Merge pull request #118 from jamesjiadazhan/jamesjiadazhan-patch6

Jamesjiadazhan patch6

NAMESPACE

@@ -22,6 +22,7 @@ export(HEI2015_DHQ3)
 export(HEI2015_NHANES_FPED)
 export(MED)
 export(MEDI)
+export(MEDI_V2)
 export(MED_ASA24)
 export(MED_DHQ3)
 export(MED_NHANES_FPED)

R/AHEI.R

@@ -70,7 +70,7 @@ AHEI = function(SERV_DATA, RESPONDENTID, GENDER, TOTALKCAL_AHEI, VEG_SERV_AHEI,
   }
 
   SERV_DATA = SERV_DATA %>%
-    mutate(SODIUM_SERV_AHEI=SODIUM_SERV_AHEI/(TOTALKCAL_AHEI/1000))
+    mutate(SODIUM_SERV_AHEI=SODIUM_SERV_AHEI/(TOTALKCAL_AHEI/2000))
 
   SODIUM_DECILE = quantile(SERV_DATA$SODIUM_SERV_AHEI, probs=seq(0, 1, by=1/11))
 

R/AHEI_DHQ3.R

@@ -38,7 +38,7 @@ AHEI_DHQ3 = function(DATA_PATH){
     dplyr::summarize(
       `Sex (1=male; 2=female)` = min(`Sex (1=male; 2=female)`),
       KCAL = sum(`Energy (kcal)`),
-      VEG_SERV = sum(`Total red/orange vegetable (cups)` + `Dark-green vegetable (cups)`*0.5 + `Other starchy vegetable (cups)` + `Other vegetable (cups)`),
+      VEG_SERV = sum(`Dark-green vegetable (cups)` + (`Total red/orange vegetable (cups)` + `Other starchy vegetable (cups)` + `Other vegetable (cups)`)/0.5),
       FRT_SERV = sum(`Total fruit (cups)`-`Juice fruit (cups)`),
       WGRAIN_SERV = sum(`Whole grain (oz)`/0.035274),
       NUTSLEG_SERV = sum(`Nuts, seeds, soy, and legumes (oz)`),
@@ -47,7 +47,7 @@ AHEI_DHQ3 = function(DATA_PATH){
       SSB_FRTJ_SERV = sum(ADDED_SUGAR_SSB_SERV/ 26),
       REDPROC_MEAT_SERV = sum((`Cured meat protein foods (oz)`/1.5) + ((`Meat from beef, pork, veal, lamb, and game protein foods (oz)`+`Meat from organ meat protein foods (oz)`)/4)),
       TRANS_SERV = (sum(`*Total trans fatty acitds (g)`*9)/KCAL)*100,
-      SODIUM_SERV = sum(`Sodium (mg)`/(KCAL/1000)),
+      SODIUM_SERV = sum(`Sodium (mg)`/(KCAL/2000)),
       ALCOHOL_SERV = sum(`Alcohol (drink(s))`)
     )
 

R/AHEI_F_ASA24.R

@@ -42,7 +42,7 @@ AHEI_F_ASA24 = function(DATA_PATH){
     dplyr::group_by(UserName) %>%
     dplyr::summarize(
       ENERGY=sum(KCAL),
-      VEG_SERV = sum(V_REDOR_TOTAL + V_DRKGR*0.5 + V_STARCHY_OTHER + V_OTHER),
+      VEG_SERV = sum(V_DRKGR + (V_REDOR_TOTAL + V_STARCHY_OTHER + V_OTHER)/0.5),
       FRT_SERV = sum(F_CITMLB+F_OTHER),
       WGRAIN_SERV = sum(G_WHOLE/0.035274),
       NUTSLEG_SERV = sum(PF_NUTSDS+PF_SOY+PF_LEGUMES),
@@ -51,7 +51,7 @@ AHEI_F_ASA24 = function(DATA_PATH){
       SSB_FRTJ_SERV = sum((ADDED_SUGAR_SSB_SERV*4 / 26)),
       REDPROC_MEAT_SERV = sum((PF_CUREDMEAT/1.5) + ((PF_MEAT+PF_ORGAN)/4)),
       TRANS_SERV = sum(0),
-      SODIUM_SERV = sum(SODI/(ENERGY/1000)),
+      SODIUM_SERV = sum(SODI/(ENERGY/2000)),
       ALCOHOL_SERV = sum(A_DRINKS)
     )
 

