## ----setup---------------------------------------------------------------
knitr::opts_chunk$set(encoding = "UTF-8")
## ------------------------------------------------------------------------
MaleA <- data.frame(Bread = 14, WholeBread = 14, Potatoes = 3, Pasta = 5,
Fruits = 14, Legumes = 3, Nuts = 5, Vegetables = 21,
Oil = "Olive Oil", OliveOil = 25, Dairy = 14,
WholeDairy = 7, Fish = 2, Poultry = 2, Eggs = 4, Meat = 3, Wine = 7)
MaleB <- data.frame(Bread = 6, WholeBread = 0, Potatoes = 6, Pasta = 4,
Fruits = 5, Legumes = 1, Nuts = 1, Vegetables = 10,
Oil = "Olive and Seeds Oil", OliveOil = 14, Dairy = 28,
WholeDairy = 28, Fish = 4, Poultry = 4, Eggs = 8, Meat = 5, Wine = 0)
library(knitr)
kable(t(rbind(MaleA = MaleA, MaleB = MaleB)))
## ------------------------------------------------------------------------
levels(MaleA$Oil)[levels(MaleA$Oil) == "Olive Oil"] <- 2
levels(MaleB$Oil)[levels(MaleB$Oil) == "Olive and Seeds Oil"] <- 1
## ------------------------------------------------------------------------
library(MedDietCalc)
MaleA1 <- computePitsavos(data = MaleA, WholeCereals = WholeBread, Fruit = Fruits,
Vegetables = Vegetables, Potatoes = Potatoes, Legumes = Legumes,
OliveOil = OliveOil, OOmeasure = "serving", Fish = Fish,
Meat = Meat, Poultry = Poultry, WholeDairy = WholeDairy,
Wine = Wine, output = "percent", frequency = "weekly")
MaleA2 <- computeSofi(data = MaleA, Fruit = Fruits, Vegetables = Vegetables,
Legumes = Legumes, Cereals = Bread + Pasta, Fish = Fish,
Meat = Meat, Dairy = Dairy, Alcohol = Wine, OliveOil = Oil,
output = "percent", frequency = "weekly")
## ------------------------------------------------------------------------
MaleB1 <- computePitsavos(data = MaleB, WholeCereals = WholeBread, Fruit = Fruits,
Vegetables = Vegetables, Potatoes = Potatoes, Legumes = Legumes,
OliveOil = OliveOil, OOmeasure = "serving", Fish = Fish,
Meat = Meat, Poultry = Poultry, WholeDairy = WholeDairy,
Wine = Wine, output = "percent", frequency = "weekly")
MaleB2 <- computeSofi(data = MaleB, Fruit = Fruits, Vegetables = Vegetables,
Legumes = Legumes, Cereals = Bread + Pasta, Fish = Fish,
Meat = Meat, Dairy = Dairy, Alcohol = Wine, OliveOil = Oil,
output = "percent", frequency = "weekly")
## ------------------------------------------------------------------------
kable(data.frame(MaleA = c(MaleA1, MaleA2), MaleB = c(MaleB1, MaleB2),
row.names = c("score1", "score2")))
## ------------------------------------------------------------------------
data(nutriSample)
risk <- computeFRESCO(data = nutriSample,
outcome = "All", simplified = TRUE,
Sex = SEXO, Age = EDAD, Smoker = ifelse(nutriSample$FUMADOR == 1, 1, 0),
BMI = nutriSample$peso/(nutriSample$altura)^2,
men = "Hombre", women = "Mujer")
hist(risk, main = "10-year estimated \n cardiovascular risk")
## ------------------------------------------------------------------------
MDS05 <- computeMDS05(data = nutriSample,
Vegetables = P41grCom + P42grCom,
Legumes = P46grCom,
FruitAndNuts = P50grCom + P52grCom + P53grCom,
Cereals = P55grCom + P56grCom + P57grCom + P59grCom +
P60grCom + P61grCom + P62grCom,
Fish = P35grCom + P36grCom + P37grCom + P38grCom,
Meat = P29grCom + P30grCom + P31grCom + P32grCom,
