diff --git a/DESCRIPTION b/DESCRIPTION index 5521390..c0e997b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,14 +1,14 @@ Package: growthcleanr Type: Package Title: Data Cleaner for Anthropometric Measurements -Version: 2.0.2 +Version: 2.0.3 Authors@R: c( - person("Daymont","Carrie", email = "cdaymont@pennstatehealth.psu.edu", role = "aut"), + person("Daymont","Carrie", email = "cdaymont@pennstatehealth.psu.edu", role = c("ctb","cre")), person("Grundmeier","Robert", role = "aut"), person("Miller","Jeffrey", role = "aut"), person("Campos","Diego", role = "aut"), person("Chudnov","Dan", role = "ctb"), - person("De los Santos","Hannah", email = "hdelossantos@mitre.org", role = c("ctb","cre")), + person("De los Santos","Hannah", email = "hdelossantos@mitre.org", role = c("ctb")), person("Cao","Lusha", role = "ctb"), person("Silva","Steffani", role = "ctb"), person("Zhang","Hanzhe", role = "ctb"), diff --git a/NEWS.md b/NEWS.md index dd21b01..cfdecca 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,14 @@ +# growthcleanr 2.0.3 - 2022-11-01 + +## 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 - 2022-09-13 ## Added diff --git a/R/growth.R b/R/growth.R index a04d53c..ab47195 100644 --- a/R/growth.R +++ b/R/growth.R @@ -204,7 +204,7 @@ cleangrowth <- function(subjid, # constants for pediatric # enumerate the different exclusion levels - exclude.levels <- c( + exclude.levels.peds <- c( 'Include', 'Unit-Error-High', 'Unit-Error-Low', @@ -235,6 +235,29 @@ cleangrowth <- function(subjid, 'Exclude-Too-Many-Errors-Other-Parameter' ) + exclude.levels.adult <- c( + "Include", + "Exclude-Adult-BIV", + "Exclude-Adult-Hundreds", + "Exclude-Adult-Unit-Errors", + "Exclude-Adult-Transpositions", + "Exclude-Adult-Weight-Cap-Identical", + "Exclude-Adult-Weight-Cap", + "Exclude-Adult-Swapped-Measurements", + "Exclude-Adult-Identical-Same-Day", + "Exclude-Adult-Extraneous-Same-Day", + "Exclude-Adult-Distinct-Pairs", + "Exclude-Adult-Distinct-3-Or-More", + "Exclude-Adult-EWMA-Extreme", + "Exclude-Adult-Distinct-Ordered-Pairs", + "Exclude-Adult-EWMA-Moderate", + "Exclude-Adult-Possibly-Impacted-By-Weight-Cap", + "Exclude-Adult-Distinct-Single", + "Exclude-Adult-Too-Many-Errors" + ) + + exclude.levels <- base::union(exclude.levels.peds, exclude.levels.adult) + # if there's no pediatric data, no need to go through this rigamarole if (nrow(data.all) > 0){ @@ -665,8 +688,7 @@ cleangrowth <- function(subjid, exclude = c(as.character(ret.df$exclude), res$result), mean_sde = c(rep(NA, nrow(ret.df)), res$mean_sde) ) - full_out[, exclude := factor(exclude, levels = unique(c(exclude.levels, - unique(exclude))))] + full_out[, exclude := factor(exclude, levels = exclude.levels)] full_out <- full_out[order(line),] # remove column added for keeping track full_out[, line := NULL] diff --git a/README.Rmd b/README.Rmd index 0e3bed1..e611469 100644 --- a/README.Rmd +++ b/README.Rmd @@ -102,6 +102,7 @@ The rest of this documentation includes: notes and suggestions for running `growthcleanr` with large data sources - [Next steps](https://carriedaymont.github.io/growthcleanr/articles/next-steps.html), notes on potential enhancements to the pediatric and adult algorithms +- [Developer guidelines](https://carriedaymont.github.io/growthcleanr/articles/developer-guidelines.html), advice for contributors to this package, including a CRAN release checklist ## Changes diff --git a/README.md b/README.md index d4e7232..01d3a0c 100644 --- a/README.md +++ b/README.md @@ -103,6 +103,10 @@ The rest of this documentation includes: - [Next steps](https://carriedaymont.github.io/growthcleanr/articles/next-steps.html), notes on potential enhancements to the pediatric and adult algorithms +- [Developer + guidelines](https://carriedaymont.github.io/growthcleanr/articles/developer-guidelines.html), + advice for contributors to this package, including a CRAN release + checklist ## Changes diff --git a/_pkgdown.yml b/_pkgdown.yml index 7934b0f..8a0c688 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -19,6 +19,7 @@ articles: - utilities - large-data-sets - next-steps + - developer-guidelines reference: - title: "Cleaning height and weight observations" diff --git a/cran-comments.md b/cran-comments.md index f05f783..16d8dd9 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,4 +1,4 @@ -# CRAN submission growthcleanr 2.0.2 (1) +# CRAN submission growthcleanr 2.0.3 ## R CMD check results There were no ERRORs, WARNINGs, or NOTEs. @@ -6,8 +6,18 @@ There were no ERRORs, WARNINGs, or NOTEs. ## Downstream dependencies There are currently no downstream dependencies for this package. + + # Previous Submissions +# CRAN submission growthcleanr 2.0.2 (1) + +## R CMD check results +There were no ERRORs, WARNINGs, or NOTEs. + +## Downstream dependencies +There are currently no downstream dependencies for this package. + # CRAN submission growthcleanr 2.0.1 (6) ## R CMD check results diff --git a/docs/404.html b/docs/404.html index c4798da..836e017 100644 --- a/docs/404.html +++ b/docs/404.html @@ -18,7 +18,7 @@ - +
@@ -41,7 +41,7 @@
  • @@ -91,7 +94,7 @@
  • - +
    • @@ -102,7 +105,7 @@
    - +
    @@ -125,7 +128,7 @@

