Merge pull request #126 from mitre/fix-missing

Fix erroneous missing data and update names

DESCRIPTION

@@ -1,24 +1,24 @@
 Package: growthcleanr
 Type: Package
 Title: Data Cleaner for Anthropometric Measurements
-Version: 2.1.0
+Version: 2.1.1
 Authors@R: c(
-    person("Daymont","Carrie", email = "[email protected]", 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 = "[email protected]", role = c("ctb")),
-    person("Cao","Lusha", role = "ctb"),
-    person("Silva","Steffani", role = "ctb"),
-    person("Zhang","Hanzhe", role = "ctb"),
-    person("Boyas","Matt", role = "ctb"),
-    person("Freedman","David", role = "ctb"),
-    person("Achilleos","Andreas", role = "ctb"),
-    person("Butts","Jessica", role = "ctb"),
-    person("Nguyen","Sheila", role = "ctb"),
-    person("Soleymani","Taraneh", role = "ctb"),
-    person("Olivier","Max", role = "ctb")
+    person("Carrie", "Daymont", email = "[email protected]", role = c("ctb","cre")),
+    person("Robert", "Grundmeier", role = "aut"),
+    person("Jeffrey", "Miller", role = "aut"),
+    person("Diego", "Campos", role = "aut"),
+    person("Dan", "Chudnov", email = "[email protected]", role = "ctb"),
+    person("Hannah", "De los Santos", email = "[email protected]", role = c("ctb")),
+    person("Lusha", "Cao", role = "ctb"),
+    person("Steffani", "Silva", role = "ctb"),
+    person("Hanzhe", "Zhang", role = "ctb"),
+    person("Matt", "Boyas", role = "ctb"),
+    person("David", "Freedman", role = "ctb"),
+    person("Andreas", "Achilleos", role = "ctb"),
+    person("Jessica", "Butts", role = "ctb"),
+    person("Sheila", "Nguyen", role = "ctb"),
+    person("Taraneh", "Soleymani", role = "ctb"),
+    person("Max", "Olivier", role = "ctb")
   )
 Description: Identifies implausible anthropometric (e.g., height,
     weight) measurements in irregularly spaced longitudinal datasets, such as those from electronic health records.

NEWS.md

@@ -1,3 +1,13 @@
+# growthcleanr 2.1.1 - 2023-03-01
+
+## Changed
+
+- Fixed missing adult measurements to be labeled "Missing" in output (#119)
+- Added tests for missingness in adult output
+- Fixed missing "-RV" codes in adult output
+- Corrected contributor names in DESCRIPTION (#120)
+- Added email for Dan Chudnov in DESCRIPTION (#95)
+
 # growthcleanr 2.1.0 - 2023-02-03
 
 ## Added

R/growth.R

@@ -160,6 +160,7 @@ cleangrowth <- function(subjid,
   N <- age_years <- batch <- exclude <- index <- line <- NULL
   newbatch <- sd.median <- sd.orig <- tanner.months <- tbc.sd <- NULL
   v <- v_adult <- whoagegrp.ht <- whoagegrp_ht <- z.orig <- NULL
+  result <- NULL
 
   # preprocessing ----
 
@@ -239,8 +240,11 @@ cleangrowth <- function(subjid,
     "Include",
     "Exclude-Adult-BIV",
     "Exclude-Adult-Hundreds",
+    "Exclude-Adult-Hundreds-RV",
     "Exclude-Adult-Unit-Errors",
+    "Exclude-Adult-Unit-Errors-RV",
     "Exclude-Adult-Transpositions",
+    "Exclude-Adult-Transpositions-RV",
     "Exclude-Adult-Weight-Cap-Identical",
     "Exclude-Adult-Weight-Cap",
     "Exclude-Adult-Swapped-Measurements",
@@ -249,6 +253,7 @@ cleangrowth <- function(subjid,
     "Exclude-Adult-Distinct-Pairs",
     "Exclude-Adult-Distinct-3-Or-More",
     "Exclude-Adult-EWMA-Extreme",
+    "Exclude-Adult-EWMA-Extreme-RV",
     "Exclude-Adult-Distinct-Ordered-Pairs",
     "Exclude-Adult-EWMA-Moderate",
     "Exclude-Adult-Possibly-Impacted-By-Weight-Cap",
@@ -652,8 +657,13 @@ cleangrowth <- function(subjid,
         .paropts = list(.packages = "data.table"),
         weight_cap = weight_cap
       )
+
+      res <- as.data.table(res)
     }
 
+    # replace result with missing if measurement or agedays are missing
+    res[is.na(measurement) | agedays < 0, result := "Missing"]
+
     if (parallel){
       stopCluster(cl)
     }

cran-comments.md

@@ -1,3 +1,13 @@
+# CRAN submission growthcleanr 2.1.1
+
+## 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 2.1.0
 
 ## R CMD check results
@@ -19,8 +29,6 @@ We have addressed each of the notes in the manual test as below:
 
 We have updated the citation accordingly.
 
-# Previous Submissions
-
 # CRAN submission growthcleanr 2.1.0 (1)
 
 ## R CMD check results