Dairy = P19grCom + P20grCom + P22grCom + P23grCom +
P24grCom + P25grCom + P26grCom + P27grCom,
Alcohol = 12 * (P94rac + P96rac + P97rac + P98rac + P99rac),
Potatoes = NULL,
MUFA = totalGrasaMonoins,
PUFA = totalGrasaPoliins,
SFA = totalGrasaSat,
Sex = SEXO, men = "Hombre", women = "Mujer", frequency = "daily",
output = "data.frame", rm.na = FALSE)
## ------------------------------------------------------------------------
kable(head(MDS05))
## ------------------------------------------------------------------------
kable(round(apply(MDS05, 2, mean),2))
## ------------------------------------------------------------------------
MDS05 <- MDS05$percent
## ------------------------------------------------------------------------
MDS12 <-
computeMDS12(data = nutriSample,
Vegetables = P41grCom + P42grCom,
Legumes = P46grCom,
FruitAndNuts = P50grCom + P52grCom + P53grCom,
Cereals = P55grCom + P56grCom + P57grCom + P59grCom +
P60grCom + P61grCom + P62grCom,
Fish = P35grCom + P36grCom + P37grCom + P38grCom,
Meat = P29grCom + P30grCom + P31grCom + P32grCom,
Dairy = P19grCom + P20grCom + P22grCom + P23grCom +
P24grCom + P25grCom + P26grCom + P27grCom,
Alcohol = 12 * (P94rac + P96rac + P97rac + P98rac + P99rac),
Potatoes = NULL,
OOprincipal = ifelse(nutriSample$AceiteTipo == 1, 1, 0),
Sex = SEXO, men = "Hombre", women = "Mujer",
frequency = "daily", output = "percent", rm.na = FALSE)
## ------------------------------------------------------------------------
Pitsavos <- computePitsavos(data = nutriSample,
WholeCereals = P56rac + ifelse(nutriSample$P63_2 == 2, nutriSample$P61rac, 0),
Fruit = P50rac + P52rac,
Vegetables = P41rac + P42rac,
Potatoes = P43rac + P44rac + P45rac,
Legumes = P46rac,
OliveOil = Aceitegr,
OOmeasure = "gr",
Fish = P35rac + P36rac + P37rac + P38rac,
Meat = P29rac + P30rac + P31rac + P32rac,
Poultry = P33rac,
WholeDairy = P19grCom + P22grCom,
Wine = P96rac,
output = "percent", frequency = "daily", rm.na = FALSE)
## ------------------------------------------------------------------------
Predimed <- computePredimed(data = nutriSample, OliveOil = Aceitegr, OOmeasure = "gr",
OOprincipal = ifelse(nutriSample$AceiteTipo == 1, 1, 0),
Vegetables = P41rac + P42rac,
Fruit = P50rac + P52rac,
RedMeat = P29rac + P31rac,
Butter = P79rac,
SoftDrinks = P89rac + P90rac,
Wine = P96rac,
Legumes = P46rac,
Fish = P35rac + P36rac + P37rac + P38rac,
Pastries = P69rac + P70rac + P71rac + P72rac + P73rac,
Nuts = P53rac,
WhiteMeat = ifelse(nutriSample$P30rac > nutriSample$P29rac, 1, 0),
Sofritos = rep(0, nrow(data)), # data lacks this variable,
# so we go on without it
output = "percent", rm.na = FALSE, frequency = "daily")
## ------------------------------------------------------------------------
MAI <- computeMAI99(data = nutriSample,
Bread = P55Kcal + P56Kcal + P57Kcal,
Cereals = P55Kcal + P56Kcal + P57Kcal + P59Kcal + P60Kcal + P61Kcal + P62Kcal,
Legumes = P46Kcal,
Potatoes = P43Kcal + P44Kcal + P46Kcal,
Vegetables = P41Kcal + P42Kcal,
FruitAndNuts = P50Kcal + P52Kcal + P53Kcal,
Fish = P35Kcal + P36Kcal + P37Kcal + P38Kcal,
Wine = P96Kcal,
Oil = AceiteKcal,
Milk = P19Kcal + P20Kcal + P21Kcal,
Cheese = P26Kcal + P27Kcal,
Meat = P29Kcal + P30Kcal + P31Kcal + P32Kcal,
Eggs = P28Kcal,
