csv2pl_vacc: Proccesses the csv created by the function format_csv and...

In arranhamlet/popvac_package: Generate population level vaccination data from a csv template.

Description

Proccesses the csv created by the function format_csv and outputs population level vaccination data for included countries.

Usage

csv2pl_vacc(campaigncsv, popdf, epi, countryiso, shplist,
  adm.setting = "adm2", format = "csv", savemodifier = NA,
  rdata.output = F, scenario = "base", GAVI.switch = "base", skew = 0)

Arguments

campaigncsv	The csv file containing the vaccination campaigns produced by the function format_csv.
popdf	The csv file generated by the function csv_to_adm2pop
epi	This is a csv containing the routine infant immunization coverage for all the countries you want to generate population vaccination coverage for.
countryiso	This is a vector of the ISO codes for all countries you want to generate population vaccination coverage for.
shplist	This is a list of second administrative division shapefiles containing each of the GADM versions you have used to input campaigns in the input csv. Uses a standardised input, for example - "list("shp2_v2.0"=shp2_v1.0,"shp2_v2.8"=shp2_v2.8)" would be used when your input csv contains GADM2 and GADM2.8 encoding. If your csv only contains a single encoding it would be - "list("shp2_v2.0"=shp2_v1.0)
adm.setting	This determines at what level the information is output. Accepts any combination of adm0 (country level), adm1 and adm2 as an input.
format	This changes the format of the output. Accepts "csv" or "rdata".
savemodifier	This adds a user generated string to the end of the name of the produced outputs.
rdata.output	This determines whether or not to output a rdata file of the results. Accepts T or F.
scenario	This changes the underlying assumptions of the population size. Base does nothing, "hiCov" reduces the population by 25 percent, "loCov" increases the population by 25 percent.
GAVI.switch	This implements different vaccination campaigns based on the column "scenario" in the campaigncsv parameter. "-all.epi" ignores the contribution of epi, "5year.mass" implements five year mass vaccination campaigns,"epi90" does...something?,"+fut.epi" includes future epi coverage.
skew	This affects how vaccination campaigns are applied. If the skew is set to -1 then campaigns are applied to the whole population, regardless of prior vaccination status. If the skew is set to 0 then campaigns are applied only to the unvaccinated population. Finally, if the skew is set to 1 then the campaigns are applied to the same population as susbsequent campaigns.

Examples

csv2pl_vacc(needs updating)

arranhamlet/popvac_package documentation built on May 10, 2019, 1:48 p.m.