    Page not found (404)

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -136,10 +139,10 @@

    Page not found (404)

    - - + + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 2a60e11..3f61f7c 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -99,7 +102,7 @@

    License

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -108,10 +111,9 @@

    License

    - - - + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index f681cee..2242508 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -103,19 +106,26 @@

    MIT License

    +<<<<<<< HEAD

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    Site built with pkgdown 2.0.7.

    +======= +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    +
    + +
    +

    Site built with pkgdown 2.0.6.

    +>>>>>>> remotes/github-carrie/upd-v2
    - - - + + diff --git a/docs/articles/adult-algorithm.html b/docs/articles/adult-algorithm.html index a3210eb..0ee36b9 100644 --- a/docs/articles/adult-algorithm.html +++ b/docs/articles/adult-algorithm.html @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,22 +106,22 @@
    - +

    Adult algorithm

    - +

    2023-02-01

    - + Source: vignettes/adult-algorithm.Rmd
    - - + +

    There will be notes in italics throughout the introductory material discussing similarities and differences between growthcleanr-adults and growthcleanr-pediatrics for those who are @@ -843,10 +846,10 @@

    14H, 14W, Error load: Too-Many-Errors<

    - - + + diff --git a/docs/articles/configuration.html b/docs/articles/configuration.html index d8cf32e..92e6114 100644 --- a/docs/articles/configuration.html +++ b/docs/articles/configuration.html @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,22 +106,22 @@
    - +

    Configuration

    - +

    2023-02-01

    - + Source: vignettes/configuration.Rmd
    - - + +

    growthcleanr offers several options for configuration, with default values set to address common cases. You may wish to experiment with the settings to discover which work best for your @@ -371,10 +374,10 @@

    Derivation process + + + + + +Developer guidelines • growthcleanr + + + + + + + + + + + + +
    +
    + + + + +
    +
    +
    +

    Developer guidelines

    + +

    2022-11-02

    + + Source: vignettes/developer-guidelines.Rmd + + +
    + + + +
    +

    CRAN Release Checklist +

    +

    When deploying updates to CRAN, here a few updates that you need to +check off before doing so:

    +
      +
    • Update version number in DESCRIPTION in format major.minor.patch +(e.g. 1.2.1)
      • +
    • Update package documentation with +devtools::document() +
      • +
    • Run devtools::check(): +
        +
      • If any problems come up that have not previously been documented in +cran-comments.md and cannot be fixed, fix them. There +should be no ERRORs or WARNINGs before submitting to CRAN.
        • +
      • Look through past CRAN submissions to make sure you haven’t +reintroduced a bug/note that has been addressed in a previous +version
        • +
      +
      • +
    • If you have made any changes to README.Rmd, re-knit to +README.md +
      • +
    • Update pkgdown site with pkgdown::build_site() +
      • +
    • Update NEWS.md with version updates
      • +
    • Update cran-comments.md in format
      • +
    • After the branch is merged, create a GitHub release
      • +
    • After the branch is merged, submit to CRAN with previously written +comments!
      • +
    +
    +
    + + + +
    + + + +
    +

