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gforge · May 14, 2014 · e556b66 · e556b66
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commit e556b66
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Showing 3 changed files with 37 additions and 30 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: comorbidities.icd10
 Type: Package
 Title: Categorizes ICD-9-CM and ICD-10 codes based on published comorbidity
     indices
-Version: 0.4
-Date: 2014-05-12
+Version: 0.5
+Date: 2014-05-14
 Author: Max Gordon
 Maintainer: Max Gordon <max@gforge.se>
 Description: Methods to categorize ICD-9-CM and ICD-10 codes into sensible
@@ -19,7 +19,8 @@ LazyLoad: yes
 URL: https://github.com/gforge/comorbidities.icd10
 BugReports: https://github.com/gforge/comorbidities.icd10/issues
 Imports:
-    plyr (>= 1.8.1)
+    plyr (>= 1.8.1),
+    stringr
 Suggests:
     testthat (>= 0.8)
 Encoding: UTF-8

diff --git a/R/peprocessors.R b/R/peprocessors.R
@@ -81,9 +81,10 @@ preproc.Swedich.ICD9 <- function(icd, icd_ver){
                 substr(icd, 1, 4),
                 icd)
 
-  # Return the icd_version info as this may be used
+    # Return the icd_version info as this may be used
   # for other purposes and save time
   attr(icd, "icd_ver") <- icd_ver
+
   return(icd)
 }
 
@@ -105,10 +106,12 @@ preproc.Swedich.ICD9 <- function(icd, icd_ver){
 #' @export
 #' @family preprocessor functions
 preproc.strip.dot <- function(icd, icd_ver){
-  if (is.data.frame(codes)) {codes <- as.matrix(codes)}
+  if (is.data.frame(icd)) {icd <- as.matrix(icd)}
 
-  icd <- gsub(".", "", codes, fixed=TRUE)
-  attr(icd, "icd_ver") <- icd_ver
+  icd <- gsub(".", "", icd, fixed=TRUE)
+  if (!missing(icd_ver)){
+    attr(icd, "icd_ver") <- icd_ver
+  }
   return(icd)
 }
 
@@ -140,11 +143,14 @@ preproc.code.splitter <- function(icd, icd_ver,
                                   trim = TRUE){
   if (trim){ icd <- str_trim(icd) }
   code_list <- strsplit(icd, split_str)
-  # Convert the icd_versions to match to the split strings
-  times <- sapply(code_list, length)
-  icd_ver <- rep(icd_ver, times=times)
-
   icd <- unlist(code_list)
-  attr(icd, "icd_ver") <- icd_ver
+
+  if (!missing(icd_ver)){
+    # Convert the icd_versions to match to the split strings
+    times <- sapply(code_list, length)
+    icd_ver <- rep(icd_ver, times=times)
+    attr(icd, "icd_ver") <- icd_ver
+  }
+
   return(icd)
 }
diff --git a/tests/testthat/test-preproc.R b/tests/testthat/test-preproc.R
@@ -37,23 +37,23 @@ test_that("code_splitter", {
 
 
 test_that("Check Swedish ICD-9 translator",{
-  expect_equal(preproc.Swedich.ICD9("456A"), "4560")
-  expect_equal(preproc.Swedich.ICD9("456X"), "4569")
+  expect_equivalent(preproc.Swedich.ICD9("456A"), "4560")
+  expect_equivalent(preproc.Swedich.ICD9("456X"), "4569")
   expect_error(preproc.Swedich.ICD9("3133"),
                info="If no letter at the fourth position there is an error")
   expect_error(preproc.Swedich.ICD9("313M"),
                info="M is not a valid letter at the fourth position and should give an error")
 
-  expect_equal(preproc.Swedich.ICD9(c("456A", "873B")),
-               c("4560", "8731"))
+  expect_equivalent(preproc.Swedich.ICD9(c("456A", "873B")),
+                    c("4560", "8731"))
 
 
-  expect_equal(preproc.Swedich.ICD9(c("456a", "873b")),
-               c("4560", "8731"))
+  expect_equivalent(preproc.Swedich.ICD9(c("456a", "873b")),
+                    c("4560", "8731"))
 
-  expect_equal(preproc.Swedich.ICD9(icd=c("456a", "873b", "M161"),
-                                    icd_ver=c(9,9,10)),
-               c("4560", "8731", "M161"))
+  expect_equivalent(preproc.Swedich.ICD9(icd=c("456a", "873b", "M161"),
+                                         icd_ver=c(9,9,10)),
+                    c("4560", "8731", "M161"))
 
   expect_error(preproc.Swedich.ICD9(icd=c("456a", "873b", "M161"),
                                     icd_ver=c(9,9,9)),
@@ -62,14 +62,14 @@ test_that("Check Swedish ICD-9 translator",{
   expect_error(preproc.Swedich.ICD9(icd=c("456a", "873b", "M161"),
                                     icd_ver=c(9,9)), 
                info="The funciton should complain if there is a mismatch between ICD-codes and the true value")
-
-  expect_equal(preproc.Swedich.ICD9(icd=c("456a", "873b", "M161"),
-                                    icd_ver=c(9,9,FALSE)),
-               c("4560", "8731", "M161"))
-
-  expect_equal(preproc.Swedich.ICD9(icd=c("456a", "873b", "M161"),
-                                    icd_ver=FALSE),
-               c("4560", "8731", "M161"))
+  
+  expect_equivalent(preproc.Swedich.ICD9(icd=c("456a", "873b", "M161"),
+                                         icd_ver=c(9,9,FALSE)),
+                    c("4560", "8731", "M161"))
+  
+  expect_equivalent(preproc.Swedich.ICD9(icd=c("456a", "873b", "M161"),
+                                         icd_ver=FALSE),
+                    c("4560", "8731", "M161"))
 })
 
 test_that("Advanced Swedish pre-processor test",{
@@ -90,7 +90,7 @@ test_that("Advanced Swedish pre-processor test",{
       icd <- preproc.code.splitter(icd, icd_ver)
       preproc.Swedich.ICD9(icd, attr(icd, "icd_ver"))
     }
-
+  
   # The most important part is that this passes
   expect_true(is.list(cmrbdt.calc(swe_test_df, 
                                   id_column="ID", icd_columns=c("MainICD", "CoICD"),