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added bindings to tidyverse colnames - fix #69 #70

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merged 1 commit into from
Jan 28, 2022
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added bindings to tidyverse colnames - fix #69 #70

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24 changes: 12 additions & 12 deletions R/utils_Exposure.R
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Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,11 @@ TreatmentExposure <- function(

# remove missing visits
dfEx <- dfEx %>%
filter( SUBJID != "" ) %>%
filter( INVID != "")
filter( .data$SUBJID != "" ) %>%
filter( .data$INVID != "")

# need to double check if any subjid has multiple INVIDs
if( anyDuplicated(dfEx %>% select(SUBJID,INVID) %>% distinct() ))
if( anyDuplicated(dfEx %>% select(.data$SUBJID,.data$INVID) %>% distinct() ))
stop( "SUBJID has multiple INVID assignments in visdt")

# Stop if snapshot date is not a date or NULL
Expand All @@ -55,27 +55,27 @@ TreatmentExposure <- function(
# Create a vector of IDs for those who are still on-going in study
if(!is.null(dfSdrg)){
completedIDs <- dfSdrg %>%
filter(SDRGYN_STD %in% c("Y","N") ) %>%
pull(SUBJID) %>%
filter(.data$SDRGYN_STD %in% c("Y","N") ) %>%
pull(.data$SUBJID) %>%
unique()
} else {
completedIDs<-c()
}

# calculate maximum treatment date
dfExRange <- dfEx %>%
select( SUBJID, INVID, EXSTDAT, EXENDAT ) %>%
group_by( SUBJID, INVID ) %>%
select( .data$SUBJID, .data$INVID, .data$EXSTDAT, .data$EXENDAT ) %>%
group_by( .data$SUBJID, .data$INVID ) %>%
summarise(
firstDoseDate = min( EXSTDAT, EXENDAT , na.rm=T),
firstDoseDate = min( .data$EXSTDAT, .data$EXENDAT , na.rm=T),
lastDoseDate = if_else(
first(SUBJID) %in% completedIDs,
as.Date(max( EXSTDAT, EXENDAT , na.rm=T)),
first(.data$SUBJID) %in% completedIDs,
as.Date(max( .data$EXSTDAT, .data$EXENDAT , na.rm=T)),
as.Date(dtSnapshot)
)
) %>%
mutate( Exposure = difftime(lastDoseDate, firstDoseDate, units="days" ) + 1) %>%
rename( SubjectID=SUBJID, SiteID=INVID)
mutate( Exposure = difftime(.data$lastDoseDate, .data$firstDoseDate, units="days" ) + 1) %>%
rename( SubjectID=.data$SUBJID, SiteID=.data$INVID)

return ( dfExRange )

Expand Down