R/AHEI_M_ASA24.R

@@ -41,7 +41,7 @@ AHEI_M_ASA24 = function(DATA_PATH){
     dplyr::group_by(UserName) %>%
     dplyr::summarize(
       ENERGY=sum(KCAL),
-      VEG_SERV = sum(V_REDOR_TOTAL + V_DRKGR*0.5 + V_STARCHY_OTHER + V_OTHER),
+      VEG_SERV = sum(V_DRKGR + (V_REDOR_TOTAL + V_STARCHY_OTHER + V_OTHER)/0.5),
       FRT_SERV = sum(F_CITMLB+F_OTHER),
       WGRAIN_SERV = sum(G_WHOLE/0.035274),
       NUTSLEG_SERV = sum(PF_NUTSDS+PF_SOY+PF_LEGUMES),
@@ -50,7 +50,7 @@ AHEI_M_ASA24 = function(DATA_PATH){
       SSB_FRTJ_SERV = sum((ADDED_SUGAR_SSB_SERV*4 / 26)),
       REDPROC_MEAT_SERV = sum((PF_CUREDMEAT/1.5) + ((PF_MEAT+PF_ORGAN)/4)),
       TRANS_SERV = sum(0),
-      SODIUM_SERV = sum(SODI/(ENERGY/1000)),
+      SODIUM_SERV = sum(SODI/(ENERGY/2000)),
       ALCOHOL_SERV = sum(A_DRINKS)
     )
 

R/AHEI_NHANES_FPED.R

@@ -65,7 +65,7 @@ AHEI_NHANES_FPED = function(FPED_IND_PATH, NUTRIENT_IND_PATH){
     dplyr::summarize(
       ENERGY=sum(DR1IKCAL),
       RIAGENDR = min(RIAGENDR),
-      VEG_SERV = sum(DR1I_V_REDOR_TOTAL + 0.5*DR1I_V_DRKGR + DR1I_V_OTHER + DR1I_V_STARCHY_OTHER),
+      VEG_SERV = sum(DR1I_V_DRKGR + (DR1I_V_REDOR_TOTAL + DR1I_V_OTHER + DR1I_V_STARCHY_OTHER)/0.5),
       FRT_SERV = sum(DR1I_F_TOTAL - DR1I_F_JUICE),
       WGRAIN_SERV = sum(DR1I_G_WHOLE/0.035274),
       NUTSLEG_SERV = sum((DR1I_V_LEGUMES*4) + DR1I_PF_NUTSDS + DR1I_PF_SOY),
@@ -74,7 +74,7 @@ AHEI_NHANES_FPED = function(FPED_IND_PATH, NUTRIENT_IND_PATH){
       SSB_FRTJ_SERV = sum((ADDED_SUGAR_SSB_SERV*4 / 26)),
       REDPROC_MEAT_SERV = sum((DR1I_PF_CUREDMEAT /1.5) + ((DR1I_PF_MEAT+DR1I_PF_ORGAN)/4)),
       TRANS_SERV = sum(0),
-      SODIUM_SERV = sum(DR1ISODI)/(ENERGY/1000),
+      SODIUM_SERV = sum(DR1ISODI)/(ENERGY/2000),
       ALCOHOL_SERV = sum(DR1I_A_DRINKS)
     )
 

