Changelog

Source: NEWS.md

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 - 2023-03-012023-03-03

Changed

• Fixed missing adult measurements to be labeled “Missing” in output (#119)
• Added tests for missingness in adult output
• Fixed missing “-RV” codes in adult output
• Corrected contributor names in DESCRIPTION (#120)
• Added email for Dan Chudnov in DESCRIPTION (#95)

growthcleanr 2.1.0 - 2023-02-032023-02-16

Added

• Use dependabot to update GitHub workflow action versions (#94)
• Use GitHub action to build and publish container image (#101)

Changed

• Updated ext_bmiz() to match Dec 2022 NCHS guidelines (#98)
• New options to keep dates, columns, unmatched rows in longwide() (#71)
• Updated CITATION to match new CRAN requirements
• Updated Dockerfile to build from repo, not CRAN

growthcleanr 2.0.3 - 2022-11-012022-11-03

Added

• CRAN release checklist now added under Developer Guidelines vignette (#99)

Changed

• All possible levels for cleangrowth() output factor now enumerated
• Updated maintainer to Carrie Daymont

growthcleanr 2.0.2 - 2022-09-132022-09-13

Added

• Package now available on CRAN: https://cran.r-project.org/package=growthcleanr

Changed

• Several updates for CRAN deployment: improved example/test runtimes, text corrections (#82); switched examples to use donttest, added CRAN comments file, updated .Rbuildignore (#84)
• Documentation updated with CRAN install (#86), fixed links (#85)
• Updated GitHub check workflow (#80) and pkgdown workflow

growthcleanr 2.0.1 - 2022-08-292022-09-01

Changed

• Updated DESCRIPTION, including authors, URLS, title, description, and imports
• Compressed files in inst/extdata for size requirements; added R.utils as import to support fread() for .gz files
• Updated license year

growthcleanr 2.0.0 - 2021-06-30

Added

• Support for cleaning adult (18-65) observations with adult_cutpoint and weightcap options (https://github.com/mitre/growthcleanr/pull/17, others)
• Added documentation describing adult algorithm, examples, and exclusions (#30), next steps (#63)
• Added tests supporting adult observations (#49)

Changed

• Removed BMI calculation from longwide(), added simple_bmi() (#47)
• Enhanced gcdriver.R to support adult options, parallel operation (https://github.com/mitre/growthcleanr/pull/23)
• Refreshed syngrowth synthetic test data, now includes adults (#50)
• Reorganized documentation from README, now using pkgdown (#30)
• Improved code layout to pass CHECK cleanly (#18, #60)

growthcleanr 1.2.6 - 2021-06-10

Changed

• Corrected four duplicated age-rows in NHANES reference medians (#40)
• Added missing non-newborn constraint in 14h.ii (thanks Lusha Cao)
• Removed Hmisc dependency (#36)
• Replaced clean_value result column name in docs with gcr_result for clarity (#35)

growthcleanr 1.2.5 - 2021-02-26

Added

• Added inst/extdata/nhanes-reference-medians.csv, reference medians for recentering derived from NHANES (described in README)

Changed

• Updated behavior of sd.recenter option to include new NHANES reference medians and explicit specification with “NHANES” or “derive” (https://github.com/mitre/growthcleanr/issues/9)
• Switched README.md to be generated from README.Rmd w/knitr (thanks
  1. (#17)
• Switched to use file.path() more consistently in R/growth.R

growthcleanr 1.2.4 - 2021-01-14

Changed

• Minor update to WHO HT velocity 3SD files to correct a small number of errors (#24). Affected files were:

  • inst/extdata/who_ht_maxvel_3sd.csv
  • inst/extdata/who_ht_vel_3sd.csv

  Although these changes were very minor, it is possible that results on data cleaned after this change may vary from previous results. The prior version of these files may be obtained by visiting the tagged release version 1.2.3 at https://github.com/carriedaymont/growthcleanr/releases/tag/1.2.3.

  The released version of growthcleanr available at that link contains the older version of both files; that older version may be used to verify reproducibility.

  Alternatively, a more recent version of growthcleanr may be used with only the affected files replaced with their older versions available at the 1.2.3 tag link above. This must be done manually.

growthcleanr 1.2.3 - 2021-01-07

Added

• New exclusion handling option on experimental carry forward adjustment

Changed

• Improved experimental carry forward adjustment handling of strings of CF values, output handling, and documentation; renamed “Missing” values
• Updated DESCRIPTION, imports, documentation to address testing issue (#12)
• Switched to R-native argparser library to support script options
• Switched to GitHub Actions for continuous integration / testing (thanks
• Improved Dockerfile to standardize user/path, simplify install (thanks

growthcleanr 1.2.2 - 2020-09-29

Added

• CITATION file, now citation("growthcleanr") works as expected

Changed

• Standardized on arrow assignment
• Moved functions previously within other functions to top level
• @import now preferred over library() for library loading
• Exported more functions
• Improved carried forward adjustment driver script, now supports line-grid (like original sweep), random, and grid-search search types, with configuration
• Added fdir option to splitinput() to specify split file directory
• Added package minimum versions to DESCRIPTION
• Fixed example code to reduce build warnings
• Improved and corrected documentation
• Re-compressed synthetic sample data (syngrowth) to improve compression

growthcleanr 1.2.1 - 2020-08-14

Added

• New tests in tests/testthat/test-utils.R and tests/testthat/test-cdc.R to support newly added functions

Changed

• Improved error handling in longwide(); fixed missing import in DESCRIPTION

growthcleanr 1.2 - 2020-07-24

Added

• New CDC BMI calculation function ext_bmiz(), comparable to SAS program published at https://www.cdc.gov/nccdphp/dnpao/growthcharts/resources/sas.htm
• Reference data file inst/extdata/CDCref_d.csv from CDC for use with ext_bmiz()
• New function longwide() for transforming cleangrowth() output for use with ext_bmiz()
• New function recode_sex() for recoding input data column values for sex to match cleangrowth() or ext_bmiz() requirements
• New exec/gcdriver.R command-line script for CLI execution of cleangrowth()
• New Dockerfile (and .dockerignore) enabling containerized use of growthcleanr
• Started test suite in tests
• New experimental function adjustcarryforward() in R/adjustcarryforward.R and driver script exec/testadjustcf.R (see README-adjustcarryforward.md for details)

Changed

• Reorganized code from R/growth.R into separate files for clarity and easier maintenance (all utility functions not directly used by cleangrowth() are now in R/utils.R)
• Updated README with details and examples for added functions

growthcleanr 1.1 - 2020-02-07

Added

• New options to add flexibility:
  • error.load.mincount and error.load.threshold
  • lt3.exclude.mode with default (same as before) and flag.both mode for handling unmatched pairs
  • sdmedian.filename and sdrecentered.filename
• New splitinput() function
• New example synthetic data set syngrowth loads automatically.

Changed

• Several updates to improve performance, including eliminating use of data.table in ewma function.
• Updated README with link to paper, detailed introduction, more installation details, examples, notes on handling large datasets, lists of parameters and exclusions.

growthcleanr 1.0.0 - 2018-09-11

Added

• Initial version posted to GitHub.