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    +
    + +
    +

    +

    Site built with pkgdown 2.0.6.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/articles/index.html b/docs/articles/index.html index 6a8da39..34f9b40 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@

    - +
    @@ -111,13 +114,15 @@

    Advanced

    Next steps
    +
    Developer guidelines
    +
    - - - + + diff --git a/docs/articles/installation.html b/docs/articles/installation.html index 82a71f8..c399033 100644 --- a/docs/articles/installation.html +++ b/docs/articles/installation.html @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,22 +106,22 @@
    - +

    Installation

    - +

    2023-02-01

    - + Source: vignettes/installation.Rmd
    - - + +

    growthcleanr has been developed and tested using R versions 3.6 and 4+. It should work using R on Windows, macOS, or Unix/Linux, although there are some additional platform-specific notes you may wish to review.

    @@ -269,7 +272,11 @@

    If you are developing the growthcleanr code itself, you can download or clone the growthcleanr source code and then install it from source. To clone the source using git:

    +<<<<<<< HEAD 
    % git clone https://github.com/carriedaymont/growthcleanr.git
    +======= +
    % git clone https://github.com/carriedaymont/growthcleanr.git
    +>>>>>>> remotes/github-carrie/upd-v2

    Once you have the growthcleanr package source, open an R session from the growthcleanr base directory. Then install growthcleanr using the R devtools package:

    @@ -301,10 +308,10 @@

    - - + + diff --git a/docs/articles/large-data-sets.html b/docs/articles/large-data-sets.html index e4e324d..e67a193 100644 --- a/docs/articles/large-data-sets.html +++ b/docs/articles/large-data-sets.html @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,22 +106,22 @@
    - +

    Working with large data sets

    - +

    2023-02-01

    - + Source: vignettes/large-data-sets.Rmd
    - - + +

    The nature of the growthcleanr algorithm is repetitive. It runs many checks over each individual subject’s measurements, in a specific sequence, and revises its assessments as it goes. Because of @@ -339,10 +342,10 @@

    Reference for gcdriver.R

    - - + + diff --git a/docs/articles/next-steps.html b/docs/articles/next-steps.html index c29c2b6..8522e44 100644 --- a/docs/articles/next-steps.html +++ b/docs/articles/next-steps.html @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,22 +106,22 @@
    - +

    Next steps

    - +

    2023-02-01

    - + Source: vignettes/next-steps.Rmd
    - - + +

    While both the pediatric and adult algorithms are considered complete, we have identified several areas for additional research and potential enhancement.

    @@ -522,10 +525,10 @@

    Error load - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,22 +106,22 @@
    - +

    Understanding growthcleanr output

    - +

    2023-02-01

    - + Source: vignettes/output.Rmd
    - - + +

    As seen in the Usage example, growthcleanr creates a vector of flags identifying which measurements should be included or excluded, and why. This vector can be @@ -552,10 +555,10 @@

    Exclusions generated by adult a

    - - + + diff --git a/docs/articles/quickstart.html b/docs/articles/quickstart.html index 6c16604..f9fe617 100644 --- a/docs/articles/quickstart.html +++ b/docs/articles/quickstart.html @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,22 +106,22 @@
    - +

    Quickstart

    - +

    2023-02-01

    - + Source: vignettes/quickstart.Rmd
    - - + +

    R setup

    @@ -488,10 +491,10 @@

    Example

    - - + + diff --git a/docs/articles/usage.html b/docs/articles/usage.html index 5a05685..8e00498 100644 --- a/docs/articles/usage.html +++ b/docs/articles/usage.html @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,22 +106,22 @@
    - +

    Usage

    - +

    2023-02-01

    - + Source: vignettes/usage.Rmd
    - - + +

    With the growthcleanr package installed as described in Installation, it can be loaded as a package:

    @@ -309,10 +312,10 @@

    Basic configuration options - +
    @@ -42,7 +42,7 @@
  • @@ -92,7 +95,7 @@
  • - +
    • @@ -103,23 +106,23 @@
    - +

    Utilities for computing pediatric BMI percentiles, Z-scores, and related tools

    - +

    2023-02-01

    - + Source: vignettes/utilities.Rmd
    - - + +

    The CDC provides a SAS macro for computing BMI percentiles and Z-scores. The function ext_bmiz(), included in growthcleanr, provides @@ -424,10 +427,10 @@

    - +
    @@ -85,65 +88,65 @@

    Authors

    - +
    • -

      Daymont Carrie. Author. +

      Daymont Carrie. Contributor, maintainer.

