JSS article, benchmarks, test improvements, documentation improvements

.Rbuildignore

@@ -1,7 +1,8 @@
 ^_config\.yml$
 aclocal\.m4$
-IGNORE.*_alt\.[Rr]$
-IGNORE.*_alt\.cpp$
+IGNORE.*_alt.*\.[Rr]$
+IGNORE.*_alt.*\.cpp$
+IGNORE.*_alt.h$
 ^appveyor\.yml$
 \.aspell$
 autom4te\.cache$
@@ -25,9 +26,8 @@ cran-comments\.md$
 .*\.gcov$
 ^\.git/.*
 ^data\/icd10_who.*$
-data-raw
-^data-raw\/.*$
-^deprecated-tests$
+^inst\/data-raw\/.*$
+^docs$
 ^Efficient.*\.md$
 icd.*\.aux$
 icd.*\.so$
@@ -56,9 +56,16 @@ standalone\/.*
 scrape_icd10_who
 ^\.settings$
 .*standalone.*
+^tests-slow$
+^tests-build$
+^tests-deprecated$
 ^todo$
 ^tools$
 ^\.travis\.yml$
 ^vignettes\/jss\.bst$
 ^vignettes\/jss\.cls$
+^vignettes\/.*_files$
+^vignettes\/.*_latexmk$
+^vignettes\/.*\.dvi$
+^vignettes\/.*\.fls$
 ^.*\.xcworkspace$

.Rinstignore

@@ -7,5 +7,4 @@ man\/icd9cm_generate_chapters_hierarchy
 man\/icd_update_everything
 man\/parse_leaf_descriptions_all
 man\/parse_leaf_desc_icd9cm_v27
-R\/benchmark\.R
 

.covrignore

@@ -1,6 +1,9 @@
 inst/include/icd_RcppExports.h
+src/RcppExports.cpp
+R/RcppExports.R
 R/parse-icd10cm-xml.R
 R/fuzz.R
 R/*_alt.R
-src/*_alt.cpp
+src/*_alt*.cpp
+src/*.h
 

.gitignore

@@ -15,6 +15,7 @@ conftest.err
 *.dll
 .DS_Store
 .externalToolBuilders
+*.gcno
 i9test.RData
 icd\.Rcheck
 icd_*.tar.gz

.travis.yml

@@ -9,33 +9,49 @@ language: r
 sudo: false
 cache: packages
 
-addons:
-  apt:
-    packages:
-      - r-cran-rodbc
-      - unixodbc-dev
+# duplicate what's in DESCRIPTION
+r_binary_packages:
+  - checkmate
+  - magrittr
+  - Rcpp
+  - stringr
+  - testthat
 
-r:
-  - oldrel
-  - release
-  - devel
-
-matrix:
-  allow_failures:
-    - r: oldrel
-
-repos:
-  CRAN: https://cloud.r-project.org
+r_packages:
+  - knitr
+  - roxygen2
+  - rmarkdown
 
 r_github_packages:
   - jimhester/covr
   - jimhester/lintr
 
+r:
+  - devel
+  - release
+  - oldrel
+
+cran: https://cloud.r-project.org
+
 warnings_are_errors: true
 
 env:
-  - LINTR_COMMENT_BOT=false ICD_STRIP=false OMP_NUM_THREADS=1 CFLAGS="-O0 -Werror -Wall -Wextra -pedantic -Wno-unused-parameter -Wno-unused-variable" CXXFLAGS="-O0 -Werror -Wall -Wextra -pedantic -Wno-unused-parameter -Wno-unused-variable" R_CHECK_CRAN_INCOMING_=FALSE _R_CHECK_FORCE_SUGGESTS_=FALSE
-  - LINTR_COMMENT_BOT=true ICD_STRIP=true OMP_NUM_THREADS=2 CFLAGS="-O3 -march=native" CXXFLAGS="-O3 -march=native" R_CHECK_CRAN_INCOMING_=FALSE _R_CHECK_FORCE_SUGGESTS_=FALSE
+  global:
+    - R_CHECK_CRAN_INCOMING_=FALSE _R_CHECK_FORCE_SUGGESTS_=FALSE
+    - LINTR_COMMENT_BOT=false
+    - ICD_COVERAGE=false
+  matrix:
+    - OMP_NUM_THREADS=1 CFLAGS="-Og -Werror -Wall -Wextra -pedantic" CXXFLAGS="-Og -Werror -Wall -Wextra -pedantic"
+    - OMP_NUM_THREADS=2 CFLAGS="-O3 -march=native" CXXFLAGS="-O3 -march=native"
+
+matrix:
+  fast_finish: true
+  include:
+  - env: LINTR_COMMENT_BOT=true
+  - env: ICD_COVERAGE=true ICD_TEST_DEPRECATED=true ICD_TEST_BUILD_DATA=true ICD_TEST_SLOW=true
+  allow_failures:
+  - r: oldrel
+  - env: ICD_COVERAGE=true ICD_TEST_DEPRECATED=true ICD_TEST_BUILD_DATA=true ICD_TEST_SLOW=true
 