R/DASHI.R

@@ -19,7 +19,7 @@
 #' @param SODIUM_SERV_DASHI The serving size of sodium, unit=mg per 2000 kcal/day
 #' @return The DASHI index/score
 #' @examples
-#' DASHI(SERV_DATA, RESPONDENTID, TOTALKCAL_DASHI, VEG_SERV_DASHI, FRT_FRTJ_SERV_DASHI, NUTSLEG_SERV_DASHI, LOWF_DAIRY_SERV_DASHI, WGRAIN_SERV_DASHI, WHITEMEAT_SERV_DASHI, REDPROC_MEAT_SERV_DASHI, FATOIL_SERV_DASHI, SWEETS_SERV_DASHI, SODIUM_SERV_DASHI)
+#' DASHI(SERV_DATA, RESPONDENTID, SERV_DATA$TOTALKCAL_DASHI, SERV_DATA$VEG_SERV_DASHI, SERV_DATA$FRT_FRTJ_SERV_DASHI, SERV_DATA$NUTSLEG_SERV_DASHI, SERV_DATA$LOWF_DAIRY_SERV_DASHI, SERV_DATA$WGRAIN_SERV_DASHI, SERV_DATA$WHITEMEAT_SERV_DASHI, SERV_DATA$REDPROC_MEAT_SERV_DASHI, SERV_DATA$FATOIL_SERV_DASHI, SERV_DATA$SWEETS_SERV_DASHI, SERV_DATA$SODIUM_SERV_DASHI)
 #' @export
 
 #Score calculation for DASHI
@@ -32,7 +32,7 @@ DASHI = function(SERV_DATA, RESPONDENTID, TOTALKCAL_DASHI, VEG_SERV_DASHI, FRT_F
   DASHI_MIN_VEG_SERV = 0
   DASHI_MAX_VEG_SERV = 4
   DASHI_MIN_FRT_FRTJ_SERV = 0
-  DASHI_MAX_FRT_FRTJ_SERV = 4
+  DASHI_MAX_FRT_FRTJ_SERV = 5
   DASHI_MIN_NUTSLEG_SERV = 0
   DASHI_MAX_NUTSLEG_SERV = 4/7
   DASHI_MIN_LOWF_DAIRY_SERV = 0
@@ -45,11 +45,11 @@ DASHI = function(SERV_DATA, RESPONDENTID, TOTALKCAL_DASHI, VEG_SERV_DASHI, FRT_F
   DASHI_MIN_REDPROC_MEAT_SERV = 1.5
   DASHI_MAX_REDPROC_MEAT_SERV = 0.5
   DASHI_MIN_FATOIL_SERV = 6
-  DASHI_MAX_FATOIL_SERV = 2
+  DASHI_MAX_FATOIL_SERV = 2.5
   DASHI_MIN_SWEETS_SERV = 4
   DASHI_MAX_SWEETS_SERV = 5/7
-  DASHI_MIN_SODIUM_SERV = 2300
-  DASHI_MAX_SODIUM_SERV = 1500
+  DASHI_MIN_SODIUM_SERV = 3000
+  DASHI_MAX_SODIUM_SERV = 1150
 
   DASHI_HEALTHY = function(actual, min, max){
     case_when(

R/DASH_ASA24.R

@@ -20,7 +20,7 @@ DASH_ASA24 = function(DATA_PATH){
     COHORT = DATA_PATH
   }
 
-  LOWF_MILK=c(11111160,11111170,11112120,11112210,11113000,11114300,11114320,11115000,11115100,11115400,11120000,11121210,11121300,11212050,11511000,11511300,11511400,11511550,11511600,11511610,11511700,11512020,11512110,11513200,11513300,11513365,11513370,11513383,11513384,11513393,11513394,11513600,11513700,11513803,11513804,11513853,11513854,11514100,11514130,11514140,11514310,11514340,11514350,11519200,11519205,11519210)
+  SKIM_MILK=c(11111170, 11113000, 11114320, 11115000, 11120000, 11121300, 11212050, 11511000, 11511300, 11511610, 11512020, 11512110, 11513300, 11513370, 11513384, 11513394, 11513700, 11513804, 11513854, 11514140, 11514350, 11519205)
   LOWF_CHEESE=c(14204010,14204020,14206010,14207010)
 
