R/ipaq.R
In nrkoehler/qscorer: Procedures for Scoring Health-related Questionnaires
Defines functions
scoring_ipaqsf
Documented in
scoring_ipaqsf
#' @title {Scoring the International Physical Activity Questionnaire (IPAQ) short form}
#' @description {\emph{The purpose of the IPAQ is to provide a set of well-developed instruments
#' that can be used internationally to obtain comparable estimates of physical activity.
#' There are two versions of the questionnaire. The short version is suitable for use in
#' national and regional surveillance systems and the long version provide more detailed
#' information often required in research work or for evaluation purposes.} (The IPAQ Group)}
#' @details
#' \itemize{
#' \item \code{Number of items:} {11}
#' \item \code{Item range:} {none}
#' \item \code{Reverse items:} {none}
#' \item \code{Score range:} {none}
#' \item \code{Cut-off-values:} {none}
#' \item \code{Minimal clinically important difference:} {none}
#' \item \code{Treatment of missing values:}
#' {not reported}
#' }
#' @references
#' Craig et al. 2003 (\url{https://doi.org/10.1249/01.MSS.0000078924.61453.FB})
#'
#' The IPAQ Group (2005). Guidelines for Data Processing and Analysis of the International Physical Activity Questionnaire. Retrieved from (\url{http://www.ipaq.ki.se})
#' @return The function returns 20 variables:
#' \itemize{
#' \item \code{vminday:} Number of minutes in vigorous physical activity per day
#' \item \code{mminday:} Number of minutes in moderate physical activity per day
#' \item \code{wminday:} Number of minutes walking per day
#' \item \code{sminday:} Number of minutes sitting per day
#' \item \code{totalhourday:} Number of hours in total (vigorous, moderate, walking, sitting) per day
#' \item \code{vminwk:} Number of minutes in vigorous physical activity per week
#' \item \code{mminwk:} Number of minutes in moderate physical activity per week
#' \item \code{wminwk:} Number of minutes walking per week
#' \item \code{sminwk:} Number of minutes sitting per week
#' \item \code{sumpa:} Total number of minutes of vigorous pa, moderate pa, and walking per week
#' \item \code{sumday:} Total number of days of vigorous pa, moderate pa, and walking per week
#' \item \code{excMin:} Flag if > 960 minutes per day
#' \item \code{excDay:} Flag if sum of days of vigorous pa, moderate pa, and walking per week > 21
#' \item \code{exc16h:} Flag if hours of daily activity and sitting exceeds 16h
#' \item \code{vminwkMET:} MET–minutes in vigorous physical activity per week
#' \item \code{mminwkMET:} MET–minutes in moderate physical activity per week
#' \item \code{wminwkMET:} MET–minutes walking per week
#' \item \code{MET:} MET–minutes in total per week
#' \item \code{kilocalories:} Kilocalories per week
#' \item \code{pacat:} Levels of physical activity (Low, Moderate, High)
#' }
#' @examples
#' \dontrun{
#' library(dplyr)
#' scoring_ipaqsf(mydata, items = items.ipaq, weight = WEIGHT)
#' }
#' @param data a \code{\link{data.frame}} containing the IPAQ items
#' orderd from 1 to 11:
#' \enumerate{
#' \item \code{VigDays:} Number of days doing vigorous physical activity per week
#' \item \code{VigHours:} Number of hours in vigorous physical activity per day
#' \item \code{VigMin:} Number of minutes in vigorous physical activity per day
#' \item \code{ModDays:} Number of days doing moderate physical activity per week
#' \item \code{ModHours:} Number of hours in moderate physical activity per day
#' \item \code{ModMin:} Number of minutes in moderate physical activity per day
#' \item \code{WalkDays:} Number of days walking per week
#' \item \code{WalkHours:} Number of hours walking per day
#' \item \code{WalkMin:} Number of minutes in walking per day
#' \item \code{SitHours:} Number of hours sitting per day
#' \item \code{SitMin:} Number of minutes sitting per day
#' }
#' @param items A character vector with the IPAQ item names ordered from 1 to 11,
#' or a numeric vector indicating the column numbers of the IPAQ items in \code{data}.
