Merge pull request carriedaymont#137 from carriedaymont/upd-v3

Update preliminary infants algorithm to main

.gitignore

@@ -19,7 +19,6 @@
 
 # produced vignettes
 vignettes/*.html
-vignettes/*.pdf
 
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: growthcleanr
 Type: Package
 Title: Data Cleaner for Anthropometric Measurements
-Version: 2.1.1
+Version: 2.2.0
 Authors@R: c(
     person("Carrie", "Daymont", email = "cdaymont@pennstatehealth.psu.edu", role = c("ctb","cre")),
     person("Robert", "Grundmeier", role = "aut"),

NAMESPACE

@@ -23,6 +23,7 @@ import(parallel)
 import(plyr, except = c(failwith, id, summarize, count, desc, mutate, arrange, rename, is.discrete, summarise, summarize))
 import(tidyr, except = extract)
 importFrom(stats,approx)
+importFrom(stats,embed)
 importFrom(stats,median)
 importFrom(stats,pnorm)
 importFrom(stats,qnorm)

NEWS.md

@@ -1,3 +1,17 @@
+# growthcleanr 2.2.0-prelim-infants - 2023-09-13
+
+## Added
+
+- Added option to cleangrowth for the preliminary infants algorithm -- expands pediatric algorithm to consider 0 - 2 years old, with infants = TRUE in cleangrowth(), with all steps implemented. Note that this option is still preliminary and should not be used for research. For more information regarding the logic of the algorithm, see the vignette 'Preliminary Infants Algorithm.' 
+
+
+# growthcleanr 3.0.0-infants-beta - 2023-03-13
+
+## Added
+
+- Added the infants beta release algorithm -- expands pediatric algorithm to consider 0 - 2 years old, with infants = TRUE in cleangrowth()
+  - Updated velocity data for the extension (#122)
+
 # growthcleanr 2.1.1 - 2023-03-01
 
 ## Changed

R/extdata.R

@@ -28,6 +28,36 @@ NULL
 #'
 NULL
 
+#' CDC Growth Percentile Table for Infants
+#'
+#' Part of default CDC-derived tables
+#'
+#' Contains percentiles for various ages, gender, and weights, pre-calculated by CDC for infants algorithm
+#'
+#' @name growth_cdc_ext_infants
+#'
+#' @section growthfile_cdc_ext_infants.csv.gz:
+#'
+#' Used in function `cleangrowth()`
+#'
+#'
+NULL
+
+#' WHO Growth Percentile Table
+#'
+#' Part of default WHO-derived tables
+#'
+#' Contains percentiles for various ages, gender, and weights, pre-calculated by WHO
+#'
+#' @name growth_who_ext
+#'
+#' @section growthfile_who.csv.gz:
+#'
+#' Used in function `cleangrowth()`
+#'
+#'
+NULL
+
 #' Length to Age Table
 #'
 #' Part of default CDC-derived tables
@@ -43,6 +73,20 @@ NULL
 #'
 NULL
 
+#' Infants reference medians
+#'
+#' Contains reference median values for default recentering in the infants
+#' algorithm
+#'
+#' @name rc-reference-medians
+#'
+#' @section rcfile-2023-08-15_format.csv.gz:
+#'
+#' Used in function `cleangrowth()`
+#'
+#'
+NULL
+
 #' NHANES reference medians
 #'
 #' Contains reference median values for default recentering, derived from NHANES
@@ -72,6 +116,22 @@ NULL
 #'
 NULL
 
+#' Tanner Growth Velocity Table for Infants
+#'
+#' Part of default CDC-derived tables
+#'
+#' Contains velocities for growth pre-calculated by CDC, used for the infants
+#' algorithm
+#'
+#' @name tanner_ht_vel_rev
+#'
+#' @section tanner_ht_vel_rev.csv.gz:
+#'
+#' Used in function `cleangrowth()`
+#'
+#'
+NULL
+
 #' Tanner Growth Velocity Table with (2\eqn{\sigma})
 #'
 #' Part of default CDC-derived tables
@@ -167,6 +227,38 @@ NULL
 #'
 NULL
 
+#' WHO Maximum Head Circumference Velocity for (3\eqn{\sigma})
+#'
+#' Part of default WHO-derived tables
+#'
+#' Contains three standard deviations for the World Health Organization values of
+#' maximum head circumference velocities.
+#'
+#' @name who_hc_maxvel
+#'
+#' @section who_hc_maxvel_3sd_infants.csv.gz:
+#'
+#' Used in function `cleangrowth()`
+#'
+#'
+NULL
+
+#' WHO Head Circumference Velocity for (3\eqn{\sigma})
+#'
+#' Part of default WHO-derived tables
+#'
+#' Contains three standard deviations for the World Health Organization values of
+#' head circumference velocities.
+#'
+#' @name who_hc_vel_3sd
+#'
+#' @section who_hc_vel_3sd_infants.csv.gz:
+#'
+#' Used in function `cleangrowth()`
+#'
+#'
+NULL
+
 #' CDC SAS BMI Input
 #'
 #' Contains input data for CDC SAS macro for calculating BMI values.
@@ -205,3 +297,31 @@ NULL
 #'
 #'
 NULL
+
+#' Fenton Growth Curves
+#'
+#' Fenton growth curves with premature infant data with sex, age, and integer
+#' weight
+#'
+#' @name fentlms_foraga
+#'
+#' @section fentlms_foraga.csv.gz:
+#'
+#' Used in function `cleangrowth()`
+#'
+#'
+NULL
+
+#' Fenton Growth Curve Z-Scores
+#'
+#' Fenton growth curves with premature infant z-scores for height and head
+#'circumference
+#'
+#' @name fentlms_forz
+#'
+#' @section fentlms_forz.csv.gz:
+#'
+#' Used in function `cleangrowth()`
+#'
+#'
+NULL