   COFFEE=c(12200100,12210200,12210210,12210260,12210270,12210280,12210310,12210400,12210420,12210430,12210440,12210505,12210520,91703600,92100000,92100500,92101000,92101500,92101600,92101610,92101630,92101700,92101800,92101810,92101820,92101850,92101851,92101900,92101901,92101903,92101904,92101905,92101906,92101910,92101911,92101913,92101917,92101918,92101919,92101920,92101921,92101923,92101925,92101926,92101928,92101930,92101931,92101933,92101935,92101936,92101938,92101950,92101955,92101960,92101965,92101970,92101975,92102000,92102010,92102020,92102030,92102040,92102050,92102060,92102070,92102080,92102090,92102100,92102110,92102400,92102401,92102450,92102500,92102501,92102502,92102503,92102504,92102505,92102510,92102511,92102512,92102513,92102514,92102515,92102600,92102601,92102602,92102610,92102611,92102612,92103000,92104000,92111000,92111010,92114000,92121000,92121001,92121010,92121020,92121030,92121040,92121041,92121050,92130000,92130001,92130005,92130006,92130010,92130011,92130020,92130021,92130030,92130031,92152000,92152010,92161000,92161001,92161002,92162000,92162001,92162002,92171000,92171010,92191100,92191105,92191200,92191400,92192000,92192030,92192040,92193000,92193005,92193020,92193025,92201010,92291300,93202000,93301400)
@@ -36,8 +36,8 @@ DASH_ASA24 = function(DATA_PATH){
   #Match participant response food frequency to the standard food frequency response code
   COHORT = COHORT %>%
     dplyr::mutate(
-      LOWF_MILK_SERV = case_when(
-        FoodCode %in% LOWF_MILK ~ D_MILK,
+      SKIM_MILK_SERV = case_when(
+        FoodCode %in% SKIM_MILK ~ D_MILK,
         TRUE ~ 0
       ),
       LOWF_CHEESECREAM_SERV = case_when(
@@ -53,11 +53,11 @@ DASH_ASA24 = function(DATA_PATH){
     dplyr::summarize(
       ENERGY=sum(KCAL),
       FRT_FRTJ_SERV = sum(F_TOTAL),
-      VEG_SERV = sum(V_REDOR_TOTAL + V_DRKGR*0.5 + V_STARCHY_OTHER + V_OTHER),
+      VEG_SERV = sum(V_DRKGR + (V_REDOR_TOTAL +  V_STARCHY_OTHER + V_OTHER)/0.5),
       NUTSLEG_SERV = sum(PF_NUTSDS+PF_SOY+PF_LEGUMES),
       WGRAIN_SERV = sum(G_WHOLE),
-      LOWF_DAIRY_SERV = sum(LOWF_MILK_SERV + LOWF_CHEESECREAM_SERV + D_YOGURT),
-      SODIUM_SERV = sum(SODI/(ENERGY/1000)),
+      LOWF_DAIRY_SERV = sum(SKIM_MILK_SERV + LOWF_CHEESECREAM_SERV + D_YOGURT),
+      SODIUM_SERV = sum(SODI/(ENERGY/2000)),
       REDPROC_MEAT_SERV = sum((PF_CUREDMEAT/1.5) + ((PF_MEAT+PF_ORGAN)/4)),
       SSB_FRTJ_SERV = sum((ADDED_SUGAR_SSB_SERV*4 / 26))
     ) 

R/DASH_DHQ3.R

@@ -23,7 +23,7 @@ DASH_DHQ3 = function(DATA_PATH){
     stop("Please use individual-level data for this function. Individual-level data should be like detail.csv")
   }
 
