CUD2V · magic-lantern · May 14, 2025 · Apr 16, 2025 · Apr 16, 2025 · May 6, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -11,3 +11,5 @@
 ^cran-comments\.md$
 ^CRAN-RELEASE$
 ^\.github$
+^inst/icd/2017
+^inst/icd/2018
diff --git a/.gitignore b/.gitignore
@@ -29,3 +29,4 @@ vignettes/*.pdf
 *.swo
 .Rproj.user
 inst/doc
+.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pccc
 Title: Pediatric Complex Chronic Conditions
-Version: 1.0.5.9000
+Version: 1.0.6
 Authors@R: c(
     person(given = "Peter", family = "DeWitt",    email = "[email protected]",             role = c("aut"),        comment = c(ORCID = "0000-0002-6391-0795")),
     person(given = "Tell",  family = "Bennett",   email = "[email protected]",    role = c("ctb"),        comment = c(ORCID = "0000-0003-1483-4236")),
@@ -12,6 +12,7 @@ Description: An implementation of the pediatric complex chronic conditions (CCC)
 Depends: R (>= 3.5.0)
 License: GPL-2
 Encoding: UTF-8
+Language: en-us
 LazyData: true
 Imports:
     dplyr (>= 1.0.0),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,19 @@
-# Version 1.0.5.9000
+# Version 1.0.6
+
+## Bug fixes
+
+* Code fixes -- most of these codes were flagging transplant but not the primary organ system; these were present in original publication but missing from this package
+    * 996.83 added to CVD - it was flagging transplant but not CVD
+    * 996.84 added to respiratory
+    * 996.81 added to renal
+    * 996.82, 996.86, 996.87 added to gi
+    * ICD10 codes added to CVD: T86.20, T86.21, T86.22
+    * M4330 is not a valid code, corrected to M433 (impacts congeni_genetic)
+    * Add Z94.0 to transplant
+
+## Extenstions
+* Update old urls and adding some links to wayback machine snapshots
+* Add key files to the package for reference
 
 ## New functions:
 * S3 method `as_tibble.pccc_codes` has been added to the package to replace the

diff --git a/R/data.R b/R/data.R
@@ -4,7 +4,7 @@
 #' \url{https://github.com/magic-lantern/icd_file_generator}. ICD codes were taken
 #' from CMS.  The ICD 9 diagnosis and procedure codes were generated with 20%
 #' missing values. Code source:
-#' \url{https://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html}
+#' \url{https://www.cms.gov/medicare/coding-billing/icd-10-codes/icd-9-cm-diagnosis-procedure-codes-abbreviated-and-full-code-titles}
 #'
 #' @format A data frame with 1000 rows and 31 variables.
 #' There is a patient identifier, ten diagnosis codes, ten procedure codes, and
@@ -51,8 +51,11 @@
 #' This dataset was produced from a tool available at
 #' \url{https://github.com/magic-lantern/icd_file_generator}. ICD codes were taken
 #' from CMS.  The code source, for both the diagnosis and produced codes can be
-#' found at \url{https://www.cms.gov/Medicare/Coding/ICD10/2017-ICD-10-CM-and-GEMs.html}
-#'
+#' found at
+#' \url{https://www.cms.gov/medicare/coding-billing/icd-10-codes/icd-10-cm-icd-10-pcs-gem-archive}
+#' with a copy of the downloaded data on the package github page,
+#' \url{https://github.com/CUD2V/pccc}
+#' 
 #' @format A data frame with 1000 rows and 31 variables.
 #' There is a patient identifier, ten diagnosis codes, ten procedure codes, and
 #' ten "other data" values, specifically:

diff --git a/R/pccc-package.R b/R/pccc-package.R
@@ -15,15 +15,15 @@
 #' For ease, a copy of the paper is included in this package.  See the examples
 #' below for instructions on opening this pdf from within R or outside of R.
 #' You can view the publication online at
-#' \url{http://bmcpediatr.biomedcentral.com/articles/10.1186/1471-2431-14-199}.
+#' \doi{10.1186/1471-2431-14-199}.
 #'
 #' Feudtner et. al. provided a SAS macro and STATA program to implement the CCC.
 #' These files are also provided for reference.  See the Examples for
 #' instructions on opening these files.
 #'
 #' Lastly, the appendix tables in the file
-#' Categories_of_CCCv2_and_Corresponding_ICD.docx have also been included with
-#' this package.
+#' \code{system.file("pccc_references", "Categories_of_CCCv2_and_Corresponding_ICD.docx", package = "pccc")}
+#' have also been included with this package.
 #'
 #' @examples
 #' \dontrun{

diff --git a/README.md b/README.md
@@ -31,7 +31,7 @@ on large datasets.
 This package provides R functions to generate the CCC categories. Because the R functions
 are built with a C++ back-end, they are very computationally efficient.
 