#' @param keep Logical, whether to keep the single items and whether to return variables containing
#' the number of non-missing items on each scale for each respondent. The default is TRUE.
#' @param weight Character vector with name of the body weight variable
#' @export
scoring_ipaqsf <- function(data, items = 1:11, keep = TRUE, weight) {
library(dplyr, warn.conflicts = FALSE)
items <- items
newvars <- c(
"VigDays", "VigHours", "VigMin", "ModDays",
"ModHours", "ModMin", "WalkDays", "WalkHours",
"WalkMin", "SitHours", "SitMin", "Weight"
)
# check for number of specified items
if (length(items) != 11) {
stop("Number of items must be 11!")
}
data <- data %>%
mutate(
VigDays = rowSums(select(., items[1])),
VigHours = rowSums(select(., items[2])),
VigMin = rowSums(select(., items[3])),
ModDays = rowSums(select(., items[4])),
ModHours = rowSums(select(., items[5])),
ModMin = rowSums(select(., items[6])),
WalkDays = rowSums(select(., items[7])),
WalkHours = rowSums(select(., items[8])),
WalkMin = rowSums(select(., items[9])),
SitHours = rowSums(select(., items[10])),
SitMin = rowSums(select(., items[11])),
Weight = rowSums(select(., weight))
) %>%
# If number of days == 0, set hours and minutes to 0
# If number of days is missing, set hours and minutes to missing
mutate_at(vars(VigHours, VigMin), list(~case_when(
VigDays == 0 ~ 0,
is.na(VigDays) ~ as.numeric(NA),
TRUE ~ .
))) %>%
mutate_at(vars(ModHours, ModMin), list(~case_when(
ModDays == 0 ~ 0,
is.na(ModDays) ~ as.numeric(NA),
TRUE ~ .
))) %>%
mutate_at(vars(WalkHours, WalkMin), list(~case_when(
WalkDays == 0 ~ 0,
is.na(WalkDays) ~ as.numeric(NA),
TRUE ~ .
))) %>%
mutate(
# If number of hours is missing, but number of minutes is not missing, set hours = 0
# If number of minutes is missing, but number of hours is not missing, set minutes = 0
VigHours = ifelse(!is.na(VigDays) & !is.na(VigMin) & is.na(VigHours), 0, VigHours),
VigMin = ifelse(!is.na(VigDays) & !is.na(VigHours) & is.na(VigMin), 0, VigMin),
ModHours = ifelse(!is.na(ModDays) & !is.na(ModMin) & is.na(ModHours), 0, ModHours),
ModMin = ifelse(!is.na(ModDays) & !is.na(ModHours) & is.na(ModMin), 0, ModMin),
WalkHours = ifelse(!is.na(WalkDays) & !is.na(WalkMin) & is.na(WalkHours), 0, WalkHours),
WalkMin = ifelse(!is.na(WalkDays) & !is.na(WalkHours) & is.na(WalkMin), 0, WalkMin),
SitHours = ifelse(!is.na(SitMin) & is.na(SitHours), 0, SitHours),
SitMin = ifelse(!is.na(SitHours) & is.na(SitMin), 0, SitMin),
# Calculate Variables
vminday = VigHours * 60 + VigMin,
mminday = ModHours * 60 + ModMin,
wminday = WalkHours * 60 + WalkMin,
sminday = SitHours * 60 + SitMin
) %>%
mutate(
totalhourday = ifelse(is.na(vminday) + is.na(mminday) + is.na(wminday) + is.na(sminday) > 2,
NA, round(rowSums(select(., ends_with("minday")), na.rm = TRUE) / 60, 1)
),
vminwk = VigDays * vminday,
mminwk = ModDays * mminday,
wminwk = WalkDays * wminday,
sminwk = sminday * 7,
sumpa = ifelse(is.na(vminday) + is.na(mminday) + is.na(wminday) > 2,
NA, rowSums(select(., matches("[vmw]minday")), na.rm = TRUE)
),
sumday = ifelse(is.na(VigDays) + is.na(ModDays) + is.na(WalkDays) > 2,
NA, rowSums(select(., ends_with("Days")), na.rm = TRUE)
),
excMin = ifelse(sumpa > 960, TRUE, FALSE),
excDay = ifelse(sumday > 21, TRUE, FALSE),
exc16h = ifelse(totalhourday > 16, TRUE, FALSE),