-  LOWF_MILK = c(5.3, 5.4, 6.3, 6.4, 10.3, 10.4)
+  SKIM_MILK = c(5.4, 6.4, 10.4)
   LOWF_CHEESE=c(50.2)
   LOWF_CREAM=c(64.2, 75.2, 80.1)
   COFFEE_TEA = c(16.1, 17.1, 64.1, 64.2, 1081.1, 1123.1, 1123.2, 1130.2, 1130.5)  
@@ -32,8 +32,8 @@ DASH_DHQ3 = function(DATA_PATH){
 
   COHORT = COHORT %>%
     dplyr::mutate(
-      LOWF_MILK_SERV = case_when(
-        `Food ID` %in% LOWF_MILK ~ `Milk (cups)`,
+      SKIM_MILK_SERV = case_when(
+        `Food ID` %in% SKIM_MILK ~ `Milk (cups)`,
         TRUE ~ 0
       ),
       LOWF_CHEESECREAM_SERV = case_when(
@@ -50,11 +50,11 @@ DASH_DHQ3 = function(DATA_PATH){
     dplyr::summarize(
       KCAL = sum(`Energy (kcal)`),
       FRT_FRTJ_SERV = sum(`Total fruit (cups)`),
-      VEG_SERV = sum(`Total red/orange vegetable (cups)` + `Dark-green vegetable (cups)`*0.5 + `Other starchy vegetable (cups)` + `Other vegetable (cups)`),
+      VEG_SERV = sum(`Dark-green vegetable (cups)` + (`Total red/orange vegetable (cups)` +  `Other starchy vegetable (cups)` + `Other vegetable (cups)`)/0.5),
       NUTSLEG_SERV = sum(`Nuts, seeds, soy, and legumes (oz)`),
       WGRAIN_SERV = sum(`Whole grain (oz)`),
-      LOWF_DAIRY_SERV = sum(LOWF_MILK_SERV+LOWF_CHEESECREAM_SERV+`Yogurt (cups)`),
-      SODIUM_SERV = sum(`Sodium (mg)`/(KCAL/1000)),
+      LOWF_DAIRY_SERV = sum(SKIM_MILK_SERV+LOWF_CHEESECREAM_SERV+`Yogurt (cups)`),
+      SODIUM_SERV = sum(`Sodium (mg)`/(KCAL/2000)),
       REDPROC_MEAT_SERV = sum((`Cured meat protein foods (oz)`/1.5) + ((`Meat from beef, pork, veal, lamb, and game protein foods (oz)`+`Meat from organ meat protein foods (oz)`)/4)),
       SSB_FRTJ_SERV = sum((ADDED_SUGAR_SSB_SERV / 26))
     )

R/DASH_NHANES_FPED.R

@@ -42,8 +42,7 @@ DASH_NHANES_FPED = function(FPED_IND_PATH, NUTRIENT_IND_PATH){
   COHORT = NUTRIENT_IND %>%
     left_join(FPED_IND, by = c("SEQN", "DR1ILINE"))
 
-
-  LOWF_MILK=c(11111160,11111170,11112120,11112210,11113000,11114300,11114320,11115000,11115100,11115400,11120000,11121210,11121300,11212050,11511000,11511300,11511400,11511550,11511600,11511610,11511700,11512020,11512110,11513200,11513300,11513365,11513370,11513383,11513384,11513393,11513394,11513600,11513700,11513803,11513804,11513853,11513854,11514100,11514130,11514140,11514310,11514340,11514350,11519200,11519205,11519210)
+  SKIM_MILK=c(11111170, 11113000, 11114320, 11115000, 11120000, 11121300, 11212050, 11511000, 11511300, 11511610, 11512020, 11512110, 11513300, 11513370, 11513384, 11513394, 11513700, 11513804, 11513854, 11514140, 11514350, 11519205)
   LOWF_CHEESE=c(14204010,14204020,14206010,14207010)
 
