# Example line list data
library(wakefield)
library(hcaidcs)
library(lubridate)
library(janitor)
library(dplyr)
set.seed(1)
line_listing <- r_data_frame(n = 500,
id,
collection = r_sample_factor(
x = c("E. coli", "MRSA", "Klebsiella spp.", "MSSA", "C. difficile")),
age, sex,
specimen_date = date_stamp(start = dmy("01/04/2016")),
onset_status = answer(x = c("HO", "CO")),
reporting_organisation_code = answer(x = c("W1A", "E17")),
ccg_code = answer(x = c("00A", "00B")),
pir_status = r_sample_factor(x = c("Trust-assigned", "CCG-assigned",
"Third-party")),
prior_hc = r_sample_factor(x = c("hoha, ha", "coha, ha", "coia", "coca",
"unknown_3_mo", "all_blank")),
patient_location = r_sample_factor(
x = c("GP", "Independent Sector Provider", "Mental Health Provider",
"NHS Acute Trust", "Non-acute NHS Provider", "Nursing Home",
"Other", "Penal Establishment", "Residential Home", "Unknown")),
patient_category = r_sample_factor(
x = c(c("A&E only", "Day patient", "Emergency Assessment", "In-patient",
"Other", "Outpatient", "Regular Attender", "Unknown")
))
)
names(line_listing) <- tolower(names(line_listing))
head(line_listing)
line_listing <- line_listing %>%
mutate_if(.predicate = is.factor, funs(as.character))
line_listing$pir_status <- ifelse(line_listing$collection != "MRSA", "",
line_listing$pir_status)
line_listing$prior_hc <- ifelse(line_listing$collection != "C. difficile", "",
line_listing$prior_hc)
line_listing %>% tabyl(onset_status)
line_listing %>% tabyl(collection)
line_listing %>% tabyl(collection, pir_status)
line_listing %>% tabyl(collection, prior_hc)
usethis::use_data(line_listing, overwrite = TRUE)
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