-The pccc package version 1.0.z implimented this version of the PCCC criteria.
+The pccc package version 1.0.z implemented this version of the PCCC criteria.
 
 ### Version 3 of the PCCC Criteria
 [Pediatric Complex Chronic Condition System Version 3](https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2821158)
@@ -49,7 +49,7 @@ match the system version) will implement version 3 of the PCCC.
 ## Installation
 
 ### From CRAN
-Relased version available on The Comprehensive R Archive Network at https://CRAN.R-project.org/package=pccc.
+Released version available on The Comprehensive R Archive Network at https://CRAN.R-project.org/package=pccc.
 
 ### Developmental version
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,12 +1,15 @@
+# Version 1.0.6
+
+## Notes:
+
+* change in the email address of the package mantainer.  The ucdenver.edu domain
+  as been replaced by the cuanzchutz.edu domain
+
 ## Test environments
-* local macOS 10.14.6 install R 3.6.3
-* ubuntu 16.04 on travis-ci (oldrel, release, devel)
-* win-builder (devel, release, oldrelease)
-* r_hub
-  * Ubuntu Linux 16.04 LTS, R-release, GCC
-  * Windows Server 2008 R2 SP1, R-devel, 32/64 bit
-  * Fedora Linux, R-devel, clang, gfortran
-  * Debian Linux, R-devel, GCC ASAN/UBSAN
+* local macOS R 4.5.0
+* 
+* 
+* 
 
 ## R CMD check results
 

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -0,0 +1,34 @@
+Zhong
+Wenjun
+Cholera due to vibrio cholerae el tor
+vctrs
+rlang
+ORCID
+testthat
+Urologic
+stringsAsFactors
+STATA
+ICD
+rda
+rds
+Feudtner
+CCCs
+CMD
+CMS
+cvd
+CVD
+Dai
+CCC
+ccc
+BMC
+Dingwei
+docx
+dplyr
+github
+icd
+Kalibera
+MCOD
+AddressSanitizer
+deprecations
+Deprecations
+dystrophy
diff --git a/inst/icd/2017/2017-GEM-DC.zip b/inst/icd/2017/2017-GEM-DC.zip
diff --git a/inst/icd/2017/2017-ICD-10-CM-Conversion-Table-.zip b/inst/icd/2017/2017-ICD-10-CM-Conversion-Table-.zip
diff --git a/inst/icd/2017/2017-ICD-10-CM-Guidelines.pdf b/inst/icd/2017/2017-ICD-10-CM-Guidelines.pdf
diff --git a/inst/icd/2017/2017-ICD10-Addendum.zip b/inst/icd/2017/2017-ICD10-Addendum.zip
diff --git a/inst/icd/2017/2017-ICD10-Code-Descriptions.zip b/inst/icd/2017/2017-ICD10-Code-Descriptions.zip
diff --git a/inst/icd/2017/2017-ICD10-Code-Tables-Index.zip b/inst/icd/2017/2017-ICD10-Code-Tables-Index.zip
diff --git a/inst/icd/2017/2017-ICD10-Duplicate-Code-.zip b/inst/icd/2017/2017-ICD10-Duplicate-Code-.zip
diff --git a/inst/icd/2017/2017-ICD10-POA-Exempt.zip b/inst/icd/2017/2017-ICD10-POA-Exempt.zip
diff --git a/inst/icd/2017/screen_shot_maybackmachine_cms_2017_icd_10_cm_and_gems.png b/inst/icd/2017/screen_shot_maybackmachine_cms_2017_icd_10_cm_and_gems.png
diff --git a/inst/icd/2018/2018-ICD-10-Addendum.zip b/inst/icd/2018/2018-ICD-10-Addendum.zip
diff --git a/inst/icd/2018/2018-ICD-10-CM-Coding-Guidelines.pdf b/inst/icd/2018/2018-ICD-10-CM-Coding-Guidelines.pdf
diff --git a/inst/icd/2018/2018-ICD-10-CM-Conversion-Table.zip b/inst/icd/2018/2018-ICD-10-CM-Conversion-Table.zip
diff --git a/inst/icd/2018/2018-ICD-10-CM-Errata.pdf b/inst/icd/2018/2018-ICD-10-CM-Errata.pdf
diff --git a/inst/icd/2018/2018-ICD-10-CM-General-Equivalence-Mappings.zip b/inst/icd/2018/2018-ICD-10-CM-General-Equivalence-Mappings.zip
diff --git a/inst/icd/2018/2018-ICD-10-Code-Descriptions.zip b/inst/icd/2018/2018-ICD-10-Code-Descriptions.zip
diff --git a/inst/icd/2018/2018-ICD-10-Table-And-Index.zip b/inst/icd/2018/2018-ICD-10-Table-And-Index.zip
diff --git a/inst/icd/2018/2018-POA-Exempt-Codes.zip b/inst/icd/2018/2018-POA-Exempt-Codes.zip
diff --git a/inst/icd/2018/screen_shot_waybackmachine_cms_2018_icd_10_cm_and_gems.png b/inst/icd/2018/screen_shot_waybackmachine_cms_2018_icd_10_cm_and_gems.png
diff --git a/inst/icd/ICD9_ICD10_comparability_file_documentation.pdf b/inst/icd/ICD9_ICD10_comparability_file_documentation.pdf
diff --git a/man/pccc-package.Rd b/man/pccc-package.Rd
diff --git a/man/pccc_icd10_dataset.Rd b/man/pccc_icd10_dataset.Rd
diff --git a/man/pccc_icd9_dataset.Rd b/man/pccc_icd9_dataset.Rd
diff --git a/src/pccc.cpp b/src/pccc.cpp
@@ -25,18 +25,26 @@ codes::codes(int v)
       "74781","74789","9960","9961","99661","99662","V421","V422","V432","V433","V450","V4581",
       "V533"};
 
