Merge pull request #76 from RTIInternational/human-readable-r-func_do…

…cumentation-update Human readable r func documentation update
RTIInternational · Feb 3, 2025 · 0d41024 · 0d41024
2 parents 3d49db0 + c415be0
commit 0d41024
Show file tree

Hide file tree

Showing 37 changed files with 7,140 additions and 1,245 deletions.
diff --git a/resources/README.md b/resources/README.md
@@ -8,14 +8,14 @@
     -- Output
 
 * [human-readable-harmonized-variable-documentation/](human-readable-harmonized-variable-documentation/)
-  * [topmed-variable-documentation.md](human-readable-harmonized-variable-documentation/topmed-variable-documentation.md)
+  * [TopMED variable documentation](human-readable-harmonized-variable-documentation/generated-doc-pages/README.md)
 
-* [merged-TOPMed-harmonized-data-file](merged-TOPMed-harmonized-data-file/)
+* [merged_TOPMed_harmonized_data_file](merged_TOPMed_harmonized_data_file/)
 
 
 ### External resources
 
-* [copies-of-certain-files-from-gdrive/](copies-of-certain-files-from-gdrive/)
-* [harmonized-variable-documentation](harmonized-variable-documentation)
+* [copies_of_external_source_files](copies_of_source_files/)
+* [harmonized-variable-documentation](../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation)
   * Symbolic link to local clone of [UW-GAC/topmed-dcc-harmonized-phenotypes](https://github.com/UW-GAC/topmed-dcc-harmonized-phenotypes/tree/master/harmonized-variable-documentation).
     Clone that repo in the same directory as this repo, and the symlink should work.
diff --git a/resources/__init__.py b/resources/__init__.py
diff --git a/resources/copies_of_external_source_files/AHA_TABLES 1(Sheet1).csv b/resources/copies_of_external_source_files/AHA_TABLES 1(Sheet1).csv
@@ -0,0 +1,81 @@
+Harmonized Variable,Harmonized Variable Description,SNOMED CT ID,NINDS CDE ID,Studies Mapped,Missing Samples (%),
+AFIB,"Atrial fibrillation (0=No, 1=Yes)",49436004,C17466; C52619,ARICFraminghamMESAREGARDS,1.26,
+AGE,Age,424144002,C00008,ARICFraminghamMESAREGARDS,1.3,
+ALCOHOL,Alcohol (servings per week),896811007,C56075,ARICFraminghamMESAREGARDS,0.46,
+ANYCHOLMED,"Taking cholesterol lowering medication (0=No, 1=Yes)",-,C58967,ARICFraminghamMESAREGARDS,1.24,
+ASPIRIN,"Taking aspirin (0=No, 1=Yes)",387458008,C10463,ARICFraminghamMESAREGARDS,1.24,
+BASE_CVD,Baseline CVD,-,-,ARICFraminghamMESA,0.65,
+BASE_STROKE,"Baseline Stroke/TIA(0=No, 1=TIA, 2=Stroke)",-,-,ARICFraminghamREGARDS,-,
+BG,Blood glucose (mg/dL) (fasting and non-fasting),-,-,Framingham,1.31,
+BMI,Body mass index (kg/m2),60621009,C11131,ARICFraminghamMESAREGARDS,1.28,
+CARSTEN,"Carotid stenosis (0=No, 1=Yes)",64586002,-,ARICFraminghamMESA,0.51,
+CENSDAY,Censor day,-,-,ARICFraminghamMESA,1.56,
+CREAT,Creatinine (mg/dL),15373003,C57972,ARICFraminghamMESAREGARDS,0.95,
+CURRSMK,"Current smoking status (0=No, 1=Yes)",77176002,C10473,ARICFraminghamMESAREGARDS,1.3,
+DAYS_SINCE_EXAM1,Time to event,-,-,Framingham,1.59,
+DEATH_IND,Death indicator,-,-,ARICFraminghamMESA,1.79,
+DEATH_IND_T2,-,-,-,MESA,1.45,
+DIAB,"Diabetes(0=No, 1=Yes)",73211009,C17480,ARICFraminghamMESAREGARDS,1.32,
+DIABP,-,271650006,C01507,ARICMESAREGARDS,1.25,
+DIABP1,"PHYSICIAN DIASTOLIC BLOOD PRESSURE, FIRST (MM HG)",-,-,Framingham,1.97,
+DIABP2,"PHYSICIAN DIASTOLIC BLOOD PRESSURE, SECOND (MM HG)",-,-,Framingham,1.24,
+EDUCLEV,"Education level (1=Less than High School, 2=High School, 3=Some College, 4=College)",276031006,C00012,ARICFraminghamMESAREGARDS,1.45,