vminday = ifelse(vminday < 10, 0, vminday),
mminday = ifelse(mminday < 10, 0, mminday),
wminday = ifelse(wminday < 10, 0, wminday),
vminwkMET = 8 * vminwk,
mminwkMET = 4 * mminwk,
wminwkMET = 3.3 * wminwk,
MET = vminwkMET + mminwkMET + wminwkMET,
kilocalories = MET * (Weight / 60),
pacat = case_when(
VigDays >= 3 & MET >= 1500 ~ "High",
sumday >= 7 & MET >= 3000 ~ "High",
VigDays >= 3 & vminday >= 20 ~ "Moderate",
ModDays + WalkDays >= 5 & mminday + wminday >= 30 ~ "Moderate",
sumday >= 5 & MET >= 600 ~ "Moderate",
is.na(VigDays) | is.na(vminday) | is.na(mminday) |
is.na(wminday) | is.na(sumday) ~ as.character(NA),
TRUE ~ "Low"
),
pacat = factor(pacat, levels = c("High", "Moderate", "Low"))
) %>%
select(-newvars) %>%
mutate_at(vars(vminwkMET:kilocalories), list(~ifelse(excMin == TRUE | excDay == TRUE, NA, .))) %>%
rename_at(vars(vminday:pacat), list(~paste0("ipaq.", .)))
# Keep single items and nvalid variables
if (keep == FALSE) {
data <- data %>% select(-items)
} else {
data <- data
}
data
}
NULL
nrkoehler/qscorer documentation built on April 5, 2020, 3:09 a.m.
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Defines functions scoring_ipaqsf
Documented in scoring_ipaqsf
#' @title {Scoring the International Physical Activity Questionnaire (IPAQ) short form}
#' @description {\emph{The purpose of the IPAQ is to provide a set of well-developed instruments
#' that can be used internationally to obtain comparable estimates of physical activity.
#' There are two versions of the questionnaire. The short version is suitable for use in
#' national and regional surveillance systems and the long version provide more detailed
#' information often required in research work or for evaluation purposes.} (The IPAQ Group)}
#' @details
#' \itemize{
#' \item \code{Number of items:} {11}
#' \item \code{Item range:} {none}
#' \item \code{Reverse items:} {none}
#' \item \code{Score range:} {none}
#' \item \code{Cut-off-values:} {none}
#' \item \code{Minimal clinically important difference:} {none}
#' \item \code{Treatment of missing values:}
#' {not reported}
#' }
#' @references
#' Craig et al. 2003 (\url{https://doi.org/10.1249/01.MSS.0000078924.61453.FB})
#'
#' The IPAQ Group (2005). Guidelines for Data Processing and Analysis of the International Physical Activity Questionnaire. Retrieved from (\url{http://www.ipaq.ki.se})
#' @return The function returns 20 variables:
#' \itemize{
#' \item \code{vminday:} Number of minutes in vigorous physical activity per day
#' \item \code{mminday:} Number of minutes in moderate physical activity per day
#' \item \code{wminday:} Number of minutes walking per day
#' \item \code{sminday:} Number of minutes sitting per day
#' \item \code{totalhourday:} Number of hours in total (vigorous, moderate, walking, sitting) per day
#' \item \code{vminwk:} Number of minutes in vigorous physical activity per week
#' \item \code{mminwk:} Number of minutes in moderate physical activity per week
#' \item \code{wminwk:} Number of minutes walking per week
#' \item \code{sminwk:} Number of minutes sitting per week
#' \item \code{sumpa:} Total number of minutes of vigorous pa, moderate pa, and walking per week
#' \item \code{sumday:} Total number of days of vigorous pa, moderate pa, and walking per week