-    dx_fixed_cvd = {"416"};
+    dx_fixed_cvd = {"416",
+      "99683" // transplant too
+    };
 
     dx_respiratory = {"32725","4160","4162","51630","51631","51637","51884","5190","2770","748","7704","V426",
       "V440","V4576","V460","V461","V550"};
 
-    dx_fixed_respiratory = {"5163"};
+    dx_fixed_respiratory = {"5163",
+      "99684" // transplant too
+    };
 
-    dx_renal = {"34461","585","5964","59653","59654","753","99668","V420","V445","V446",
+    dx_renal = {"34461","585","5964","59653","59654","753","99668",
+      "99681", //transplant
+      "V420","V445","V446",
       "V451","V4573","V4574","V536","V555","V556","V56"};
 
     dx_gi = {"4530","5364","555","556","5571","5602","5647","5714","5715","5716","5717",
-      "5718","5719","7503","751","V427","V4283","V4284","V441","V442","V443","V444","V5350",
+      "5718","5719","7503","751",
+      "99682", "99686", "99687", // transplant
+      "V427","V4283","V4284","V441","V442","V443","V444","V5350",
       "V5351","V5359","V551","V552","V553","V554"};
 
     dx_hemato_immu = {"042","043","044","135","279","2820","2821","2822","2823","2824","2825",
@@ -126,6 +134,25 @@ codes::codes(int v)
       "T85190A","T85192A","T85199A","T8579XA","Z982","Z4541","Z4542", "Q851"};
 
     dx_fixed_neuromusc = {"G80"};
+    // NOTE: G80 and G80.3 are listed in pccc/inst/pccc_references/Categories_of_CCCv2_and_Corresponding_ICD.docx
+    // However, it appears that during some dev work the following was
+    // determined for PCCC V2
+    // G80.0 -- include
+    // G80.1 -- include
+    // G80.2 -- exclude
+    // G80.3 -- include
+    // G80.4 -- include
+    // G80.5 -- (not a valid ICD code)
+    // G80.6 -- (not a valid ICD code)
+    // G80.7 -- (not a valid ICD code)
+    // G80.8 -- include
+    // G80.9 -- exclude
+    //
+    // For version 3, all the G80.x codes will be included
+    // See Supplement 3 from
+    // Feinstein JA, Hall M, Davidson A, Feudtner C. Pediatric Complex Chronic
+    // Condition System Version 3. JAMA Netw Open. 2024;7(7):e2420579.
+    // doi:10.1001/jamanetworkopen.2024.20579
 