    • -

      Grundmeier Robert. Author. +

      Grundmeier Robert. Author.

    • -

      Miller Jeffrey. Author. +

      Miller Jeffrey. Author.

    • -

      Campos Diego. Author. +

      Campos Diego. Author.

    • -

      Chudnov Dan. Contributor. +

      Chudnov Dan. Contributor.

    • -

      De los Santos Hannah. Contributor, maintainer. +

      De los Santos Hannah. Contributor.

    • -

      Cao Lusha. Contributor. +

      Cao Lusha. Contributor.

    • -

      Silva Steffani. Contributor. +

      Silva Steffani. Contributor.

    • -

      Zhang Hanzhe. Contributor. +

      Zhang Hanzhe. Contributor.

    • -

      Boyas Matt. Contributor. +

      Boyas Matt. Contributor.

    • -

      Freedman David. Contributor. +

      Freedman David. Contributor.

    • -

      Achilleos Andreas. Contributor. +

      Achilleos Andreas. Contributor.

    • -

      Butts Jessica. Contributor. +

      Butts Jessica. Contributor.

    • -

      Nguyen Sheila. Contributor. +

      Nguyen Sheila. Contributor.

    • -

      Soleymani Taraneh. Contributor. +

      Soleymani Taraneh. Contributor.

    @@ -178,7 +181,7 @@

    Citation

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -187,10 +190,9 @@

    Citation

    - - - + + diff --git a/docs/index.html b/docs/index.html index 06152f0..94642fc 100644 --- a/docs/index.html +++ b/docs/index.html @@ -20,7 +20,7 @@ - +
    @@ -43,7 +43,7 @@
  • @@ -93,7 +96,7 @@
  • - +
    • @@ -104,7 +107,7 @@
    - +
    @@ -162,6 +165,8 @@

    Advanced topics:Working with large datasets, notes and suggestions for running growthcleanr with large data sources
  • Next steps, notes on potential enhancements to the pediatric and adult algorithms
    • +
  • +Developer guidelines, advice for contributors to this package, including a CRAN release checklist

    • @@ -202,11 +207,10 @@

    Citation

    Developers

      -
    • Daymont Carrie
      Author
      • +
    • Daymont Carrie
      Contributor, maintainer
    • Grundmeier Robert
      Author
    • Miller Jeffrey
      Author
    • Campos Diego
      Author
      • -
    • De los Santos Hannah
      Contributor, maintainer
    • More about authors...
    @@ -225,7 +229,7 @@

    Dev status

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -236,10 +240,10 @@

    Dev status

    - - + + diff --git a/docs/news/index.html b/docs/news/index.html index 24a40d0..d76884f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -85,6 +88,18 @@

    Changelog

    Source: NEWS.md
    +
    +

    growthcleanr 2.0.3 - 2022-11-01

    +
    +

    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

    @@ -281,7 +296,7 @@

    Added -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -290,10 +305,9 @@

    Added - +
    @@ -25,7 +25,7 @@

    - +
    @@ -93,7 +96,7 @@

    CDC BMI reference data

    CDCref_d.csv.gz

    - +

    Used for extended BMI computation

    @@ -107,7 +110,7 @@

    CDCref_d.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -116,10 +119,9 @@

    CDCref_d.csv.gz

    - - - + + diff --git a/docs/reference/acf_answers.html b/docs/reference/acf_answers.html index ff99e43..a9d4c8e 100644 --- a/docs/reference/acf_answers.html +++ b/docs/reference/acf_answers.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +
    @@ -163,7 +166,7 @@

    Arguments

    Value

    - +

    A data frame, containing an index "n" of rows, corresponding to the original order of the input vectors, and "acf_answers", containing the answers @@ -180,19 +183,26 @@

    Value

    +<<<<<<< HEAD

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    Site built with pkgdown 2.0.7.

    +======= +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    +
    + +
    +

    Site built with pkgdown 2.0.6.

