#' Getting Invalid Examples and Summaries for Patient_State
#'
#' This function will generate two data frames: first, a frame to be used later to extract invalid examples from;
#' second, a frame that contains facility-level summaries for counts and percentages of invalid Patient_State.
#'
#' The valid values were taken from the `PHVS_State_FIPS_5-2_V1.xls` file from
#' Public Health Information Network Vocabulary Access and Distribution System value sets
#' (https://phinvads.cdc.gov/vads/ViewView.action?name=Syndromic%20Surveillance). The package will
#' be updated as the CDC provides new or different codes that are considered valid or invalid.
#'
#' You can view the concept codes that are considered valid by calling `data("state")`. This data frame
#' leaves off the zeros in front of single-digit codes; codes with zeros in front of them are explicitly added
#' in the code for the function.
#'
#' @param data The raw data from BioSense on which you will do the invalid patient state checks.
#' @return A list of two data frames: examples and summary for the Patient_State.
#' @import dplyr
#' @export
county_invalid <- function(data) {
# generating valid values
data("county",envir=environment())
valid_county_values <- county %>% # take data
select(Concept.Code) %>% # the variable we want is called concept code
filter(!is.na(Concept.Code)) %>% # get rid of any nas
c() %>% # turn this into a vector
unlist() %>% # unlist them from the concept name object
unname() # remove names
# generate examples
county_examples <- data %>% # take data
select(c(C_Biosense_Facility_ID, C_BioSense_ID, C_Patient_County)) %>% # taking just the variables we need
mutate(Invalid_Patient_County=case_when(
is.na(C_Patient_County) ~ NA, # if na then keep na
C_Patient_County %in% valid_county_values ~ FALSE, # if county is found in valid values, false
!C_Patient_County %in% valid_county_values ~ TRUE # if it isn't, then true
))
# generate summary
county_summary <- county_examples %>% # take the examples
group_by(C_BioSense_ID) %>% # group by patient visit
mutate(Any_Invalid_Patient_County=case_when(
all(is.na(Invalid_Patient_County)) ~ NA, # if all is na, keep na
sum(Invalid_Patient_County, na.rm=TRUE) == 0 ~ FALSE, # if none are true, then invalid is false
TRUE ~ TRUE # otherwise, true
)) %>%
slice(1) %>% # take one row per patient visit
ungroup() %>% # explicitly ungroup
group_by(C_Biosense_Facility_ID) %>% # group by facility
summarise(Patient_County.Percent=round(mean(Any_Invalid_Patient_County, na.rm=TRUE)*100,2), # percent
Patient_County.Count=sum(Any_Invalid_Patient_County, na.rm=TRUE)) # count
return(
list(county_examples=county_examples,
county_summary=county_summary)
)
}
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