     dx_cvd = {"I270","I271","I272","I2781","I2789","I279","I340","I348","I360","I368","I370",
       "I378","I42","I43","I44","I45","I47","I48","I490","I491","I493","I494","I495","I498","I499",
@@ -134,6 +161,7 @@ codes::codes(int v)
       "Z951","T82519A","T82529A","T82539A","T82599A","T82110A","T82111A","T82120A","T82121A",
       "T82190A","T82191A","T8201XA","T8202XA","T8203XA","T8209XA","T82211A","T82212A","T82213A",
       "T82218A","T82221A","T82222A","T82223A","T82228A","T82518A","T82528A","T82538A","T82598A",
+      "T8620", "T8621", "T8622",
       "T826XXA","T827XXA","Z941","Z950","Z952","Z95810","Z95811","Z95812","Z95818","Z953","Z45010",
       "Z45018","Z4502","Z4509","Z959"};
 
@@ -163,7 +191,7 @@ codes::codes(int v)
       "E830","E831","E833","E834","E88","H498","E85","E009","E230","E232","E222","E233","E237",
       "E240","E242","E243","E248","E249","E2681","E250","E258","E259","Z4681","Z794","Z9641"};
 
-    dx_congeni_genetic = {"E343","K449","M410","M412","M4130","M418","M419","M4330","M965","Q722","Q750",
+    dx_congeni_genetic = {"E343","K449","M410","M412","M4130","M418","M419","M433","M965","Q722","Q750",
       "Q752","Q759","Q760","Q761","Q762","Q764","Q765","Q766","Q767","Q77","Q780","Q781","Q782",
       "Q783","Q784","Q788","Q789","Q790","Q791","Q792","Q793","Q794","Q799","Q795","Q8740","Q8781",
       "Q8789","Q897","Q899","Q909","Q913","Q914","Q917","Q928","Q93","Q950","Q969","Q97","Q98",
@@ -195,7 +223,7 @@ codes::codes(int v)
 
     dx_transplant = {"T8600","T8601","T8602","T8609","T8610","T8611","T8612","T8620","T8621","T8622",
       "T86810","T86811","T86819","T8640","T8641","T8642","T86890","T86891","T86899","T86850",
-      "T86851","T86859","T865","T8690","T8691","T8692","T8699"};
+      "T86851","T86859","T865","T8690","T8691","T8692","T8699","Z940"};
 
     pc_neuromusc = {"0016070","0016071","0016072","0016073","0016074","0016075","0016076","0016077",
       "0016078","001607B","00160J0","00160J1","00160J2","00160J4","00160J5","00160J6","00160J7",

diff --git a/tests/icd10_test_result.rds b/tests/icd10_test_result.rds
diff --git a/tests/icd9_test_result.rds b/tests/icd9_test_result.rds
diff --git a/tests/test_ccc_icd10.R b/tests/test_ccc_icd10.R
@@ -21,7 +21,7 @@ ccc_out <- ccc(data.frame(id = letters[1:3],
 ccc_out$id <- as.factor(ccc_out$id)
 rnd_test <- readRDS("random_data_test_result.rds")
 rnd_test$id <- as.factor(rnd_test$id)
-stopifnot(all.equal(ccc_out, rnd_test))
+stopifnot(isTRUE(all.equal(ccc_out, rnd_test)))
 
 
 #test_that("icd 10 data set with all parameters - result should be unchanged.", {
@@ -33,5 +33,10 @@ df <-
       pc_cols = dplyr::starts_with("pc"),
       icdv    = 10)
 
-stopifnot(all.equal(df, readRDS("icd10_test_result.rds")))
+expected <- readRDS("icd10_test_result.rds")
 
+stopifnot(isTRUE(all.equal(df, expected)))
+
+################################################################################
+#                                 End of File                                  #
+################################################################################