AnimalFats = P29grGrasa + P30grGrasa + P31grGrasa +
P32grGrasa + P33grGrasa + P34grGrasa ,
SoftDrinks = P89Kcal + P90Kcal,
Pastries = P69Kcal + P70Kcal + P71Kcal + P72Kcal + P73Kcal,
Sugar = P84Kcal,
Kcal = totalKcal,
output = "index", rm.na = FALSE)
## ------------------------------------------------------------------------
MDQI <- computeMDQI(data = nutriSample,
FruitAndVegetables = P50grCom + P52grCom + P41grCom + P42grCom,
OliveOil = Aceitegr,
OOmeasure = "gr",
Fish = P35grCom + P36grCom + P37grCom + P38grCom,
Cereals = P55grCom + P56grCom + P57grCom + P59grCom +
P60grCom + P61grCom + P62grCom,
Meat = P29grCom + P30grCom + P31grCom + P32grCom,
SatFats = totalGrasaSat,
Cholesterol = totalCol,
Kcal = totalKcal,
invert = TRUE,
frequency = "daily", output = "percent", rm.na = FALSE)
## ------------------------------------------------------------------------
Cardio <- computeCardio(data = nutriSample,
OliveOil = Aceitegr,
OOmeasure = "gr",
Fruit = P50rac + P52rac,
Vegetables = P41rac + P42rac,
Legumes = P46rac,
Fish = P35rac + P36rac + P37rac + P38rac,
Wine = P96rac,
Meat = P29rac + P30rac + P31rac + P32rac,
RefinedBread = P55rac,
RefinedRice = P61rac,
WholeBread = P56rac,
frequency = "daily", output = "percent", rm.na = FALSE)
## ------------------------------------------------------------------------
MDP02 <- computeMDP02(data = nutriSample,
OliveOil = Aceitegr,
OOmeasure = "gr",
Fiber = totalFibra,
Fruit = P50grCom,
Vegetables = P41grCom + P42grCom,
Fish = P35grCom + P36grCom + P37grCom + P38grCom,
Alcohol = 12 * (P94rac + P96rac + P97rac + P98rac + P99rac),
Meat = P29grCom + P30grCom + P31grCom + P32grCom,
RefinedCereals = P55grCom + P61grCom,
output = "percent", rm.na = FALSE, frequency = "daily")
## ------------------------------------------------------------------------
RMed <- computeRMED(data = nutriSample,
Kcal = totalKcal,
FruitAndNuts = P50grCom + P52grCom + P53grCom,
Vegetables = P41grCom + P42grCom,
Legumes = P46grCom,
Cereals = P55grCom + P56grCom + P57grCom + P59grCom +
P60grCom + P61grCom + P62grCom,
Fish = P35grCom + P36grCom + P37grCom + P38grCom,
OliveOil = Aceitegr,
Meat = P29grCom + P30grCom + P31grCom + P32grCom,
Dairy= P19grCom + P20grCom + P22grCom + P23grCom +
P24grCom + P25grCom + P26grCom + P27grCom,
Alcohol = 12 * (P94rac + P96rac + P97rac + P98rac + P99rac),
Sex = SEXO, men = "Hombre", women = "Mujer",
frequency = "daily", output = "percent", rm.na = FALSE)
## ------------------------------------------------------------------------
# kind of Olive Oil consumded is stored in a different way than asked by formula:
# data has: 1 = olive oil, 2 = seeds oil, 3 = both,
# formula wants use of olive oil: 0 = occasional use, 1 = frequent use, 2 = regular use
# so we first change it:
Oil <- ifelse(nutriSample$AceiteTipo == 2, 0,
ifelse(nutriSample$AceiteTipo == 3, 1,
ifelse(nutriSample$AceiteTipo == 1, 2, 0)))
Sofi <- computeSofi(data = nutriSample,
Fruit = P50rac + P52rac,
Vegetables = P41rac + P42rac,
Legumes = P46rac,
Cereals = P55rac + P56rac + P57rac + P59rac + P60rac + P61rac + P62rac,
Fish = P35rac + P36rac + P37rac + P38rac,
Meat = P29rac + P30rac + P31rac + P32rac,
Dairy = P19rac + P20rac + P20rac + P22rac + P23rac +
P24rac + P25rac + P26rac + P27rac,
