data-raw/vaccination_data.R

In arisp99/CAvaccines: An Analysis of CA Vaccination Rates and Disease Occurrence

# In order to run the following script, must first set the path to the data
# folder. Fill in the path and uncomment the line below
# path_to_data = ""

# Run function to get county level vaccination data
county_2008 <- extract_vaccination(paste(path_to_data, "2007-08CAKindergartenData.xls", sep = "/"), "2008",  c(6, 7314), "KA0708")
county_2009 <- extract_vaccination(paste(path_to_data, "2008-09CAKindergartenData.xls", sep = "/"), "2009",  c(6, 7179), "KA0809")
county_2010 <- extract_vaccination(paste(path_to_data, "2009-10CAKindergartenData.xls", sep = "/"), "2010",  c(6, 7130), "KA0910")
county_2011 <- extract_vaccination(paste(path_to_data, "2010-11CAKindergartenData.xls", sep = "/"), "2011",  c(6, 7170), "KA1011")
county_2012 <- extract_vaccination(paste(path_to_data, "2011-12CAKindergartenData.xls", sep = "/"), "2012",  c(6, 7332), "Sheet1")
county_2013 <- extract_vaccination(paste(path_to_data, "2012-13CAKindergartenData.xls", sep = "/"), "2013",  c(6, 7642), "KA1213")

# 2014 is experiencing problems for an unknown reason. Exclude it for simplicity.
county_2014 <- extract_vaccination(paste(path_to_data, "2013-14CAKindergartenData.xls", sep = "/"), "2014",  c(6, 7386), "KA1314")

county_2015 <- extract_vaccination(paste(path_to_data, "2014-15CAKindergartenData.xlsx", sep = "/"), "2015",  c(6, 7470), "Sheet1")
county_2016 <- extract_vaccination(paste(path_to_data, "2015-16CAKindergartenData.xls",  sep = "/"), "2016",  c(6, 7427), "KA1516")
county_2017 <- extract_vaccination(paste(path_to_data, "2016-17KindergartenData.xlsx",   sep = "/"), "2017",  c(5, 6919), "Enrollment 20 or More")

# We do not have incidence data on 2018 cases
# yr_2018 <- system.file("extdata", "2017-18CA_KindergartenDataLetter.xlsx", package = "CAvaccines")
# county_2018 <- extract_vaccination(yr_2018, "2018",  c(5, 6735), "Enrollment 20 or More")

# Combine all the datasets together
county_vaccination <-
  dplyr::bind_rows(county_2008, county_2009, county_2010, county_2011,
                   county_2012, county_2013, county_2014, county_2015,
                   county_2016, county_2017)

# Convert year into a factor
county_vaccination$Year <- as.factor(county_vaccination$Year)

# Save county level vaccination data in data/ folder
usethis::use_data(county_vaccination, overwrite = TRUE)