   COFFEE=c(12200100,12210200,12210210,12210260,12210270,12210280,12210310,12210400,12210420,12210430,12210440,12210505,12210520,91703600,92100000,92100500,92101000,92101500,92101600,92101610,92101630,92101700,92101800,92101810,92101820,92101850,92101851,92101900,92101901,92101903,92101904,92101905,92101906,92101910,92101911,92101913,92101917,92101918,92101919,92101920,92101921,92101923,92101925,92101926,92101928,92101930,92101931,92101933,92101935,92101936,92101938,92101950,92101955,92101960,92101965,92101970,92101975,92102000,92102010,92102020,92102030,92102040,92102050,92102060,92102070,92102080,92102090,92102100,92102110,92102400,92102401,92102450,92102500,92102501,92102502,92102503,92102504,92102505,92102510,92102511,92102512,92102513,92102514,92102515,92102600,92102601,92102602,92102610,92102611,92102612,92103000,92104000,92111000,92111010,92114000,92121000,92121001,92121010,92121020,92121030,92121040,92121041,92121050,92130000,92130001,92130005,92130006,92130010,92130011,92130020,92130021,92130030,92130031,92152000,92152010,92161000,92161001,92161002,92162000,92162001,92162002,92171000,92171010,92191100,92191105,92191200,92191400,92192000,92192030,92192040,92193000,92193005,92193020,92193025,92201010,92291300,93202000,93301400)
@@ -60,8 +59,8 @@ DASH_NHANES_FPED = function(FPED_IND_PATH, NUTRIENT_IND_PATH){
         DR1IFDCD.x %in% SSB ~ DR1I_ADD_SUGARS,
         TRUE ~ 0
       ),
-      LOWF_MILK_SERV = case_when(
-        DR1IFDCD.x %in% LOWF_MILK ~ DR1I_D_MILK,
+      SKIM_MILK_SERV = case_when(
+        DR1IFDCD.x %in% SKIM_MILK ~ DR1I_D_MILK,
         TRUE ~ 0
       ),
       LOWF_CHEESECREAM_SERV = case_when(
@@ -73,11 +72,11 @@ DASH_NHANES_FPED = function(FPED_IND_PATH, NUTRIENT_IND_PATH){
     dplyr::summarize(
       ENERGY = sum(DR1IKCAL),
       FRT_FRTJ_SERV = sum(DR1I_F_TOTAL),
-      VEG_SERV = sum(DR1I_V_REDOR_TOTAL + 0.5*DR1I_V_DRKGR + DR1I_V_OTHER + DR1I_V_STARCHY_OTHER),
+      VEG_SERV = sum(DR1I_V_DRKGR + (DR1I_V_REDOR_TOTAL +  DR1I_V_OTHER + DR1I_V_STARCHY_OTHER)/0.5),
       NUTSLEG_SERV = sum((DR1I_V_LEGUMES*4) + DR1I_PF_NUTSDS + DR1I_PF_SOY),
       WGRAIN_SERV = sum(DR1I_G_WHOLE),
-      LOWF_DAIRY_SERV = sum(LOWF_MILK_SERV+LOWF_CHEESECREAM_SERV+DR1I_D_YOGURT),
-      SODIUM_SERV = sum(DR1ISODI)/(ENERGY/1000),
+      LOWF_DAIRY_SERV = sum(SKIM_MILK_SERV+LOWF_CHEESECREAM_SERV+DR1I_D_YOGURT),
+      SODIUM_SERV = sum(DR1ISODI)/(ENERGY/2000),
       REDPROC_MEAT_SERV = sum((DR1I_PF_CUREDMEAT /1.5) + ((DR1I_PF_MEAT+DR1I_PF_ORGAN)/4)),
       SSB_FRTJ_SERV = sum((ADDED_SUGAR_SSB_SERV*4 / 26)),