From 7e99356f88ab5147d28bfe338e01bda701a18016 Mon Sep 17 00:00:00 2001 From: "Dr. Hannah De los Santos" Date: Wed, 13 Sep 2023 10:58:29 -0400 Subject: [PATCH] Update pkgdown site --- docs/404.html | 5 +- docs/LICENSE-text.html | 5 +- docs/LICENSE.html | 5 +- docs/articles/adult-algorithm.html | 7 +- docs/articles/configuration.html | 7 +- docs/articles/developer-guidelines.html | 7 +- docs/articles/index.html | 7 +- docs/articles/installation.html | 25 ++- docs/articles/large-data-sets.html | 61 +++--- docs/articles/next-steps.html | 125 +++++------ docs/articles/output.html | 7 +- docs/articles/prelim-infants-algorithm.html | 195 ++++++++++++++++++ docs/articles/quickstart.html | 7 +- docs/articles/usage.html | 91 ++++---- docs/articles/utilities.html | 109 +++++----- docs/authors.html | 5 +- docs/index.html | 5 +- docs/news/index.html | 12 +- docs/pkgdown.yml | 5 +- docs/reference/CDCref_d.html | 5 +- docs/reference/acf_answers.html | 5 +- docs/reference/adjustcarryforward.html | 5 +- docs/reference/bmianthro.html | 5 +- docs/reference/cleangrowth.html | 11 +- docs/reference/ewma.html | 5 +- docs/reference/ext_bmiz.html | 5 +- docs/reference/growth_cdc_ext.html | 5 +- docs/reference/index.html | 5 +- docs/reference/lenanthro.html | 5 +- docs/reference/longwide.html | 5 +- docs/reference/nhanes-reference-medians.html | 5 +- docs/reference/read_anthro.html | 11 +- docs/reference/recode_sex.html | 5 +- docs/reference/sd_median.html | 5 +- docs/reference/simple_bmi.html | 5 +- docs/reference/splitinput.html | 5 +- docs/reference/syngrowth.html | 5 +- docs/reference/tanner_ht_vel.html | 5 +- docs/reference/tanner_ht_vel_with_2sd.html | 5 +- .../test_syngrowth_sas_output_compare.html | 5 +- docs/reference/test_syngrowth_wide.html | 5 +- docs/reference/testacf.html | 5 +- docs/reference/weianthro.html | 5 +- docs/reference/who_ht_maxvel.html | 5 +- docs/reference/who_ht_maxvel_2sd.html | 5 +- docs/reference/who_ht_vel_2sd.html | 5 +- docs/reference/who_ht_vel_3sd.html | 5 +- docs/sitemap.xml | 3 + 48 files changed, 594 insertions(+), 251 deletions(-) create mode 100644 docs/articles/prelim-infants-algorithm.html diff --git a/docs/404.html b/docs/404.html index 923920a9..29a5d7f3 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -81,6 +81,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 844d06e4..ee8b400f 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 252207b8..43aa2909 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/articles/adult-algorithm.html b/docs/articles/adult-algorithm.html index 5330a3e0..63be10fc 100644 --- a/docs/articles/adult-algorithm.html +++ b/docs/articles/adult-algorithm.html @@ -33,7 +33,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • @@ -113,7 +116,7 @@

    Adult algorithm

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/adult-algorithm.Rmd diff --git a/docs/articles/configuration.html b/docs/articles/configuration.html index 0e3d5d29..bf48b7cb 100644 --- a/docs/articles/configuration.html +++ b/docs/articles/configuration.html @@ -33,7 +33,7 @@ growthcleanr - 2.1.1 + 2.2.0
    @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • @@ -113,7 +116,7 @@

    Configuration

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/configuration.Rmd diff --git a/docs/articles/developer-guidelines.html b/docs/articles/developer-guidelines.html index 77869b15..30ecbb5f 100644 --- a/docs/articles/developer-guidelines.html +++ b/docs/articles/developer-guidelines.html @@ -33,7 +33,7 @@ growthcleanr - 2.1.1 + 2.2.0
    @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • @@ -113,7 +116,7 @@

    Developer guidelines

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/developer-guidelines.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 1ced39cb..6d7b5df0 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0
    @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference @@ -116,6 +119,8 @@

    Advanced

    Developer guidelines
    +
    Preliminary infants algorithm
    +
    diff --git a/docs/articles/installation.html b/docs/articles/installation.html index 9d18ac2c..e0785ab6 100644 --- a/docs/articles/installation.html +++ b/docs/articles/installation.html @@ -33,7 +33,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • @@ -113,7 +116,7 @@

    Installation

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/installation.Rmd @@ -184,8 +187,8 @@

    macOS threads. You will know it worked successfully if, when you load the data.table library in R, you see something like the following:

    -
    library(data.table)
-data.table 1.12.2 using 2 threads (see ?getDTthreads).  Latest news: r-datatable.com
    +
    library(data.table)
+data.table 1.12.2 using 2 threads (see ?getDTthreads).  Latest news: r-datatable.com

    That data.table reports “using 2 threads” indicates that installation has succeeded. If the message reports using only one thread, see the advice under the “OpenMP @@ -208,7 +211,7 @@

    Docker

    To install and run growthcleanr using Docker, open the PowerShell on Windows, or open the Terminal on macOS, and enter this docker command:

    -
    docker run -it ghcr.io/mitre/growthcleanr/gcr-image:latest R
    +
    docker run -it ghcr.io/mitre/growthcleanr/gcr-image:latest R

    The image tag latest in the example above will refer to the latest version of the package available on the main branch of the mitre/growthcleanr repository, which is typically in close sync with the upstream carriedaymont/growthcleanr @@ -216,7 +219,7 @@

    Docker growthcleanr. To explicitly choose a release by name, replace latest with the release tag, e.g. for the released package v2.1.0:

    -
    docker run -it ghcr.io/mitre/growthcleanr/gcr-image:v2.1.0 R
    +
    docker run -it ghcr.io/mitre/growthcleanr/gcr-image:v2.1.0 R

    Whichever package you use, the first time this command is run, it might take a few minutes to download and extract several necessary components, but this should be fully automated. If successful, you @@ -228,8 +231,8 @@

    Docker your own data. For example, if you are on Windows, and your data is in C:\Users\exampleuser\analysis, specify a mapping using the added -v step below:

    -
    docker run -it -v C:\Users\exampleusers\analysis:/usr/src/app \
-    ghcr.io/mitre/growthcleanr/gcr-image:latest R
    +
    docker run -it -v C:\Users\exampleusers\analysis:/usr/src/app \
+    ghcr.io/mitre/growthcleanr/gcr-image:latest R

