting_severe", "stunting", "not_stunting",
+#'   "outlier")`.
 #' @note Input vectors are recycled by [vctrs::vec_recycle_common()], and must
 #'   adhere to the [vctrs] recycling rules. This function assumes that your
 #'   measurements were taken according to the WHO guidelines, which stipulate
@@ -200,10 +201,11 @@ classify_stunting <- function(lenht_cm, age_days, gest_days, sex,
 #'
 #' @inheritParams classify_sfga
 #' @inheritParams classify_stunting
-#' @return Factor of wasting classifications with same length as longest input.
-#'   If `outliers = FALSE`, levels are `c("wasting_severe", "wasting",
-#'   "not_wasting", "overweight")`. If `outliers = TRUE`, levels are
-#'   `c("wasting_severe", "wasting", "not_wasting", "overweight", "outlier")`.
+#' @returns An object of class factor with the same length as the longest input
+#'   vector, containing wasting classifications. Its levels are
+#'   `c("wasting_severe", "wasting", "not_wasting", "overweight")` if `outliers
+#'   = FALSE` (the default), else `c("wasting_severe", "wasting", "not_wasting",
+#'   "overweight", "outlier")`.
 #' @note Input vectors will be recycled by [vctrs::vec_recycle_common()].
 #'   Implausible z-score bounds are sourced from the referenced WHO report, and
 #'   classification cut-offs from the DHS manual.
@@ -256,11 +258,11 @@ classify_wasting <- function(weight_kg, lenht_cm, gest_days, age_days, sex,
 #'
 #' @inheritParams classify_sfga
 #' @inherit classify_stunting params references
-#' @return Factor of weight-for-age classifications with same length as longest
-#'   input. If `outliers = FALSE`, levels are `c("underweight_severe",
-#'   "underweight", "normal", "overweight")`. If `outliers = TRUE`, levels are
-#'   `c("underweight_severe", "underweight", "normal", "overweight",
-#'   "outlier")`.
+#' @returns An object of class factor with the same length as the longest input
+#'   vector, containing weight-for-age classifications. Its levels are
+#'   `c("underweight_severe", "underweight", "normal", "overweight")` if
+#'   `outliers = FALSE` (the default), else `c("underweight_severe",
+#'   "underweight", "normal", "overweight", "outlier")`.
 #' @inherit classify_wasting note
 #' @examples
 #' classify_wfa(

R/data.R

@@ -1,4 +1,4 @@
-#' gigs: Assess Growth in Infants and Newborns
+#' gigs: Assess Fetal, Newborn, and Child Growth with International Standards
 #'
 #' Convert between anthropometric measures and z-scores/centiles using WHO
 #' and INTERGROWTH-21<sup>st</sup> growth standards. This includes functions for