 before_script:
  - ls -aR
@@ -48,7 +64,8 @@ before_script:
 after_success:
  - ls -aR
  - cat ./icd.Rcheck/tests/test-all.Rout
- - Rscript -e "covr::codecov(quiet = FALSE)"
+ - if [ "$ICD_COVERAGE" = "true" ]; then
+     Rscript -e "covr::codecov(quiet = FALSE)"; fi
  - Rscript -e "lintr::lint_package()"
 
 notifications:

DESCRIPTION

@@ -1,13 +1,14 @@
 Package: icd
 Title: Tools for Working with ICD-9 and ICD-10 Codes, and
     Finding Comorbidities
-Version: 3.0.0
-Date: 2018-04-20
+Version: 3.1.2
+Date: 2018-05-05
 Authors@R: 
     c(person(given = "Jack O.",
              family = "Wasey",
              role = c("aut", "cre", "cph"),
-             email = "jack@jackwasey.com"),
+             email = "jack@jackwasey.com",
+             comment = c(ORCID = "0000-0003-3738-4637")),
       person(given = "William",
              family = "Murphy",
              role = "ctb",
@@ -38,12 +39,12 @@ Maintainer: Jack O. Wasey <jack@jackwasey.com>
 Description: Calculate comorbidities, Charlson scores, perform
     fast and accurate validation, conversion, manipulation, filtering and
     comparison of ICD-9 and ICD-10 codes. This package enables a work flow
-    from raw lists of ICD codes in hospital billing databases to
+    from raw lists of ICD codes in hospital databases to
     comorbidities. ICD-9 and ICD-10 comorbidity mappings from Quan (Deyo
     and Elixhauser versions), Elixhauser and AHRQ included.  Common
     ambiguities and code formats are handled.
 License: GPL-3
-URL: https://github.com/jackwasey/icd
+URL: https://jackwasey.github.io/icd/
 BugReports: https://github.com/jackwasey/icd/issues
 Depends:
     R (>= 3.4)
@@ -58,8 +59,9 @@ Suggests:
     RODBC,
     roxygen2 (>= 5.0.0),
     rmarkdown,
+    rticles,
     stringr,
-    testthat,
+    testthat (>= 0.11.1),
     xml2
 LinkingTo:
     Rcpp,
@@ -75,53 +77,3 @@ Copyright: See file (inst/)COPYRIGHTS
 LazyData: true
 LazyDataCompression: xz
 RoxygenNote: 6.0.1
-Collate: 
-    'RcppExports.R'
-    'as_char_no_warn.R'
-    'attr.R'
-    'catch-routine-registration.R'
-    'children.R'
-    'children_alt.R'
-    'convert.R'
-    'class.R'
-    'comorbid.R'
-    'comorbid_alt.R'
-    'condense.R'
-    'datadocs.R'
-    'diff_comorbid.R'
-    'env.R'
-    'explain-table.R'
-    'explain.R'
-    'factor_nosort.R'
-    'filter.R'
-    'generate_mappings.R'
-    'generate_spelling.R'
-    'generate_sysdata.R'
-    'guess.R'
-    'hcc.R'
-    'icd-package.R'
-    'manip.R'
-    'parse-ahrq-ccs.R'
-    'parse-comorbid.R'
-    'parse-icd10.R'
-    'parse-icd10cm-xml.R'
-    'parse-rtf.R'
-    'parse.R'
-    'parse_hcc.R'
-    'print.icd_comorbidity_map.R'
-    'ranges.R'
-    'ranges_alt.R'
-    'real.R'
-    'sas.R'
-    'save_in_data_dir.R'
-    'score.R'
-    'sort.R'
-    'sort_alt.R'
-    'to_data_raw.R'
-    'unzip_single.R'
-    'util-file.R'
-    'util-test.R'
-    'util.R'
-    'valid.R'
-    'z-deprecated.R'
-    'zzz.R'