    Note that the slashes in file paths reverse direction from the reference to the folder location on your Windows machine (before the colon) to the folder location on the Docker container (after the colon); @@ -242,8 +245,8 @@

    Docker

    If you are on macOS, and your data is in /Users/exampleuser/analysis, specify a folder mapping like this:

    -
    docker run -it -v /Users/exampleuser/analysis:/usr/src/app \
-    ghcr.io/mitre/growthcleanr/gcr-image:latest R
    +
    docker run -it -v /Users/exampleuser/analysis:/usr/src/app \
+    ghcr.io/mitre/growthcleanr/gcr-image:latest R

    If you mapped a folder, then inside the Docker environment’s R prompt, when you then issue a command like list.files(), you should see a list of the same files in the R session that you see in @@ -283,7 +286,7 @@

    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:

    -
    git clone https://github.com/carriedaymont/growthcleanr.git
    +
    git clone https://github.com/carriedaymont/growthcleanr.git

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

    diff --git a/docs/articles/large-data-sets.html b/docs/articles/large-data-sets.html index 8340f110..c662a1bc 100644 --- a/docs/articles/large-data-sets.html +++ b/docs/articles/large-data-sets.html @@ -33,7 +33,7 @@ growthcleanr - 2.1.1 + 2.2.0

    @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • @@ -113,7 +116,7 @@

    Working with large data sets

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/large-data-sets.Rmd @@ -222,12 +225,12 @@

    Splitting input datasets

    To invoke exec/gcdriver.R on a single input file using Rscript:

    -
    Rscript exec/gcdriver.R --quietly --sdrecenter nhanes mydata.csv mydata-cleaned.csv
    +
    Rscript exec/gcdriver.R --quietly --sdrecenter nhanes mydata.csv mydata-cleaned.csv

    If you have many small files saved, for example, as mydata.00001.csv, mydata.00002.csv, etc., this driver can be invoked using parallel:

    -
    ls mydata.?????.csv | parallel -j2 --eta \
-  "Rscript exec/gcdriver.R --quietly --sdrecenter nhanes {} {}-clean.csv"
    +
    ls mydata.?????.csv | parallel -j2 --eta \
+  "Rscript exec/gcdriver.R --quietly --sdrecenter nhanes {} {}-clean.csv"

    This lists your input files, and passes the filename list to parallel to use in invoking the driver script, one file at a time, and to process as parallel jobs as resources are available. Each run of the job then @@ -275,7 +278,7 @@

    Batch splitting for adult data
    Rscript exec/gcdriver.R --numbatches 4 --adult_split 50 my-large-input.csv my-large-input-cleaned.csv

    +
    Rscript exec/gcdriver.R --numbatches 4 --adult_split 50 my-large-input.csv my-large-input-cleaned.csv
  • @@ -113,7 +116,7 @@

    Next steps

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/next-steps.Rmd @@ -157,7 +160,7 @@

    Running the experimentgrowthcleanr as described in the main README.md file, save it to a CSV file for exec/testadjustcf.R:

    -
    > fwrite(cleaned_data, "cleaned.csv", row.names = F)
    +
    > fwrite(cleaned_data, "cleaned.csv", row.names = F)

    For testacf(), keep cleaned_data in your environment. Note that the column names should be as described for cleaned_data the Example under Quickstart.

    @@ -167,7 +170,7 @@

    Running the experiment -
    Rscript exec/testadjustcf.R cleaned.csv
    +
    Rscript exec/testadjustcf.R cleaned.csv

    To use testacf(), run the following in the console (with cleaned_data in the environment):

    @@ -351,42 +354,42 @@ 
    Running the experimentFor example, for a 9-step sweep with the default search type,
 random, the parameters passed to the function in each pass
 will be:
    
-
    run minfactor   maxfactor   banddiff    banddiff_plus   min_ht.exp_under    min_ht.exp_over max_ht.exp_under    max_ht.exp_over
-1   0.494454649 0.331710969 1.681997601 5.438065292 0.371428523 -0.200524185    0.296497153 0.244186167
-2   0.198872727 0.918207332 0.0261138   0.361051567 0.370286443 -0.618056939    0.318943811 0.280842425
-3   0.057848889 0.343496154 2.957211272 3.448713172 0.758593493 -0.240298769    0.189112731 0.586874211
-4   0.034874339 0.462954204 0.949754412 2.697612725 1.694048784 -0.563224398    0.237626234 0.410851815
-5   0.5 2   3   5.5 2   0   0.33    1.5
-6   0.621874695 3.545623892 4.918346826 10.84063427 2.996152267 0.904217721 0.585439346 1.787876622
-7   0.896005213 2.192603083 3.885669706 7.492214661 3.581171147 0.319534914 0.537161064 2.25658771
-8   0.670031176 2.90689554  5.990111082 9.239964036 3.676927744 0.082569093 0.568586483 2.645760535
-9   0.98603125  2.169401426 5.718063961 6.950459617 2.91380773  0.816289079 0.457654322 2.540503306
    
+
    run minfactor   maxfactor   banddiff    banddiff_plus   min_ht.exp_under    min_ht.exp_over max_ht.exp_under    max_ht.exp_over
+1   0.494454649 0.331710969 1.681997601 5.438065292 0.371428523 -0.200524185    0.296497153 0.244186167
+2   0.198872727 0.918207332 0.0261138   0.361051567 0.370286443 -0.618056939    0.318943811 0.280842425
+3   0.057848889 0.343496154 2.957211272 3.448713172 0.758593493 -0.240298769    0.189112731 0.586874211
+4   0.034874339 0.462954204 0.949754412 2.697612725 1.694048784 -0.563224398    0.237626234 0.410851815
+5   0.5 2   3   5.5 2   0   0.33    1.5
+6   0.621874695 3.545623892 4.918346826 10.84063427 2.996152267 0.904217721 0.585439346 1.787876622
+7   0.896005213 2.192603083 3.885669706 7.492214661 3.581171147 0.319534914 0.537161064 2.25658771
+8   0.670031176 2.90689554  5.990111082 9.239964036 3.676927744 0.082569093 0.568586483 2.645760535
+9   0.98603125  2.169401426 5.718063961 6.950459617 2.91380773  0.816289079 0.457654322 2.540503306
    
 
    In a 9-step sweep with a line-grid search type, the
 parameters passed to the function in each pass will be:
    
