Merge pull request #70 from marinak-ebi/debug-eye

Update `CategoryMap.conf` for renaming categories

Author: marinak-ebi

Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/R/main.R

@@ -106,7 +106,7 @@ mainAgeing = function(file = NULL                                    ,
   EA2LAMApping                   = read.csv(file = file.path(local(), 'EA2LA_parameter_mappings_2019-09-24.csv'))
   MetaDataList                   = read.csv(file = file.path(local(), 'metadataParameters.csv'))
   exceptionList                  = unique(c(exceptionList,MetaDataList$parameter_stable_id))
-  # CategoricalCategoryBlackList   = readFile(file = 'CategoricalCategoryBlackList.list')
+  
   # Main subdirectory/working directory
   message0('Preparing the working directory ...')
   cwd = getwd()

Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/CategoricalCategoryBlackList.list

@@ -4,9 +4,10 @@ no data for both eyes:NA
 No data:NA
 not defined:NA
 unobservable:NA
+no data left eye:NA
+no data right eye:NA
 no data left eye, present right eye:present right eye
 no data right eye, present left eye:present left eye
 no data left eye, right eye abnormal:right eye abnormal
 no data right eye, left eye abnormal:left eye abnormal
 Is_this_file_finished_with_a_new_line_question_mark:0
-

Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/CategoryMap.conf

@@ -426,3 +426,139 @@ ALTICSLA_EYE_092_003
 ALTHRWLLA_EYE_092_001
 ALTHRWLLA_EYE_092_002
 ALTHRWLLA_EYE_092_003
+HRWLLA_EYE_001_001
+HRWLLA_EYE_002_001
+HRWLLA_EYE_003_001
+HRWLLA_EYE_004_001
+HRWLLA_EYE_005_001
+HRWLLA_EYE_006_001
+HRWLLA_EYE_007_001
+HRWLLA_EYE_008_001
+HRWLLA_EYE_009_001
+HRWLLA_EYE_010_001
+HRWLLA_EYE_011_001
+HRWLLA_EYE_012_001
+HRWLLA_EYE_013_001
+HRWLLA_EYE_014_001
+HRWLLA_EYE_015_001
+HRWLLA_EYE_016_001
+HRWLLA_EYE_017_001
+HRWLLA_EYE_018_001
+HRWLLA_EYE_019_001
+HRWLLA_EYE_020_001
+HRWLLA_EYE_021_001
+HRWLLA_EYE_022_001
+HRWLLA_EYE_023_001
+HRWLLA_EYE_024_001
+HRWLLA_EYE_025_001
+HRWLLA_EYE_026_001
+HRWLLA_EYE_027_001
+HRWLLA_EYE_080_001
+HRWLLA_EYE_081_001
+HRWLLA_EYE_082_001
+HRWLLA_EYE_083_001
+HRWLLA_EYE_084_001
+HRWLLA_EYE_085_001
+HRWLLA_EYE_086_001
+JAXLA_EYE_001_001
+JAXLA_EYE_002_001
+JAXLA_EYE_003_001
+JAXLA_EYE_004_001
+JAXLA_EYE_005_001
+JAXLA_EYE_006_001
+JAXLA_EYE_007_001
+JAXLA_EYE_008_001
+JAXLA_EYE_009_001
+JAXLA_EYE_010_001
+JAXLA_EYE_011_001
+JAXLA_EYE_012_001
+JAXLA_EYE_013_001
+JAXLA_EYE_014_001
+JAXLA_EYE_015_001
+JAXLA_EYE_016_001
+JAXLA_EYE_017_001
+JAXLA_EYE_018_001
+JAXLA_EYE_019_001
+JAXLA_EYE_020_001
+JAXLA_EYE_021_001
+JAXLA_EYE_022_001
+JAXLA_EYE_023_001
+JAXLA_EYE_024_001
+JAXLA_EYE_025_001
+JAXLA_EYE_026_001
+JAXLA_EYE_027_001
+JAXLA_EYE_080_001
+JAXLA_EYE_081_001
+JAXLA_EYE_082_001
+JAXLA_EYE_083_001
+JAXLA_EYE_084_001
+JAXLA_EYE_085_001
+JAXLA_EYE_086_001
+RBRCLA_EYE_001_001
+RBRCLA_EYE_002_001
+RBRCLA_EYE_003_001
+RBRCLA_EYE_004_001
+RBRCLA_EYE_005_001
+RBRCLA_EYE_006_001
+RBRCLA_EYE_007_001
+RBRCLA_EYE_008_001
+RBRCLA_EYE_009_001
+RBRCLA_EYE_010_001
+RBRCLA_EYE_011_001
+RBRCLA_EYE_012_001
+RBRCLA_EYE_013_001
+RBRCLA_EYE_014_001
+RBRCLA_EYE_015_001
+RBRCLA_EYE_016_001
+RBRCLA_EYE_017_001
+RBRCLA_EYE_018_001
+RBRCLA_EYE_019_001
+RBRCLA_EYE_020_001
+RBRCLA_EYE_021_001
+RBRCLA_EYE_022_001
+RBRCLA_EYE_023_001
+RBRCLA_EYE_024_001
+RBRCLA_EYE_025_001
+RBRCLA_EYE_026_001
+RBRCLA_EYE_027_001
+RBRCLA_EYE_080_001
+RBRCLA_EYE_081_001
+RBRCLA_EYE_082_001
+RBRCLA_EYE_083_001
+RBRCLA_EYE_084_001
+RBRCLA_EYE_085_001
+RBRCLA_EYE_086_001
+BCMLA_EYE_001_001
+BCMLA_EYE_002_001
+BCMLA_EYE_003_001
+BCMLA_EYE_004_001
+BCMLA_EYE_005_001
+BCMLA_EYE_006_001
+BCMLA_EYE_007_001
+BCMLA_EYE_008_001
+BCMLA_EYE_009_001
+BCMLA_EYE_010_001
+BCMLA_EYE_011_001
+BCMLA_EYE_012_001
+BCMLA_EYE_013_001
+BCMLA_EYE_014_001
+BCMLA_EYE_015_001
+BCMLA_EYE_016_001
+BCMLA_EYE_017_001
+BCMLA_EYE_018_001
+BCMLA_EYE_019_001
+BCMLA_EYE_020_001
+BCMLA_EYE_021_001
+BCMLA_EYE_022_001
+BCMLA_EYE_023_001
+BCMLA_EYE_024_001
+BCMLA_EYE_025_001
+BCMLA_EYE_026_001
+BCMLA_EYE_027_001
+BCMLA_EYE_080_001
+BCMLA_EYE_081_001
+BCMLA_EYE_082_001
+BCMLA_EYE_083_001
+BCMLA_EYE_084_001
+BCMLA_EYE_085_001
+BCMLA_EYE_086_001