R/ig_fet.R

@@ -101,32 +101,37 @@
 #' **56(3):359-370** \doi{10.1002/uog.21990}
 #' @examples
 #' # Convert centiles to values
-#' p <- 0.25 # 25th centile
-#' ig_fet_centile2value(p = p, x = 280, acronym = "hcfga") |>
+#' ig_fet_centile2value(p = c(0.25, 0.5, 0.75), # 25th, 50th, 75th centile
+#'                      x = 279:281,
+#'                      acronym = "hcfga") |>
 #'   round(digits = 2)
 #'
 #' # Or z-scores to values
-#' z <- qnorm(p)
-#' ig_fet_zscore2value(z = z, x = 280, acronym = "hcfga") |>
+#' ig_fet_zscore2value(z = qnorm(c(0.25, 0.5, 0.75)),
+#'                     x = 279:281,
+#'                     acronym = "hcfga") |>
 #'   round(digits = 2)
 #'
 #' # Specify which standard to use with the acronym parameter...
-#' ig_fet_zscore2value(z = z, x = 280, acronym = "acfga") |>
+#' ig_fet_zscore2value(z = -1:1,
+#'                     x = 279:281,
+#'                     acronym = "acfga") |>
 #'   round(digits = 2)
 #'
 #' # ... or by using a standard-specific function
-#' ig_fet_acfga_zscore2value(z = z, gest_days = 280) |>
+#' ig_fet_acfga_zscore2value(z = -1:1,
+#'                           gest_days = 279:281) |>
 #'   round(digits = 2)
 #'
 #' # Inputs are recycled to the input of the longest length
-#' ig_fet_efwfga_zscore2value(z = seq(0.1, 0.9, by = 0.2),
-#'                            gest_days = 280) |>
+#' ig_fet_acfga_zscore2value(z = 0,
+#'                           gest_days = 279:281) |>
 #'   round(digits = 2)
 #'
-#' # Bad inputs will not stop the function but will instead return NA - here 91
-#' # days for gest_days is outside the bounds of the INTERGROWTH-21st Fetal
-#' # Growth standard for head circumference-for-GA
-#' ig_fet_hcfga_zscore2value(z = z, gest_days = c(91, 98, 224, 266)) |>
+#' # Bad inputs will not stop the function but will instead produce `NA`s in the
+#' # output - by default gigs will issue useful warnings
+#' ig_fet_hcfga_centile2value(p = c(-0.5, 0.15, 0.5, 0.85),
+#'                            gest_days = c(91, 98, 224, NA)) |>
 #'   round(digits = 2)
 #' @rdname ig_fet_zscore2value
 #' @export
@@ -632,31 +637,36 @@ ig_fet_cmfga_centile2value <- function(p, gest_days) {
 #' @inherit shared_value2zscore_returns return
 #' @examples
 #' # Convert values to centiles
-#' y <- 335
-#' ig_fet_value2centile(y = y, x = 280, acronym = "hcfga") |>
+#' ig_fet_value2centile(y = 335:345,
+#'                      x = 260:270,
+#'                      acronym = "hcfga") |>
 #'   round(digits = 2)
 #'
 #' # Or values to z-scores
-#' ig_fet_value2zscore(y = y, x = 280, acronym = "hcfga") |>
+#' ig_fet_value2zscore(y = 335:345,
+#'                     x = 260:270,
+#'                     acronym = "hcfga") |>
 #'   round(digits = 2)
 #'
 #' # Specify which standard to use with the acronym parameter...
-#' ig_fet_value2zscore(y = 340, x = 280, acronym = "acfga") |>
+#' ig_fet_value2zscore(y = 335:345,
+#'                     x = 260:270,
+#'                     acronym = "acfga") |>
 #'   round(digits = 2)
 #'
 #' # ... or by using a standard-specific function
-#' ig_fet_acfga_value2zscore(abdocirc_mm = 340, gest_days = 280) |>
+#' ig_fet_acfga_value2zscore(abdocirc_mm = 335:345,
+#'                           gest_days = 260:270) |>
 #'   round(digits = 2)
 #'
 #' # Inputs are recycled to the input of the longest length
 #' ig_fet_efwfga_value2zscore(efw_g = seq(3200, 3500, by = 50),
 #'                            gest_days = 280) |>
 #'   round(digits = 2)
 #'
-#' # Bad inputs will not stop the function but will instead return NA - here 90
-#' # days for `gest_days` is outside the bounds of the INTERGROWTH-21st Fetal
-#' # Growth standards
-#' ig_fet_hcfga_value2zscore(headcirc_mm = c(90, 100, 300, 310),
+#' # Bad inputs will not stop the function but will instead produce `NA`s in the
+#' # output - by default gigs will issue useful warnings
+#' ig_fet_hcfga_value2zscore(headcirc_mm = c(90, 100, 300, NaN),
 #'                           gest_days = c(91, 98, 224, 266)) |>
 #'   round(digits = 2)
 #' @rdname ig_fet_value2zscore

R/ig_fet_estimation.R

@@ -10,10 +10,12 @@
 #' @note Inputs are recycled using [vctrs::vec_recycle_common()].
 #' @examples
 #' # Estimate fetal weight in grams
-#' ig_fet_estimate_fetal_weight(abdocirc_mm = 31, headcirc_mm = 26.5)
+#' ig_fet_estimate_fetal_weight(abdocirc_mm = 31:33,
+#'                              headcirc_mm = 25:27)
 #'
 #' # Input vectors are recycled using vctrs::vec_recycle_common
-#' ig_fet_estimate_fetal_weight(abdocirc_mm = 25, headcirc_mm = 24:26)
+#' ig_fet_estimate_fetal_weight(abdocirc_mm = 25.0,
+#'                              headcirc_mm = 24:26)
 #' @returns Numeric vector with estimated fetal weight(s) in g, with the same
 #'   length as the longest input vector.
 #' @seealso Get z-scores/centiles for estimated fetal weights at known
@@ -67,21 +69,24 @@ ig_fet_estimate_fetal_weight <- function(abdocirc_mm, headcirc_mm) {
 #'   finally with head circumference alone.
 #' @examples
 #' # Estimate gestational age in days using crown-rump length (most accurate)
-#' ig_fet_estimate_ga(crl_mm = 25)
+#' ig_fet_estimate_ga(crl_mm = 40:45)
 #'
 #' # Estimate gestational age in days using head circumference and femur length
 #' # (second-most accurate)
-#' ig_fet_estimate_ga(headcirc_mm = 250, femurlen_mm = 55)
+#' ig_fet_estimate_ga(headcirc_mm = 250:255, femurlen_mm = 55:60)
 #'
 #' # Estimate gestational age in days using head circumference only (least
 #' # accurate)
-#' ig_fet_estimate_ga(headcirc_mm = 250)
+#' ig_fet_estimate_ga(headcirc_mm = 250:255)
 #'
 #' # The function defaults to CRL if available
-#' ig_fet_estimate_ga(crl_mm = 25, headcirc_mm = 250, femurlen_mm = 55)
+#' ig_fet_estimate_ga(crl_mm = 40:45,
+#'                    headcirc_mm = 250:255,
+#'                    femurlen_mm = 55:60)
 #'
 #' # Inputs are recycled using [vctrs::vec_recycle_common]
-#' ig_fet_estimate_ga(headcirc_mm = 249:251, femurlen_mm = 55)
+#' ig_fet_estimate_ga(headcirc_mm = 252,
+#'                    femurlen_mm = 55:60)
 #' @returns A numeric vector with estimated gestational ages in days. This
 #'   vector will have a length equal to the outputs from
 #'   [vctrs::vec_recycle_common()].