-
    run  minfactor  maxfactor  banddiff  banddiff_plus  min_ht.exp_under  min_ht.exp_over  max_ht.exp_under  max_ht.exp_over
-1    0          0          0         0              0                 -1               0                 0
-2    0.125      0.5        0.75      1.375          0.5               -0.75            0.0825            0.375
-3    0.25       1          1.5       2.75           1                 -0.5             0.165             0.75
-4    0.375      1.5        2.25      4.125          1.5               -0.25            0.2475            1.125
-5    0.5        2          3         5.5            2                 0                0.33              1.5
-6    0.625      2.5        3.75      6.875          2.5               0.25             0.4125            1.875
-7    0.75       3          4.5       8.25           3                 0.5              0.495             2.25
-8    0.875      3.5        5.25      9.625          3.5               0.75             0.5775            2.625
-9    1          4          6         11             4                 1                0.66              3
    
+
    run  minfactor  maxfactor  banddiff  banddiff_plus  min_ht.exp_under  min_ht.exp_over  max_ht.exp_under  max_ht.exp_over
+1    0          0          0         0              0                 -1               0                 0
+2    0.125      0.5        0.75      1.375          0.5               -0.75            0.0825            0.375
+3    0.25       1          1.5       2.75           1                 -0.5             0.165             0.75
+4    0.375      1.5        2.25      4.125          1.5               -0.25            0.2475            1.125
+5    0.5        2          3         5.5            2                 0                0.33              1.5
+6    0.625      2.5        3.75      6.875          2.5               0.25             0.4125            1.875
+7    0.75       3          4.5       8.25           3                 0.5              0.495             2.25
+8    0.875      3.5        5.25      9.625          3.5               0.75             0.5775            2.625
+9    1          4          6         11             4                 1                0.66              3
    
 
    In a 3-step sweep with a full-grid search type, with the
 --param CSV/param data frame specified as in
 the above example, the parameters passed to the function in each pass
 will be:
    
-
    run minfactor maxfactor banddiff banddiff_plus min_ht.exp_under min_ht.exp_over max_ht.exp_under max_ht.exp_over
-1       0.0         3        3           5.5                0               0              0.5             1.5
-2       0.5         3        3           5.5                0               0              0.5             1.5
-3       1.0         3        3           5.5                0               0              0.5             1.5
-4       0.0         3        3           5.5                2               0              0.5             1.5
-5       0.5         3        3           5.5                2               0              0.5             1.5
-6       1.0         3        3           5.5                2               0              0.5             1.5
-7       0.0         3        3           5.5                4               0              0.5             1.5
-8       0.5         3        3           5.5                4               0              0.5             1.5
-9       1.0         3        3           5.5                4               0              0.5             1.5
    
+
    run minfactor maxfactor banddiff banddiff_plus min_ht.exp_under min_ht.exp_over max_ht.exp_under max_ht.exp_over
+1       0.0         3        3           5.5                0               0              0.5             1.5
+2       0.5         3        3           5.5                0               0              0.5             1.5
+3       1.0         3        3           5.5                0               0              0.5             1.5
+4       0.0         3        3           5.5                2               0              0.5             1.5
+5       0.5         3        3           5.5                2               0              0.5             1.5
+6       1.0         3        3           5.5                2               0              0.5             1.5
+7       0.0         3        3           5.5                4               0              0.5             1.5
+8       0.5         3        3           5.5                4               0              0.5             1.5
+9       1.0         3        3           5.5                4               0              0.5             1.5
    
 
    For the script, the output in the working directory will contain the
 sweep parameters, like the above, in a file called
 test_adjustcarrforward_DATE_TIME_parameters.csv, and the
@@ -398,7 +401,7 @@ 
    Running the experimenttestacf_res entry.
    
 
    For example, a 5-step sweep with the line-grid search
 would be run with this command:
    
-
    Rscript exec/textadjustcf.R --gridlength 5 --searchtype line-grid cleaned.csv
    
+
    Rscript exec/textadjustcf.R --gridlength 5 --searchtype line-grid cleaned.csv
    
 
    or with this function execution:
    
 
     result_list <- testacf(
@@ -410,12 +413,12 @@ 
    Running the experimenttest_adjustcarrforward_DATE_TIME_parameters.csv
 (script)/params data frame of result_list
 (function) would be:
    
-
    run  minfactor  maxfactor  banddiff  banddiff_plus  min_ht.exp_under  min_ht.exp_over  max_ht.exp_under  max_ht.exp_over
-1    0          0          0         0              0                 -1               0                 0
-2    0.25       1          1.5       2.75           1                 -0.5             0.165             0.75
-3    0.5        2          3         5.5            2                 0                0.33              1.5
-4    0.75       3          4.5       8.25           3                 0.5              0.495             2.25
-5    1          4          6         11             4                 1                0.66              3
    
+
    run  minfactor  maxfactor  banddiff  banddiff_plus  min_ht.exp_under  min_ht.exp_over  max_ht.exp_under  max_ht.exp_over
+1    0          0          0         0              0                 -1               0                 0
+2    0.25       1          1.5       2.75           1                 -0.5             0.165             0.75
+3    0.5        2          3         5.5            2                 0                0.33              1.5
+4    0.75       3          4.5       8.25           3                 0.5              0.495             2.25
+5    1          4          6         11             4                 1                0.66              3
    
 
    Note that an odd-numbered length will include the default values in
 the middle run of the sweep (hence the examples with 5 and 9 step
 sweeps).
    
@@ -423,31 +426,31 @@ 
    Running the experimenttest_adjustcarrforward_DATE_TIME.csv
 (script)/testacf_res data frame of result_list
 (function) would be:
    
-
    id     subjid    sex  agedays  param     measurement  gcr_result                      run-1      run-2      run-3      run-4      run-5
-1510   775155    0    889      HEIGHTCM  84.9         Exclude-Extraneous-Same-Day Missing    Missing    Missing    Missing    Missing
-1511   775155    0    889      HEIGHTCM  89.06        Include                     No Change  No Change  No Change  No Change  No Change
-1512   775155    0    1071     HEIGHTCM  92.5         Include                     No Change  No Change  No Change  No Change  No Change
-1513   775155    0    1253     HEIGHTCM  96.2         Include                     No Change  No Change  No Change  No Change  No Change
-1514   775155    0    1435     HEIGHTCM  96.2         Exclude-Carried-Forward     No Change  No Change  Include    Include    Include
-1515   775155    0    1435     HEIGHTCM  99.692       Include                     No Change  No Change  No Change  No Change  No Change
-1516   775155    0    1806     HEIGHTCM  106.1        Include                     No Change  No Change  No Change  No Change  No Change
-1517   775155    0    2177     HEIGHTCM  112.3        Include                     No Change  No Change  No Change  No Change  No Change
-1518   775155    0    889      WEIGHTKG  13.1         Include                     No Change  No Change  No Change  No Change  No Change
    