    +>>>>>>> remotes/github-carrie/upd-v2
    - - - + + diff --git a/docs/reference/adjustcarryforward.html b/docs/reference/adjustcarryforward.html index 1582e75..e12bc60 100644 --- a/docs/reference/adjustcarryforward.html +++ b/docs/reference/adjustcarryforward.html @@ -9,7 +9,7 @@ - +
    @@ -31,7 +31,7 @@
    - +
    @@ -230,7 +233,7 @@

    Arguments

    Value

    - +

    Re-evaluated exclusion assessments based on height velocity.

    @@ -264,19 +267,26 @@

    Examples

    +<<<<<<< HEAD

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    Site built with pkgdown 2.0.7.

    +======= +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    +
    + +
    +

    Site built with pkgdown 2.0.6.

    +>>>>>>> remotes/github-carrie/upd-v2
    - - - + + diff --git a/docs/reference/bmianthro.html b/docs/reference/bmianthro.html index 20f68a3..75a15ce 100644 --- a/docs/reference/bmianthro.html +++ b/docs/reference/bmianthro.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@

    - +
    @@ -97,7 +100,7 @@

    Details

    bmianthro.txt.gz

    - +

    Used in function cleangrowth()

    @@ -111,7 +114,7 @@

    bmianthro.txt.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -120,10 +123,9 @@

    bmianthro.txt.gz

    - - - + + diff --git a/docs/reference/cleangrowth.html b/docs/reference/cleangrowth.html index 7d20555..4042029 100644 --- a/docs/reference/cleangrowth.html +++ b/docs/reference/cleangrowth.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -273,7 +276,7 @@

    Arguments

    Value

    - +

    Vector of exclusion codes for each of the input measurements.

    @@ -312,10 +315,17 @@

    Examples

    measurement = df_stats$measurement, parallel = TRUE, num.batches = 2) +<<<<<<< HEAD #> Warning: <anonymous>: ... may be used in an incorrect context: ‘.fun(piece, ...)’ #> Warning: <anonymous>: ... may be used in an incorrect context: ‘.fun(piece, ...)’ #> Warning: <anonymous>: ... may be used in an incorrect context: ‘.fun(piece, ...)’ #> Warning: <anonymous>: ... may be used in an incorrect context: ‘.fun(piece, ...)’ +======= +#> Warning: <anonymous>: ... may be used in an incorrect context: '.fun(piece, ...)' +#> Warning: <anonymous>: ... may be used in an incorrect context: '.fun(piece, ...)' +#> Warning: <anonymous>: ... may be used in an incorrect context: '.fun(piece, ...)' +#> Warning: <anonymous>: ... may be used in an incorrect context: '.fun(piece, ...)' +>>>>>>> remotes/github-carrie/upd-v2 # }
    @@ -327,19 +337,26 @@

    Examples

    +<<<<<<< HEAD

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    Site built with pkgdown 2.0.7.

    +======= +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    +
    + +
    +

    Site built with pkgdown 2.0.6.

    +>>>>>>> remotes/github-carrie/upd-v2
    - - - + + diff --git a/docs/reference/ewma.html b/docs/reference/ewma.html index ca7d1ae..4f1011e 100644 --- a/docs/reference/ewma.html +++ b/docs/reference/ewma.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -114,7 +117,7 @@

    Arguments

    Value

    - +

    Data frame with 3 variables:

    • The first variable (ewma.all) contains the EWMA at observation time excluding only the actual observation for that time point.

      • @@ -160,10 +163,9 @@

      Examples

    - - - + + diff --git a/docs/reference/ext_bmiz.html b/docs/reference/ext_bmiz.html index a0267f5..9b9fe31 100644 --- a/docs/reference/ext_bmiz.html +++ b/docs/reference/ext_bmiz.html @@ -8,7 +8,7 @@ - +
    @@ -30,7 +30,7 @@
    - +
    @@ -145,7 +148,7 @@

    Arguments

    Value

    - +

    Expanded data frame containing computed BMI values

    @@ -232,10 +235,9 @@

    Examples

    - - - + + diff --git a/docs/reference/growth_cdc_ext.html b/docs/reference/growth_cdc_ext.html index d10d5d7..29f6d36 100644 --- a/docs/reference/growth_cdc_ext.html +++ b/docs/reference/growth_cdc_ext.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -97,7 +100,7 @@