+EVENT,Event code,-,-,Framingham,-,
+EVENT_DESC,Formatted value of EVENT,-,-,Framingham,-,
+EVENT_NAME_O,-,-,-,ARICMESA,-,
+EVENT_T2_O,-,-,-,ARICMESA,1.44,
+EVENT_VAL_C,-,-,-,ARICMESA,0.8,
+FAM_INCOME,Family income,224168007,-,ARICFraminghamMESAREGARDS,0.56,
+FASTING,-,-,-,REGARDS,-,
+FASTING_12HR,-,-,-,ARIC,0.66,
+FASTING_8HR,-,-,-,ARIC,0.66,
+FASTING_BG,Fasting blood glucose (>: 8 hours) (mg/dL),271062006,C54941,FraminghamMESA,1.53,
+FH_STROKE,"Family history of stroke, Mother or Father (0=No, 1=Yes)",443877004,C20253,ARICFraminghamMESAREGARDS,0.83,
+FRUITS,Fruits (servings per week),-,C10056,ARICFraminghamREGARDS,2.65,
+GENHLTH,"General Health (Exams 5-7, 4-category)",-,-,ARICFramingham,2.63,
+GENHLTH2,"General Health (Exams 8-9, 5-category)",-,-,ARICFraminghamMESAREGARDS,1.45,
+GLUCOSE,-,-,-,ARICREGARDS,0.33,
+HDL,HDL cholesterol (mg/dL),9422000,C18146,ARICFraminghamMESAREGARDS,1.3,
+HGT_CM,Height (centimeters),1153637007,C01522,ARICFraminghamMESAREGARDS,1.28,
+HRX,"Treated for hypertension (0=No, 1=Yes)",302192008,C58930,ARICFraminghamMESAREGARDS,1.31,
+HXCVD,History of cardiovascular disease,49601007,C21869; C17477; C17479,ARICFraminghamMESAREGARDS,1.12,
+HXHRTD,History of heart disease,56265001,C21869; C17477; C17479,ARICFraminghamMESAREGARDS,0.43,
+HXMI,History of MI(REGARDS model),22298006,C0450,ARICFraminghamMESAREGARDS,1.12,
+HXMI_SR,-,22298006,C0450,REGARDS,-,
+HXPAD,-,-,-,REGARDS,-,
+HXTIA,-,-,-,REGARDS,-,
+HYPT,-,-,-,MESA,1.25,
+ID_C,-,-,-,ARIC,-,
+INSULIN,"Taking insulin (0=No, 1=Yes)",67866001,C20268,ARICFraminghamMESAREGARDS,1.24,
+LDL,-,-,-,ARICMESAREGARDS,0.83,
+LVH,Left ventricular hypertrophy on ECG,55827005,C10735,ARICFraminghamMESAREGARDS,1.29,
+MESAID,-,-,-,MESA,-,
+NONSTATIN,"Taking non-statin medication (0=No, 1=Yes)",-,-,FraminghamMESA,1.24,
+PID,UNIQUE PARTICIPANT ID,-,-,Framingham,-,
+RACE_C,Race,103579009,C00030,ARICFraminghamMESAREGARDS,-,
+REGARDS_SUBJ_ID,-,-,-,REGARDS,-,
+SEX_C,Participant gender (character),-,-,ARICFraminghamMESAREGARDS,-,
+SEX_N,"Participant gender (1=Male, 0=Female)",-,-,ARICFraminghamMESAREGARDS,-,
+SODIUM,Sodium intake (mg/day),1148504005,C54943,ARICFraminghamREGARDS,-,
+STATE,Site location (state),398070004,-,ARICFraminghamMESAREGARDS,-,
+STATIN,"Taking statin medication (0=No, 1=Yes)",315053001,C54963,ARICFraminghamMESAREGARDS,1.24,
+STATNONSTAT,"Taking statin/non-statin combination (0=No, 1=Yes)",-,-,Framingham,-,
+STROKE,-,-,-,REGARDS,-,
+STROKE10,-,-,-,REGARDS,0.33,
+STROKE - ALL CAUSE,-,-,-,REGARDS,-,
+STROKE - HEMORRHAGIC,-,-,-,REGARDS,-,
+STROKE - ISCHEMIC,-,-,-,REGARDS,-,
+SYSBP,-,386536003,C01565,ARICMESAREGARDS,1.25,
+SYSBP1,"PHYSICIAN SYSTOLIC BLOOD PRESSURE, FIRST (MM HG)",-,-,Framingham,1.97,
+SYSBP2,"PHYSICIAN SYSTOLIC BLOOD PRESSURE, SECOND (MM HG)",-,-,Framingham,1.24,
+T2STROKE,-,-,-,REGARDS,0.33,
+T2STROKE10,-,-,-,REGARDS,0.33,
+T2STROKE10_YRS,-,-,-,REGARDS,0.33,
+T2STROKE_YRS,-,-,-,REGARDS,0.33,
+TC,Total cholesterol (mg/dL),121868005,C18168,ARICFraminghamMESAREGARDS,1.29,
+TRIG,Total Triglycerides (mg/dL),14740000,C18169,ARICFraminghamMESAREGARDS,1.29,
+VALVDIS,"Valvular heart disease (0=No, 1=Yes)",368009,C22435,FraminghamMESA,2.56,
+VEGETABLES,Vegetables (servings per week),401070008,C10056,ARICFraminghamREGARDS,2.64,
+VISDAY,Visit day (days since exam 1),-,-,ARICFraminghamMESA,1.52,
+VISIT,Visit,-,-,ARICFraminghamMESA,-,
+WGT,Weight (lbs),726527001,C01541,ARICFraminghamMESAREGARDS,,