+
    id     subjid    sex  agedays  param     measurement  gcr_result                      run-1      run-2      run-3      run-4      run-5
+1510   775155    0    889      HEIGHTCM  84.9         Exclude-Extraneous-Same-Day Missing    Missing    Missing    Missing    Missing
+1511   775155    0    889      HEIGHTCM  89.06        Include                     No Change  No Change  No Change  No Change  No Change
+1512   775155    0    1071     HEIGHTCM  92.5         Include                     No Change  No Change  No Change  No Change  No Change
+1513   775155    0    1253     HEIGHTCM  96.2         Include                     No Change  No Change  No Change  No Change  No Change
+1514   775155    0    1435     HEIGHTCM  96.2         Exclude-Carried-Forward     No Change  No Change  Include    Include    Include
+1515   775155    0    1435     HEIGHTCM  99.692       Include                     No Change  No Change  No Change  No Change  No Change
+1516   775155    0    1806     HEIGHTCM  106.1        Include                     No Change  No Change  No Change  No Change  No Change
+1517   775155    0    2177     HEIGHTCM  112.3        Include                     No Change  No Change  No Change  No Change  No Change
+1518   775155    0    889      WEIGHTKG  13.1         Include                     No Change  No Change  No Change  No Change  No Change
    
 
    The fifth row in the example above demonstrates the results of the
 experimental script; for runs 1 and 2, the result is not changed, but
 for runs 3-5, the measurement is adjusted for reinclusion. To
 demonstrate the range, the following is an extract of measurements only
 marked as carried forward exclusions by cleangrowth():
    
-
    id     subjid     sex  agedays  param     measurement  gcr_result                   run-1      run-2      run-3      run-4      run-5
-1514   775155     0    1435     HEIGHTCM  96.2         Exclude-Carried-Forward  No Change  No Change  Include    Include    Include
-1521   775155     0    1435     WEIGHTKG  15.3         Exclude-Carried-Forward  No Change  No Change  No Change  No Change  No Change
-7952   1340377    1    1806     HEIGHTCM  107.1        Exclude-Carried-Forward  No Change  Include    Include    Include    Include
-7967   1340377    1    1806     WEIGHTKG  18.4         Exclude-Carried-Forward  No Change  No Change  No Change  No Change  No Change
-41775  3643526    1    1253     HEIGHTCM  87.808       Exclude-Carried-Forward  Include    Include    Include    Include    Include
-44901  3706097    0    4032     HEIGHTCM  138.8        Exclude-Carried-Forward  No Change  Include    Include    Include    Include
-30011  5792371    1    3661     HEIGHTCM  145.4        Exclude-Carried-Forward  No Change  Include    Include    Include    Include
-30013  5792371    1    4032     HEIGHTCM  145.4        Exclude-Carried-Forward  No Change  No Change  No Change  No Change  No Change
-30016  5792371    1    1071     WEIGHTKG  15.9         Exclude-Carried-Forward  No Change  No Change  No Change  No Change  No Change
    
+
    id     subjid     sex  agedays  param     measurement  gcr_result                   run-1      run-2      run-3      run-4      run-5
+1514   775155     0    1435     HEIGHTCM  96.2         Exclude-Carried-Forward  No Change  No Change  Include    Include    Include
+1521   775155     0    1435     WEIGHTKG  15.3         Exclude-Carried-Forward  No Change  No Change  No Change  No Change  No Change
+7952   1340377    1    1806     HEIGHTCM  107.1        Exclude-Carried-Forward  No Change  Include    Include    Include    Include
+7967   1340377    1    1806     WEIGHTKG  18.4         Exclude-Carried-Forward  No Change  No Change  No Change  No Change  No Change
+41775  3643526    1    1253     HEIGHTCM  87.808       Exclude-Carried-Forward  Include    Include    Include    Include    Include
+44901  3706097    0    4032     HEIGHTCM  138.8        Exclude-Carried-Forward  No Change  Include    Include    Include    Include
+30011  5792371    1    3661     HEIGHTCM  145.4        Exclude-Carried-Forward  No Change  Include    Include    Include    Include
+30013  5792371    1    4032     HEIGHTCM  145.4        Exclude-Carried-Forward  No Change  No Change  No Change  No Change  No Change
+30016  5792371    1    1071     WEIGHTKG  15.9         Exclude-Carried-Forward  No Change  No Change  No Change  No Change  No Change
    
 
    Some of these values are not adjusted at all; one is from run 1 on, a
 few are from run 2 on, and one is from run 3 on.
    
 
    
diff --git a/docs/articles/output.html b/docs/articles/output.html
index e2dabd0f..6cf34fb5 100644
--- a/docs/articles/output.html
+++ b/docs/articles/output.html
@@ -33,7 +33,7 @@
       
       
         growthcleanr
-        2.1.1
+        2.2.0
    @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +

  • @@ -113,7 +116,7 @@

    Understanding growthcleanr output

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/output.Rmd diff --git a/docs/articles/prelim-infants-algorithm.html b/docs/articles/prelim-infants-algorithm.html new file mode 100644 index 00000000..6539e63d --- /dev/null +++ b/docs/articles/prelim-infants-algorithm.html @@ -0,0 +1,195 @@ + + + + + + + +Preliminary infants algorithm • growthcleanr + + + + + + + + + + + + +
    +
    + + + + +
    +
    +
    +

    Preliminary infants algorithm

    + +

    2023-09-13

    + + Source: vignettes/prelim-infants-algorithm.Rmd + + +
    + + + +

    Now available is the in-development release of the infants algorithm, +which expands pediatric algorithm to clean 0 - 2 and revises its steps. +This is strongly not recommended for general use, and still contains +bugs. Possible bugs are enumerated below, and provide a starting point +for potential developers:

    +
      +
    • Same day exclusions are over called in weight and head +circumference
      • +
    • Carried forward exclusions are mis-called within that step
      • +
    • Same day exclusions are mis-called within that step
      • +
    • Raw differences step are over called in height
      • +
    • EWMA results missed in height
      • +
    • Carried forward results are missed in head circumference
      • +
    • Various smaller misalignments across exclusion results
      • +
    +

    If you would still like to use this in-development feature, you can +do this in the cleangrowth algorithm by turning on the option +prelim_infants:

    +
    +# prepare data as a data.table
+data <- as.data.table(source_data)
+ 
+# set the data.table key for better indexing
+setkey(data, subjid, param, agedays)
+ 
+# generate new exclusion flag field using function
+cleaned_data <- 
+  data[, gcr_result := cleangrowth(subjid, param, agedays, sex, measurement,
+                                   prelim_infants = TRUE)]
    +

    For information on the steps in the infants algorithm, please see this +document.