    Details

    growthfile_cdc_ext.csv.gz

    - +

    Used in function cleangrowth()

    @@ -111,7 +114,7 @@

    growthfile_cdc_ext.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -120,10 +123,9 @@

    growthfile_cdc_ext.csv.gz

    - - - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index b3a8fc7..1f49183 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -223,7 +226,7 @@

    Datasets

    @@ -25,7 +25,7 @@

    - +
    @@ -97,7 +100,7 @@

    Details

    lenanthro.txt.gz

    - +

    Used in function cleangrowth()

    @@ -111,7 +114,7 @@

    lenanthro.txt.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -120,10 +123,9 @@

    lenanthro.txt.gz

    - - - + + diff --git a/docs/reference/longwide.html b/docs/reference/longwide.html index 81c9244..45f5862 100644 --- a/docs/reference/longwide.html +++ b/docs/reference/longwide.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -149,7 +152,7 @@

    Arguments

    Value

    - +

    Returns a data frame transformed from long to wide. Includes only values flagged with indicated inclusion types. Note that, for each subject, heights without corresponding weights for a given age (and vice versa) will be dropped.

    @@ -183,19 +186,26 @@

    Examples

    +<<<<<<< HEAD

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    Site built with pkgdown 2.0.7.

    +======= +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    +
    + +
    +

    Site built with pkgdown 2.0.6.

    +>>>>>>> remotes/github-carrie/upd-v2
    - - - + + diff --git a/docs/reference/nhanes-reference-medians.html b/docs/reference/nhanes-reference-medians.html index ada4a21..b5d299a 100644 --- a/docs/reference/nhanes-reference-medians.html +++ b/docs/reference/nhanes-reference-medians.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +
    @@ -95,7 +98,7 @@

    NHANES reference medians

    nhanes-reference-medians.csv.gz

    - +

    Used in function cleangrowth()

    @@ -109,7 +112,7 @@

    nhanes-reference-medians.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -118,10 +121,9 @@

    nhanes-reference-medians.csv.gz

    - - - + + diff --git a/docs/reference/read_anthro.html b/docs/reference/read_anthro.html index 1a24039..58f892b 100644 --- a/docs/reference/read_anthro.html +++ b/docs/reference/read_anthro.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -106,7 +109,7 @@

    Arguments

    Value

    - +

    Function for calculating BMI based on measurement, age in days, sex, and measurement value.

    @@ -138,10 +141,9 @@

    Examples

    - - - + + diff --git a/docs/reference/recode_sex.html b/docs/reference/recode_sex.html index 8abb322..d1c2144 100644 --- a/docs/reference/recode_sex.html +++ b/docs/reference/recode_sex.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +
    @@ -136,7 +139,7 @@

    Arguments

    Value

    - +

    Returns a data table with recoded sex variables.

    @@ -164,19 +167,26 @@

    Examples

    +<<<<<<< HEAD

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    Site built with pkgdown 2.0.7.

    +======= +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    +
    + +
    +

    Site built with pkgdown 2.0.6.

    +>>>>>>> remotes/github-carrie/upd-v2
    - - - + + diff --git a/docs/reference/sd_median.html b/docs/reference/sd_median.html index 4a0e5a7..de4b564 100644 --- a/docs/reference/sd_median.html +++ b/docs/reference/sd_median.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -114,7 +117,7 @@

    Arguments

    Value

    - +

    Table of data with median SD-scores per day of life by gender and parameter.

    @@ -157,10 +160,9 @@

    Examples

    - - - + + diff --git a/docs/reference/simple_bmi.html b/docs/reference/simple_bmi.html index 4656d37..47f267f 100644 --- a/docs/reference/simple_bmi.html +++ b/docs/reference/simple_bmi.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +
    @@ -113,7 +116,7 @@

    Arguments

    Value

    - +

    Returns a data table with the added column "bmi"

    @@ -157,10 +160,9 @@

    Examples

    - - - + + diff --git a/docs/reference/splitinput.html b/docs/reference/splitinput.html index 199ba51..cd00e47 100644 --- a/docs/reference/splitinput.html +++ b/docs/reference/splitinput.html @@ -7,7 +7,7 @@ - +
    @@ -29,7 +29,7 @@
    - +
    @@ -132,7 +135,7 @@

