Resolved merge conflicts in generated docs, refs carriedaymont#98

mitre · Feb 1, 2023 · 9e0ae59 · 9e0ae59
2 parents 36b3d8e + cf71b00
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,13 +1,23 @@
-# CRAN submission growthcleanr 2.0.2 (1)
+# CRAN submission growthcleanr 2.0.3
 
 ## R CMD check results
 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
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html