NAMESPACE

@@ -29,6 +29,8 @@ S3method(expand_minor,icd9)
 S3method(expand_range,character)
 S3method(expand_range,icd10cm)
 S3method(expand_range,icd9)
+S3method(expand_range_major,default)
+S3method(expand_range_major,icd10cm)
 S3method(expand_range_major,icd9)
 S3method(explain,default)
 S3method(explain,icd10)
@@ -52,13 +54,21 @@ S3method(get_invalid,comorbidity_map)
 S3method(get_invalid,default)
 S3method(get_invalid,icd10)
 S3method(get_invalid,icd9)
+S3method(get_major,icd10)
+S3method(get_major,icd9)
 S3method(get_valid,character)
 S3method(get_valid,icd10)
 S3method(get_valid,icd10cm)
 S3method(get_valid,icd9)
+S3method(get_visit_name,data.frame)
+S3method(get_visit_name,matrix)
 S3method(guess_version,character)
 S3method(guess_version,data.frame)
 S3method(guess_version,factor)
+S3method(guess_version,icd10)
+S3method(guess_version,icd10cm)
+S3method(guess_version,icd9)
+S3method(guess_version,icd9cm)
 S3method(is_billable,default)
 S3method(is_billable,icd10)
 S3method(is_billable,icd10cm)
@@ -68,6 +78,10 @@ S3method(is_defined,default)
 S3method(is_defined,icd10)
 S3method(is_defined,icd10cm)
 S3method(is_defined,icd9)
+S3method(is_major,default)
+S3method(is_major,icd10)
+S3method(is_major,icd10cm)
+S3method(is_major,icd9)
 S3method(is_valid,comorbidity_map)
 S3method(is_valid,default)
 S3method(is_valid,icd10)

NEWS.md

@@ -1,10 +1,12 @@
 # Version 3.0
- * function names without 'icd_' prefix, old names kept for compatiblity, but easier now to write `comorbid(patient_data)` and `icd::comorbid` may also be used.
- * Comorbidities for ICD-10 codes now 1.5 - 2 orders of magnitude faster using matrix multiplication to solve problem under the hood
+ * major improvement in comorbidity calculation speed using matrix multiplication behind the scenes. ICD-10 codes were slower than ICD-9 code comorbidities before, and are now 1.5 - 2 orders of magnitude faster.
  * Added AHRQ clinical condition software (CCS) classification for ICD-9 and ICD-10, thanks to Vitaly Druker, fixes #127
- * Assume C++11, which is now four years old, and enables code simplification.
- * rename all functions to remove the icd_, people can use the concise icd:: if library(icd) was not callled.
- * deprecated rarely or unused code, including %i9in% 
+ * added 'charlson' synonyms for 'quan_deyo', e.g. Charlson comorbidities can now be found using `comorbid_charlson(patient_data)`
+ * Added AHRQ clinical condition software (CCS) classification for ICD-9 and ICD-10, thanks to Vitaly Druker, fixes #127
+ * function names have lost the 'icd_' prefix, old names kept for compatiblity, but easier now to write `comorbid(patient_data)`, and `icd::comorbid` may also be used, and which many consider good practice.
+ * Assume C++11, which is now four years old, enabling code simplification
+ * rename all functions to remove the icd_, people can use the concise icd:: if library(icd) was not callled
+ * deprecated rarely or unused code, including %i9in%
 
 # Version 2.4.1
  * updated HCC to include 2017 data, thanks to @anobel fixes #136