#' \item \code{excMin:} Flag if > 960 minutes per day
#' \item \code{excDay:} Flag if sum of days of vigorous pa, moderate pa, and walking per week > 21
#' \item \code{exc16h:} Flag if hours of daily activity and sitting exceeds 16h
#' \item \code{vminwkMET:} MET–minutes in vigorous physical activity per week
#' \item \code{mminwkMET:} MET–minutes in moderate physical activity per week
#' \item \code{wminwkMET:} MET–minutes walking per week
#' \item \code{MET:} MET–minutes in total per week
#' \item \code{kilocalories:} Kilocalories per week
#' \item \code{pacat:} Levels of physical activity (Low, Moderate, High)
#' }
#' @examples
#' \dontrun{
#' library(dplyr)
#' scoring_ipaqsf(mydata, items = items.ipaq, weight = WEIGHT)
#' }
#' @param data a \code{\link{data.frame}} containing the IPAQ items
#' orderd from 1 to 11:
#' \enumerate{
#' \item \code{VigDays:} Number of days doing vigorous physical activity per week
#' \item \code{VigHours:} Number of hours in vigorous physical activity per day
#' \item \code{VigMin:} Number of minutes in vigorous physical activity per day
#' \item \code{ModDays:} Number of days doing moderate physical activity per week
#' \item \code{ModHours:} Number of hours in moderate physical activity per day
#' \item \code{ModMin:} Number of minutes in moderate physical activity per day
#' \item \code{WalkDays:} Number of days walking per week
#' \item \code{WalkHours:} Number of hours walking per day
#' \item \code{WalkMin:} Number of minutes in walking per day
#' \item \code{SitHours:} Number of hours sitting per day
#' \item \code{SitMin:} Number of minutes sitting per day
#' }
#' @param items A character vector with the IPAQ item names ordered from 1 to 11,
#' or a numeric vector indicating the column numbers of the IPAQ items in \code{data}.
#' @param keep Logical, whether to keep the single items and whether to return variables containing
#' the number of non-missing items on each scale for each respondent. The default is TRUE.
#' @param weight Character vector with name of the body weight variable
#' @export
scoring_ipaqsf <- function(data, items = 1:11, keep = TRUE, weight) {
library(dplyr, warn.conflicts = FALSE)
items <- items
newvars <- c(
"VigDays", "VigHours", "VigMin", "ModDays",
"ModHours", "ModMin", "WalkDays", "WalkHours",
"WalkMin", "SitHours", "SitMin", "Weight"
)
# check for number of specified items
if (length(items) != 11) {
stop("Number of items must be 11!")
}
data <- data %>%
mutate(
VigDays = rowSums(select(., items[1])),
VigHours = rowSums(select(., items[2])),
VigMin = rowSums(select(., items[3])),
ModDays = rowSums(select(., items[4])),
ModHours = rowSums(select(., items[5])),
ModMin = rowSums(select(., items[6])),
WalkDays = rowSums(select(., items[7])),
WalkHours = rowSums(select(., items[8])),
WalkMin = rowSums(select(., items[9])),
SitHours = rowSums(select(., items[10])),
SitMin = rowSums(select(., items[11])),
Weight = rowSums(select(., weight))
) %>%
# If number of days == 0, set hours and minutes to 0
# If number of days is missing, set hours and minutes to missing
mutate_at(vars(VigHours, VigMin), list(~case_when(
VigDays == 0 ~ 0,
is.na(VigDays) ~ as.numeric(NA),
TRUE ~ .
))) %>%
mutate_at(vars(ModHours, ModMin), list(~case_when(
ModDays == 0 ~ 0,
is.na(ModDays) ~ as.numeric(NA),
TRUE ~ .