    +

    This algorithm expansion also contains information on smoothing +z-scores between observations of 2 and 4 years old. If you would like to +use this in your work, code can be found in growth.R lines 525-555.

    +

    If you have any feedback on this in-development feature, would like +to provide feedback on the algorithm logic or code, or discuss other +collaborations, please contact the maintainer of this package, Carrie +Daymont.

    +
    + + + +
    + + + +
    +

    +

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

    +
    + +
    +

    +

    Site built with pkgdown 2.0.7.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/articles/quickstart.html b/docs/articles/quickstart.html index f2313936..6b4a567e 100644 --- a/docs/articles/quickstart.html +++ b/docs/articles/quickstart.html @@ -33,7 +33,7 @@ growthcleanr - 2.1.1 + 2.2.0
    @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • @@ -113,7 +116,7 @@

    Quickstart

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/quickstart.Rmd diff --git a/docs/articles/usage.html b/docs/articles/usage.html index 25a80391..59fa8c95 100644 --- a/docs/articles/usage.html +++ b/docs/articles/usage.html @@ -33,7 +33,7 @@ growthcleanr - 2.1.1 + 2.2.0
    @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • @@ -113,7 +116,7 @@

    Usage

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/usage.Rmd @@ -152,45 +155,45 @@

    Basic operations using ex

    It can be used as in the following example. Note that processing the example data with cleangrowth() will likely take a few minutes to complete.

    -
    library(data.table)
-library(dplyr)
-
-# Convert the `syngrowth` data frame to a `data.table`
-data <- as.data.table(syngrowth)
-
-# `setkey()` creates an efficient sorting key on the `data.table`; this is required
-# for `cleangrowth()`
-setkey(data, subjid, param, agedays)
-
-# Add a column `gcr_result` using `cleangrowth`
-cleaned_data <- data[, gcr_result := cleangrowth(subjid, param, agedays, sex, measurement)]
-
-# View a sample of the results
-head(cleaned_data)
-      id                               subjid sex  agedays    param measurement                  gcr_result
-1: 83330 002986c5-354d-bb9d-c180-4ce26813ca28   1 20489.22 HEIGHTCM       151.1                     Include
-2: 83332 002986c5-354d-bb9d-c180-4ce26813ca28   1 20860.22 HEIGHTCM       151.1                     Include
-3: 83334 002986c5-354d-bb9d-c180-4ce26813ca28   1 20860.22 HEIGHTCM       150.6 Exclude-Same-Day-Extraneous
-4: 83335 002986c5-354d-bb9d-c180-4ce26813ca28   1 21231.22 HEIGHTCM       151.1                     Include
-5: 83337 002986c5-354d-bb9d-c180-4ce26813ca28   1 21602.22 HEIGHTCM       151.1                     Include
-6: 83339 002986c5-354d-bb9d-c180-4ce26813ca28   1 21623.22 HEIGHTCM       151.1                     Include
-
-# Summarize results by result type
-cleaned_data %>% group_by(gcr_result) %>% tally(sort=TRUE)
-# A tibble: 26 x 2
-   gcr_result                      n
-   <fct>                       <int>
- 1 Include                     61652
- 2 Exclude-Extraneous-Same-Day 11263
- 3 Exclude-Carried-Forward      7093
- 4 Exclude-Same-Day-Extraneous  4010
- 5 Exclude-Same-Day-Identical    623
- 6 Exclude-SD-Cutoff             175
- 7 Exclude-EWMA-8                139
- 8 Exclude-Distinct-3-Or-More    125
- 9 Exclude-BIV                   108
-10 Exclude-EWMA-Extreme           99
-# … with 16 more rows
    +
    library(data.table)
+library(dplyr)
+
+# Convert the `syngrowth` data frame to a `data.table`
+data <- as.data.table(syngrowth)
+
+# `setkey()` creates an efficient sorting key on the `data.table`; this is required
+# for `cleangrowth()`
+setkey(data, subjid, param, agedays)
+
+# Add a column `gcr_result` using `cleangrowth`
+cleaned_data <- data[, gcr_result := cleangrowth(subjid, param, agedays, sex, measurement)]
+
+# View a sample of the results
+head(cleaned_data)
+      id                               subjid sex  agedays    param measurement                  gcr_result
+1: 83330 002986c5-354d-bb9d-c180-4ce26813ca28   1 20489.22 HEIGHTCM       151.1                     Include
+2: 83332 002986c5-354d-bb9d-c180-4ce26813ca28   1 20860.22 HEIGHTCM       151.1                     Include
+3: 83334 002986c5-354d-bb9d-c180-4ce26813ca28   1 20860.22 HEIGHTCM       150.6 Exclude-Same-Day-Extraneous
+4: 83335 002986c5-354d-bb9d-c180-4ce26813ca28   1 21231.22 HEIGHTCM       151.1                     Include
+5: 83337 002986c5-354d-bb9d-c180-4ce26813ca28   1 21602.22 HEIGHTCM       151.1                     Include
+6: 83339 002986c5-354d-bb9d-c180-4ce26813ca28   1 21623.22 HEIGHTCM       151.1                     Include
+
+# Summarize results by result type
+cleaned_data %>% group_by(gcr_result) %>% tally(sort=TRUE)
+# A tibble: 26 x 2
+   gcr_result                      n
+   <fct>                       <int>
+ 1 Include                     61652
+ 2 Exclude-Extraneous-Same-Day 11263
+ 3 Exclude-Carried-Forward      7093
+ 4 Exclude-Same-Day-Extraneous  4010
+ 5 Exclude-Same-Day-Identical    623
+ 6 Exclude-SD-Cutoff             175
+ 7 Exclude-EWMA-8                139
+ 8 Exclude-Distinct-3-Or-More    125
+ 9 Exclude-BIV                   108
+10 Exclude-EWMA-Extreme           99
+# … with 16 more rows

    If you are able to run these steps and see a similar result, you have the growthcleanr package installed correctly. The resulting cleaned_data can be reviewed, subsetted, and compared in @@ -257,9 +260,9 @@

    Basic configuration options
    Warning messages:
-1: <anonymous>: ... may be used in an incorrect context: ‘.fun(piece, ...)’
-2: <anonymous>: ... may be used in an incorrect context: ‘.fun(piece, ...)’

    +
    Warning messages:
+1: <anonymous>: ... may be used in an incorrect context: ‘.fun(piece, ...)’
+2: <anonymous>: ... may be used in an incorrect context: ‘.fun(piece, ...)’