    Arguments

    Value

    - +

    the count number referring to the last split file written

    @@ -175,10 +178,9 @@

    Examples

    - - - + + diff --git a/docs/reference/syngrowth.html b/docs/reference/syngrowth.html index 9c126a5..fcafd15 100644 --- a/docs/reference/syngrowth.html +++ b/docs/reference/syngrowth.html @@ -5,7 +5,7 @@ - +
    @@ -27,7 +27,7 @@
    - +
    @@ -125,10 +128,9 @@

    Details

    - - - + + diff --git a/docs/reference/tanner_ht_vel.html b/docs/reference/tanner_ht_vel.html index 188b859..13fba35 100644 --- a/docs/reference/tanner_ht_vel.html +++ b/docs/reference/tanner_ht_vel.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -97,7 +100,7 @@

    Details

    tanner_ht_vel.csv.gz

    - +

    Used in function cleangrowth()

    @@ -111,7 +114,7 @@

    tanner_ht_vel.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -120,10 +123,9 @@

    tanner_ht_vel.csv.gz

    - - - + + diff --git a/docs/reference/tanner_ht_vel_with_2sd.html b/docs/reference/tanner_ht_vel_with_2sd.html index 62977d7..192363a 100644 --- a/docs/reference/tanner_ht_vel_with_2sd.html +++ b/docs/reference/tanner_ht_vel_with_2sd.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -98,7 +101,7 @@

    Details

    tanner_ht_vel_with_2sd.csv.gz

    - +

    Used in function acf_answers()

    @@ -112,7 +115,7 @@

    tanner_ht_vel_with_2sd.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -121,10 +124,9 @@

    tanner_ht_vel_with_2sd.csv.gz

    - - - + + diff --git a/docs/reference/test_syngrowth_sas_output_compare.html b/docs/reference/test_syngrowth_sas_output_compare.html index e6972c1..1ef7aba 100644 --- a/docs/reference/test_syngrowth_sas_output_compare.html +++ b/docs/reference/test_syngrowth_sas_output_compare.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -93,7 +96,7 @@

    CDC SAS BMI Output

    test_syngrowth_sas_output_compare.csv.gz

    - +

    Used to test function ext_bmiz()

    @@ -107,7 +110,7 @@

    test_syngrowth_sas_output_compare.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -116,10 +119,9 @@

    test_syngrowth_sas_output_compare.csv.gz

    - - - + + diff --git a/docs/reference/test_syngrowth_wide.html b/docs/reference/test_syngrowth_wide.html index b77b883..f1e5ecc 100644 --- a/docs/reference/test_syngrowth_wide.html +++ b/docs/reference/test_syngrowth_wide.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -93,7 +96,7 @@

    CDC SAS BMI Input

    test_syngrowth_wide.csv.gz

    - +

    Used to test function ext_bmiz()

    @@ -107,7 +110,7 @@

    test_syngrowth_wide.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -116,10 +119,9 @@

    test_syngrowth_wide.csv.gz

    - - - + + diff --git a/docs/reference/testacf.html b/docs/reference/testacf.html index 73c73eb..b4cb2e4 100644 --- a/docs/reference/testacf.html +++ b/docs/reference/testacf.html @@ -6,7 +6,7 @@ - +
    @@ -28,7 +28,7 @@
    - +
    @@ -167,7 +170,7 @@

    Arguments

    Value

    - +

    A list containing: testacf_res: data frame with adjustcarryforward results for each run, @@ -183,7 +186,7 @@

    Value

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -192,10 +195,9 @@

    Value

    - - - + + diff --git a/docs/reference/weianthro.html b/docs/reference/weianthro.html index dbffdba..130329a 100644 --- a/docs/reference/weianthro.html +++ b/docs/reference/weianthro.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -97,7 +100,7 @@

    Details

    weianthro.csv.gz

    - +

    Used in function cleangrowth()

    @@ -111,7 +114,7 @@

    weianthro.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -120,10 +123,9 @@

    weianthro.csv.gz

    - - - + + diff --git a/docs/reference/who_ht_maxvel.html b/docs/reference/who_ht_maxvel.html index 557334f..c8f5c6a 100644 --- a/docs/reference/who_ht_maxvel.html +++ b/docs/reference/who_ht_maxvel.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -98,7 +101,7 @@

    Details

    who_ht_maxvel_3sd.csv.gz

    - +

    Used in function cleangrowth()