))) %>%
mutate_at(vars(WalkHours, WalkMin), list(~case_when(
WalkDays == 0 ~ 0,
is.na(WalkDays) ~ as.numeric(NA),
TRUE ~ .
))) %>%
mutate(
# If number of hours is missing, but number of minutes is not missing, set hours = 0
# If number of minutes is missing, but number of hours is not missing, set minutes = 0
VigHours = ifelse(!is.na(VigDays) & !is.na(VigMin) & is.na(VigHours), 0, VigHours),
VigMin = ifelse(!is.na(VigDays) & !is.na(VigHours) & is.na(VigMin), 0, VigMin),
ModHours = ifelse(!is.na(ModDays) & !is.na(ModMin) & is.na(ModHours), 0, ModHours),
ModMin = ifelse(!is.na(ModDays) & !is.na(ModHours) & is.na(ModMin), 0, ModMin),
WalkHours = ifelse(!is.na(WalkDays) & !is.na(WalkMin) & is.na(WalkHours), 0, WalkHours),
WalkMin = ifelse(!is.na(WalkDays) & !is.na(WalkHours) & is.na(WalkMin), 0, WalkMin),
SitHours = ifelse(!is.na(SitMin) & is.na(SitHours), 0, SitHours),
SitMin = ifelse(!is.na(SitHours) & is.na(SitMin), 0, SitMin),
# Calculate Variables
vminday = VigHours * 60 + VigMin,
mminday = ModHours * 60 + ModMin,
wminday = WalkHours * 60 + WalkMin,
sminday = SitHours * 60 + SitMin
) %>%
mutate(
totalhourday = ifelse(is.na(vminday) + is.na(mminday) + is.na(wminday) + is.na(sminday) > 2,
NA, round(rowSums(select(., ends_with("minday")), na.rm = TRUE) / 60, 1)
),
vminwk = VigDays * vminday,
mminwk = ModDays * mminday,
wminwk = WalkDays * wminday,
sminwk = sminday * 7,
sumpa = ifelse(is.na(vminday) + is.na(mminday) + is.na(wminday) > 2,
NA, rowSums(select(., matches("[vmw]minday")), na.rm = TRUE)
),
sumday = ifelse(is.na(VigDays) + is.na(ModDays) + is.na(WalkDays) > 2,
NA, rowSums(select(., ends_with("Days")), na.rm = TRUE)
),
excMin = ifelse(sumpa > 960, TRUE, FALSE),
excDay = ifelse(sumday > 21, TRUE, FALSE),
exc16h = ifelse(totalhourday > 16, TRUE, FALSE),
vminday = ifelse(vminday < 10, 0, vminday),
mminday = ifelse(mminday < 10, 0, mminday),
wminday = ifelse(wminday < 10, 0, wminday),
vminwkMET = 8 * vminwk,
mminwkMET = 4 * mminwk,
wminwkMET = 3.3 * wminwk,
MET = vminwkMET + mminwkMET + wminwkMET,
kilocalories = MET * (Weight / 60),
pacat = case_when(
VigDays >= 3 & MET >= 1500 ~ "High",
sumday >= 7 & MET >= 3000 ~ "High",
VigDays >= 3 & vminday >= 20 ~ "Moderate",
ModDays + WalkDays >= 5 & mminday + wminday >= 30 ~ "Moderate",
sumday >= 5 & MET >= 600 ~ "Moderate",
is.na(VigDays) | is.na(vminday) | is.na(mminday) |
is.na(wminday) | is.na(sumday) ~ as.character(NA),
TRUE ~ "Low"
),
pacat = factor(pacat, levels = c("High", "Moderate", "Low"))
) %>%
select(-newvars) %>%
mutate_at(vars(vminwkMET:kilocalories), list(~ifelse(excMin == TRUE | excDay == TRUE, NA, .))) %>%
rename_at(vars(vminday:pacat), list(~paste0("ipaq.", .)))
# Keep single items and nvalid variables
if (keep == FALSE) {
data <- data %>% select(-items)
} else {
data <- data
}
data
}
NULL
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