    This set of warnings is coming from one of growthcleanr’s dependencies, and does not indicate either failure or improper execution.

    diff --git a/docs/articles/utilities.html b/docs/articles/utilities.html index 5b8d14ba..dc133873 100644 --- a/docs/articles/utilities.html +++ b/docs/articles/utilities.html @@ -33,7 +33,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -82,6 +82,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • @@ -114,7 +117,7 @@

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

    -

    2023-03-13

    +

    2023-09-13

    Source: vignettes/utilities.Rmd @@ -188,27 +191,27 @@

    Converting long g

    Note that this assumes that cleaned_data has the same structure as described in Quickstart - Data preparation:

    -
    names(cleaned_data)
-[1] "id"          "subjid"      "sex"         "agedays"     "param"       "measurement" "gcr_result"
    +
    names(cleaned_data)
+[1] "id"          "subjid"      "sex"         "agedays"     "param"       "measurement" "gcr_result"

    The wide dataset cleaned_data_wide will include rows with aligned height and weight measurements drawn from the observations in cleaned_data marked by cleangrowth() for inclusion. As such, it will be a shorter dataset (fewer rows) based on fewer observations.

    -
    dim(cleaned_data)
-[1] 85728     7
-
-dim(cleaned_data_wide)
-[1] 26701     9
-
-head(cleaned_data_wide)
-                                subjid    agey     agem sex   wt wt_id    ht ht_id  agedays
-1 002986c5-354d-bb9d-c180-4ce26813ca28 56.0964 673.1568   2 71.7 83331 151.1 83330 20489.22
-2 002986c5-354d-bb9d-c180-4ce26813ca28 57.1122 685.3464   2 73.2 83333 151.1 83332 20860.22
-3 002986c5-354d-bb9d-c180-4ce26813ca28 58.1279 697.5348   2 74.6 83336 151.1 83335 21231.22
-4 002986c5-354d-bb9d-c180-4ce26813ca28 59.1437 709.7244   2 72.8 83338 151.1 83337 21602.22
-5 002986c5-354d-bb9d-c180-4ce26813ca28 59.2012 710.4144   2 72.4 83340 151.1 83339 21623.22
-6 002986c5-354d-bb9d-c180-4ce26813ca28 60.1594 721.9128   2 69.4 83343 151.1 83342 21973.22
    +
    dim(cleaned_data)
+[1] 85728     7
+
+dim(cleaned_data_wide)
+[1] 26701     9
+
+head(cleaned_data_wide)
+                                subjid    agey     agem sex   wt wt_id    ht ht_id  agedays
+1 002986c5-354d-bb9d-c180-4ce26813ca28 56.0964 673.1568   2 71.7 83331 151.1 83330 20489.22
+2 002986c5-354d-bb9d-c180-4ce26813ca28 57.1122 685.3464   2 73.2 83333 151.1 83332 20860.22
+3 002986c5-354d-bb9d-c180-4ce26813ca28 58.1279 697.5348   2 74.6 83336 151.1 83335 21231.22
+4 002986c5-354d-bb9d-c180-4ce26813ca28 59.1437 709.7244   2 72.8 83338 151.1 83337 21602.22
+5 002986c5-354d-bb9d-c180-4ce26813ca28 59.2012 710.4144   2 72.4 83340 151.1 83339 21623.22
+6 002986c5-354d-bb9d-c180-4ce26813ca28 60.1594 721.9128   2 69.4 83343 151.1 83342 21973.22

    In this example, the subject identifiers previously marked as subjid are now in the id column; individual identifiers for observations of a single parameter are not present.

    @@ -216,15 +219,15 @@

    Converting long g your input set uses different column names. For example, if my_cleaned_data specifies age in days as aged and parameter type as type, specify each, with quotes:

    -
    head(my_cleaned_data)
-     id subjid sex    aged     type measurement                  gcr_result
-1: 1510 775155   0     889 HEIGHTCM       84.90 Exclude-Extraneous-Same-Day
-2: 1511 775155   0     889 HEIGHTCM       89.06                     Include
-3: 1518 775155   0     889 WEIGHTKG       13.10                     Include
-4: 1512 775155   0    1071 HEIGHTCM       92.50                     Include
-5: 1519 775155   0    1071 WEIGHTKG       14.70                     Include
-6: 1513 775155   0    1253 HEIGHTCM       96.20                     Include
-longwide(my_cleaned_data, agedays = "aged", param = "type")
    +
    head(my_cleaned_data)
+     id subjid sex    aged     type measurement                  gcr_result
+1: 1510 775155   0     889 HEIGHTCM       84.90 Exclude-Extraneous-Same-Day
+2: 1511 775155   0     889 HEIGHTCM       89.06                     Include
+3: 1518 775155   0     889 WEIGHTKG       13.10                     Include
+4: 1512 775155   0    1071 HEIGHTCM       92.50                     Include
+5: 1519 775155   0    1071 WEIGHTKG       14.70                     Include
+6: 1513 775155   0    1253 HEIGHTCM       96.20                     Include
+longwide(my_cleaned_data, agedays = "aged", param = "type")

    By default, longwide() will only transform records flagged by cleangrowth() for inclusion. To include more categories assigned by cleangrowth(), use the @@ -287,32 +290,32 @@

    Computing BMI percentiles and Z- ‘Male’ for male subjects and any of ‘2’, ‘g’, ‘G’, ‘Girls’, ‘f’, ‘F’, ‘female’, or ‘Female’ for female subjects), ext_bmiz() can be called:

    -
    cleaned_data_bmiz <- ext_bmiz(cleaned_data_bmi)
-head(cleaned_data_bmiz)
-                                 subjid    agey      age   sex    wt wt_id    ht ht_id agedays      bmi      bmiz
-                                 <char>   <num>    <num> <int> <num> <int> <num> <int>   <int>    <num>     <num>
-1: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 10.0233 120.2796     2  35.4    17 141.6    15    3661 17.65537 0.3236612
-2: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 11.0390 132.4680     2  39.2    19 147.9    18    4032 17.92048 0.1734315
-3: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 12.0548 144.6576     2  44.8    21 155.1    20    4403 18.62320 0.1832443
-4: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 12.5914 151.0968     2  47.8    23 158.7    22    4599 18.97903 0.1829183
-5: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 13.0705 156.8460     2  50.5    26 160.8    24    4774 19.53077 0.2586449
-6: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad  3.9288  47.1456     2  16.6     2 102.6     1    1435 15.76933 0.3453978
-       bmip       waz       wp       haz       hp      p95      p97   bmip95   mod_bmiz   mod_waz   mod_haz
-      <num>     <num>    <num>     <num>    <num>    <num>    <num>    <num>      <num>     <num>     <num>
-1: 62.69027 0.3498817 63.67862 0.5140553 69.63933 22.96109 24.57902 76.89254 0.18485501 0.2399201 0.5008944
-2: 56.88438 0.2311645 59.14065 0.5002225 69.15408 24.13836 25.90525 74.24067 0.09543668 0.1556259 0.4955022
-3: 57.26968 0.3237374 62.69316 0.4803298 68.45036 25.26981 27.17179 73.69745 0.10065274 0.2201655 0.4855100
-4: 57.25689 0.3812700 64.84986 0.5153244 69.68368 25.83904 27.80781 73.45100 0.10011666 0.2596479 0.5212281
-5: 60.20454 0.4440465 67.14955 0.4849566 68.61464 26.32757 28.35405 74.18371 0.14353771 0.3024342 0.4885546
-6: 63.51023 0.4369963 66.89430 0.5348018 70.36065 18.02950 18.60078 87.46409 0.24462581 0.3332011 0.5224816
-      sigma original_bmip original_bmiz sev_obese obese
-      <num>         <num>         <num>     <int> <int>
-1: 4.443536      62.69027     0.3236612         0     0
-2: 4.797031      56.88438     0.1734315         0     0
-3: 5.148292      57.26968     0.1832443         0     0
-4: 5.332930      57.25689     0.1829183         0     0
-5: 5.497248      60.20454     0.2586449         0     0
-6: 2.274792      63.51023     0.3453978         0     0
    +
    cleaned_data_bmiz <- ext_bmiz(cleaned_data_bmi)
+head(cleaned_data_bmiz)
+                                 subjid    agey      age   sex    wt wt_id    ht ht_id agedays      bmi      bmiz
+                                 <char>   <num>    <num> <int> <num> <int> <num> <int>   <int>    <num>     <num>
+1: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 10.0233 120.2796     2  35.4    17 141.6    15    3661 17.65537 0.3236612
+2: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 11.0390 132.4680     2  39.2    19 147.9    18    4032 17.92048 0.1734315
+3: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 12.0548 144.6576     2  44.8    21 155.1    20    4403 18.62320 0.1832443
+4: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 12.5914 151.0968     2  47.8    23 158.7    22    4599 18.97903 0.1829183
+5: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad 13.0705 156.8460     2  50.5    26 160.8    24    4774 19.53077 0.2586449
+6: 001aa16d-bf0e-a077-3b3d-5ab8b58545ad  3.9288  47.1456     2  16.6     2 102.6     1    1435 15.76933 0.3453978
+       bmip       waz       wp       haz       hp      p95      p97   bmip95   mod_bmiz   mod_waz   mod_haz
+      <num>     <num>    <num>     <num>    <num>    <num>    <num>    <num>      <num>     <num>     <num>
+1: 62.69027 0.3498817 63.67862 0.5140553 69.63933 22.96109 24.57902 76.89254 0.18485501 0.2399201 0.5008944
+2: 56.88438 0.2311645 59.14065 0.5002225 69.15408 24.13836 25.90525 74.24067 0.09543668 0.1556259 0.4955022
+3: 57.26968 0.3237374 62.69316 0.4803298 68.45036 25.26981 27.17179 73.69745 0.10065274 0.2201655 0.4855100
+4: 57.25689 0.3812700 64.84986 0.5153244 69.68368 25.83904 27.80781 73.45100 0.10011666 0.2596479 0.5212281
+5: 60.20454 0.4440465 67.14955 0.4849566 68.61464 26.32757 28.35405 74.18371 0.14353771 0.3024342 0.4885546
+6: 63.51023 0.4369963 66.89430 0.5348018 70.36065 18.02950 18.60078 87.46409 0.24462581 0.3332011 0.5224816
+      sigma original_bmip original_bmiz sev_obese obese
+      <num>         <num>         <num>     <int> <int>
+1: 4.443536      62.69027     0.3236612         0     0
+2: 4.797031      56.88438     0.1734315         0     0
+3: 5.148292      57.26968     0.1832443         0     0
+4: 5.332930      57.25689     0.1829183         0     0
+5: 5.497248      60.20454     0.2586449         0     0
+6: 2.274792      63.51023     0.3453978         0     0

    The output columns include:

    diff --git a/docs/authors.html b/docs/authors.html index 49fbcb39..0b4da03e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/index.html b/docs/index.html index ec278bf6..49211d6f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -34,7 +34,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -83,6 +83,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • diff --git a/docs/news/index.html b/docs/news/index.html index 2534ae67..e5c77e64 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference @@ -88,6 +91,13 @@

    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

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 53be6f20..dcb87f3e 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.19.2 +pandoc: 3.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: @@ -9,8 +9,9 @@ articles: large-data-sets: large-data-sets.html next-steps: next-steps.html output: output.html + prelim-infants-algorithm: prelim-infants-algorithm.html quickstart: quickstart.html usage: usage.html utilities: utilities.html -last_built: 2023-03-13T17:25Z +last_built: 2023-09-13T14:53Z diff --git a/docs/reference/CDCref_d.html b/docs/reference/CDCref_d.html index 25da7942..8cc180d8 100644 --- a/docs/reference/CDCref_d.html +++ b/docs/reference/CDCref_d.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0
    @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/acf_answers.html b/docs/reference/acf_answers.html index 663e603b..4cf76465 100644 --- a/docs/reference/acf_answers.html +++ b/docs/reference/acf_answers.html @@ -18,7 +18,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -63,6 +63,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/adjustcarryforward.html b/docs/reference/adjustcarryforward.html index 87680c73..172c45da 100644 --- a/docs/reference/adjustcarryforward.html +++ b/docs/reference/adjustcarryforward.html @@ -23,7 +23,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -68,6 +68,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/bmianthro.html b/docs/reference/bmianthro.html index 74319d28..4d685a75 100644 --- a/docs/reference/bmianthro.html +++ b/docs/reference/bmianthro.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/cleangrowth.html b/docs/reference/cleangrowth.html index 0b35e97d..5818b201 100644 --- a/docs/reference/cleangrowth.html +++ b/docs/reference/cleangrowth.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference @@ -120,7 +123,7 @@

    Clean growth measurements

    adult_cutpoint = 20, weight_cap = Inf, adult_columns_filename = "", - infants = FALSE + prelim_infants = FALSE ) @@ -275,8 +278,8 @@

    Arguments

    for post-analysis. For more information on this output, please see README.

    -
    infants
    -

    TRUE/FALSE. Run the beta-release of the infants algorithm (expands pediatric algorithm to clean 0 - 2). Defaults to FALSE.