Alcohol = P94rac + P96rac + P97rac + P98rac + P99rac,
OliveOil = Oil,
output = "percent", rm.na = FALSE, frequency = "daily")
rm(Oil)
## ------------------------------------------------------------------------
Goulet <- computeGoulet(data = nutriSample,
WholeCereals = P56rac + ifelse(nutriSample$P63_2 == 2, nutriSample$P61rac, 0),
Vegetables = P41rac + P42rac,
Fruit = P50rac + P52rac,
LegumesAndNuts = P46rac + P53rac + P75rac,
OliveOil = Aceitegr,
OOmeasure = "gr",
Olives = P54rac,
Dairy = P19rac + P20rac + P20rac + P22rac + P23rac + P24rac + P25rac + P26rac + P27rac,
Fish = P35rac + P36rac + P37rac + P38rac,
Poultry = P33rac,
Eggs = P28rac,
Sweets = P69rac + P70rac + P71rac + P72rac + P73rac,
Meat = P29rac + P30rac + P31rac + P32rac,
output = "percent", frequency = "daily", rm.na = FALSE)
## ------------------------------------------------------------------------
# kind of Olive Oil consumded is stored in a different way than asked by formula:
# data has: 1 = olive oil, 2 = seeds oil, 3 = both,
# formula wants:
# 0 = olive oil is not usually consumed.
# 1 = olive oil and other vegetable oils are usually consumed.
# 2 = only olive oil is usually consumed
# so we first change it:
Oil <- ifelse(nutriSample$AceiteTipo == 2, 0,
ifelse(nutriSample$AceiteTipo == 3, 1,
ifelse(nutriSample$AceiteTipo == 1, 2, 0)))
MSDPS <- computeMSDPS(data = nutriSample,
# group of arguments about food consumption:
WholeCereals = P56rac + ifelse(nutriSample$P63_2 == 2, nutriSample$P61rac, 0),
Fruit = P50rac + P52rac,
Vegetables = P41rac + P42rac,
Dairy = P19rac + P20rac + P20rac + P22rac + P23rac +
P24rac + P25rac + P26rac + P27rac,
Wine = P96rac,
Fish = P35rac + P36rac + P37rac + P38rac,
Poultry = P33rac,
LegumesAndMore = P46rac + P53rac + P54rac,
Potatoes = P43grCom + P44grCom + P45grCom,
Eggs = P28rac,
Sweets = P69rac + P70rac + P71rac + P72rac + P73rac,
Meat = P29rac + P30rac + P31rac + P32rac,
OOprincipal = Oil,
# group of arguments about energy intake to compute correction factor:
WholeCerealsK = P56Kcal + ifelse(nutriSample$P63_2 == 2, nutriSample$P61Kcal, 0),
FruitK = P50Kcal + P52Kcal,
VegetablesK = P41Kcal + P42Kcal,
DairyK = P19Kcal + P20Kcal + P21Kcal + P22Kcal + P23Kcal +
P24Kcal + P25Kcal + P26Kcal + P27Kcal,
WineK = P96Kcal,
FishK = P35Kcal + P36Kcal + P37Kcal + P38Kcal,
PoultryK = P33Kcal,
LegumesAndMoreK = P46Kcal + P53Kcal + P54Kcal,
PotatoesK = P43grCom + P44grCom + P45grCom,
EggsK = P28Kcal,
SweetsK = P69Kcal + P70Kcal + P71Kcal + P72Kcal + P73Kcal,
MeatK = P29Kcal + P30Kcal + P31Kcal + P32Kcal,
OliveOilK = AceiteKcal,
Kcal = totalKcal,
# final arguments:
Sex = SEXO, men = "Hombre", women = "Mujer",
output = "percent", frequency = "daily", rm.na = FALSE)
## ------------------------------------------------------------------------
scores <- data.frame(MDS05, MDS12, Pitsavos, Predimed, MDQI, Cardio,
MDP02, RMed, Sofi, Goulet, MSDPS, MAI)
knitr::kable(head(scores))
## ------------------------------------------------------------------------
knitr::kable(round(cor(scores, use = "pairwise.complete.obs"), 2))
## ------------------------------------------------------------------------
for(i in 1:ncol(scores)){
hist(scores[ ,i], main="", xlab=names(scores)[i], xlim=c(0,100))
}