    @@ -112,7 +115,7 @@

    who_ht_maxvel_3sd.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -121,10 +124,9 @@

    who_ht_maxvel_3sd.csv.gz

    - - - + + diff --git a/docs/reference/who_ht_maxvel_2sd.html b/docs/reference/who_ht_maxvel_2sd.html index 3dffac0..686f495 100644 --- a/docs/reference/who_ht_maxvel_2sd.html +++ b/docs/reference/who_ht_maxvel_2sd.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -98,7 +101,7 @@

    Details

    who_ht_maxvel_2sd.csv.gz

    - +

    Used in function acf_answers()

    @@ -112,7 +115,7 @@

    who_ht_maxvel_2sd.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -121,10 +124,9 @@

    who_ht_maxvel_2sd.csv.gz

    - - - + + diff --git a/docs/reference/who_ht_vel_2sd.html b/docs/reference/who_ht_vel_2sd.html index 5b56410..cb07f7d 100644 --- a/docs/reference/who_ht_vel_2sd.html +++ b/docs/reference/who_ht_vel_2sd.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -98,7 +101,7 @@

    Details

    who_ht_vel_2sd.csv.gz

    - +

    Used in function acf_answers()

    @@ -112,7 +115,7 @@

    who_ht_vel_2sd.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -121,10 +124,9 @@

    who_ht_vel_2sd.csv.gz

    - - - + + diff --git a/docs/reference/who_ht_vel_3sd.html b/docs/reference/who_ht_vel_3sd.html index ca497d3..ec59fb3 100644 --- a/docs/reference/who_ht_vel_3sd.html +++ b/docs/reference/who_ht_vel_3sd.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -98,7 +101,7 @@

    Details

    who_ht_vel_3sd.csv.gz

    - +

    Used in function cleangrowth()

    @@ -112,7 +115,7 @@

    who_ht_vel_3sd.csv.gz

    -

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego, De los Santos Hannah.

    +

    Developed by Daymont Carrie, Grundmeier Robert, Miller Jeffrey, Campos Diego.

    @@ -121,10 +124,9 @@

    who_ht_vel_3sd.csv.gz

    - - - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index db0605b..6a9d0ea 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -15,6 +15,9 @@ /articles/configuration.html + + /articles/developer-guidelines.html + /articles/index.html @@ -46,10 +49,13 @@ /index.html - /news/index.html + /LICENSE-text.html - /reference/CDCref_d.html + /LICENSE.html + + + /news/index.html /reference/acf_answers.html @@ -60,6 +66,9 @@ /reference/bmianthro.html + + /reference/CDCref_d.html + /reference/cleangrowth.html @@ -112,13 +121,13 @@ /reference/tanner_ht_vel_with_2sd.html - /reference/test_syngrowth_sas_output_compare.html + /reference/testacf.html - /reference/test_syngrowth_wide.html + /reference/test_syngrowth_sas_output_compare.html - /reference/testacf.html + /reference/test_syngrowth_wide.html /reference/weianthro.html @@ -135,4 +144,4 @@ /reference/who_ht_vel_3sd.html - + \ No newline at end of file diff --git a/vignettes/developer-guidelines.Rmd b/vignettes/developer-guidelines.Rmd new file mode 100644 index 0000000..352ee64 --- /dev/null +++ b/vignettes/developer-guidelines.Rmd @@ -0,0 +1,23 @@ +--- +title: "Developer guidelines" +date: "`r Sys.Date()`" +vignette: > + %\VignetteIndexEntry{Developer Guidelines} %\VignetteEngine{knitr::rmarkdown} + %\usepackage[utf8]{inputenc} +--- + +## CRAN Release Checklist + +When deploying updates to CRAN, here a few updates that you need to check off before doing so: + +- Update version number in DESCRIPTION in format major.minor.patch (e.g. 1.2.1) +- Update package documentation with `devtools::document()` +- Run `devtools::check()`: + - If any problems come up that have not previously been documented in `cran-comments.md` and cannot be fixed, fix them. There should be no ERRORs or WARNINGs before submitting to CRAN. + - Look through past CRAN submissions to make sure you haven't reintroduced a bug/note that has been addressed in a previous version +- If you have made any changes to `README.Rmd`, re-knit to `README.md` +- Update pkgdown site with `pkgdown::build_site()` +- Update NEWS.md with version updates +- Update cran-comments.md in format +- After the branch is merged, create a GitHub release +- After the branch is merged, submit to CRAN with previously written comments!