    +
    prelim_infants
    +

    TRUE/FALSE. Run the in-development release of the infants algorithm (expands pediatric algorithm to improve performance for children 0 – 2 years). Not recommended for use in research. For more information regarding the logic of the algorithm, see the vignette 'Preliminary Infants Algorithm.' Defaults to FALSE.

    diff --git a/docs/reference/ewma.html b/docs/reference/ewma.html index 3eb48c6a..acf54758 100644 --- a/docs/reference/ewma.html +++ b/docs/reference/ewma.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0
    @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/ext_bmiz.html b/docs/reference/ext_bmiz.html index ae6d3bd6..c8cf2dad 100644 --- a/docs/reference/ext_bmiz.html +++ b/docs/reference/ext_bmiz.html @@ -22,7 +22,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -67,6 +67,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/growth_cdc_ext.html b/docs/reference/growth_cdc_ext.html index 5f613c6d..29952d9a 100644 --- a/docs/reference/growth_cdc_ext.html +++ b/docs/reference/growth_cdc_ext.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/index.html b/docs/reference/index.html index a409c56f..0456d281 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/lenanthro.html b/docs/reference/lenanthro.html index 38a315b3..199f31c2 100644 --- a/docs/reference/lenanthro.html +++ b/docs/reference/lenanthro.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/longwide.html b/docs/reference/longwide.html index 0909e9e3..7b4760f0 100644 --- a/docs/reference/longwide.html +++ b/docs/reference/longwide.html @@ -19,7 +19,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -64,6 +64,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/nhanes-reference-medians.html b/docs/reference/nhanes-reference-medians.html index 5c875b13..c54e458d 100644 --- a/docs/reference/nhanes-reference-medians.html +++ b/docs/reference/nhanes-reference-medians.html @@ -18,7 +18,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -63,6 +63,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/read_anthro.html b/docs/reference/read_anthro.html index 5bc801b5..358a1d21 100644 --- a/docs/reference/read_anthro.html +++ b/docs/reference/read_anthro.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference @@ -94,7 +97,7 @@

    Function to calculate z-scores and csd-scores based on anthro tables.

    - 
    read_anthro(path = "", cdc.only = FALSE, infants = FALSE)
    + 
    read_anthro(path = "", cdc.only = FALSE, prelim_infants = FALSE)
    @@ -107,8 +110,8 @@

    Arguments

    Whether or not only CDC data should be used. Defaults to false.

    -
    infants
    -

    boolean on if beta infants version is being used. will be merged in to main algorithm.

    +
    prelim_infants
    +

    TRUE/FALSE. Run the in-development release of the infants algorithm (expands pediatric algorithm to improve performance for children 0 – 2 years). Not recommended for use in research. For more information regarding the logic of the algorithm, see the vignette 'Preliminary Infants Algorithm.' Defaults to FALSE.

    diff --git a/docs/reference/recode_sex.html b/docs/reference/recode_sex.html index 06f5b597..1dde31d8 100644 --- a/docs/reference/recode_sex.html +++ b/docs/reference/recode_sex.html @@ -18,7 +18,7 @@ growthcleanr - 2.1.1 + 2.2.0
    @@ -63,6 +63,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/sd_median.html b/docs/reference/sd_median.html index d3ef2ca5..a659e553 100644 --- a/docs/reference/sd_median.html +++ b/docs/reference/sd_median.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/simple_bmi.html b/docs/reference/simple_bmi.html index c04d2f53..4ae274ca 100644 --- a/docs/reference/simple_bmi.html +++ b/docs/reference/simple_bmi.html @@ -18,7 +18,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -63,6 +63,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/splitinput.html b/docs/reference/splitinput.html index a5cd2398..4ff94ec5 100644 --- a/docs/reference/splitinput.html +++ b/docs/reference/splitinput.html @@ -21,7 +21,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -66,6 +66,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/syngrowth.html b/docs/reference/syngrowth.html index 01b0c010..dd4038c3 100644 --- a/docs/reference/syngrowth.html +++ b/docs/reference/syngrowth.html @@ -19,7 +19,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -64,6 +64,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/tanner_ht_vel.html b/docs/reference/tanner_ht_vel.html index 4a94e9ed..a108b9b8 100644 --- a/docs/reference/tanner_ht_vel.html +++ b/docs/reference/tanner_ht_vel.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/tanner_ht_vel_with_2sd.html b/docs/reference/tanner_ht_vel_with_2sd.html index 57afa61e..bed09a29 100644 --- a/docs/reference/tanner_ht_vel_with_2sd.html +++ b/docs/reference/tanner_ht_vel_with_2sd.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/test_syngrowth_sas_output_compare.html b/docs/reference/test_syngrowth_sas_output_compare.html index 742fa140..5ee61a13 100644 --- a/docs/reference/test_syngrowth_sas_output_compare.html +++ b/docs/reference/test_syngrowth_sas_output_compare.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/test_syngrowth_wide.html b/docs/reference/test_syngrowth_wide.html index b108b1bb..a2b77ce9 100644 --- a/docs/reference/test_syngrowth_wide.html +++ b/docs/reference/test_syngrowth_wide.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/testacf.html b/docs/reference/testacf.html index 613eae99..569d3726 100644 --- a/docs/reference/testacf.html +++ b/docs/reference/testacf.html @@ -20,7 +20,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -65,6 +65,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/weianthro.html b/docs/reference/weianthro.html index e2ac4690..c29bdf7c 100644 --- a/docs/reference/weianthro.html +++ b/docs/reference/weianthro.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/who_ht_maxvel.html b/docs/reference/who_ht_maxvel.html index 47851509..87bf1931 100644 --- a/docs/reference/who_ht_maxvel.html +++ b/docs/reference/who_ht_maxvel.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/who_ht_maxvel_2sd.html b/docs/reference/who_ht_maxvel_2sd.html index abf89d3d..bc062d92 100644 --- a/docs/reference/who_ht_maxvel_2sd.html +++ b/docs/reference/who_ht_maxvel_2sd.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/who_ht_vel_2sd.html b/docs/reference/who_ht_vel_2sd.html index 35a0a069..da52a7b8 100644 --- a/docs/reference/who_ht_vel_2sd.html +++ b/docs/reference/who_ht_vel_2sd.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/reference/who_ht_vel_3sd.html b/docs/reference/who_ht_vel_3sd.html index 93b8969a..4d0bfa3e 100644 --- a/docs/reference/who_ht_vel_3sd.html +++ b/docs/reference/who_ht_vel_3sd.html @@ -17,7 +17,7 @@ growthcleanr - 2.1.1 + 2.2.0 @@ -62,6 +62,9 @@
  • Developer guidelines
    • +
  • + Preliminary infants algorithm +
  • Reference diff --git a/docs/sitemap.xml b/docs/sitemap.xml index e2066ded..7fe67a64 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -27,6 +27,9 @@ /articles/output.html + + /articles/prelim-infants-algorithm.html + /articles/quickstart.html