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Merge pull request #22 from asbates/consistent-week-naming

consistent week naming for `pi_mortality` and `ilinet`
master
boB Rudis 3 years ago
committed by GitHub
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commit
8831b9a87e
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  1. 3
      DESCRIPTION
  2. 5
      NEWS.md
  3. 2
      R/aaa.R
  4. 8
      R/pi-mortality.r
  5. 2
      man/pi_mortality.Rd

3
DESCRIPTION

@ -15,7 +15,8 @@ Authors@R: c(
person("Sebastian", "Meyer", email = "seb.meyer@fau.de", role = "ctb",
comment = c(ORCID = "0000-0002-1791-9449")),
person("James", "Turtle", email = "jturtle@predsci.com", role = "ctb",
comment = c(ORCID = "0000-0003-0735-7769"))
comment = c(ORCID = "0000-0003-0735-7769")),
person("Andrew", "Bates", role = "ctb")
)
Maintainer: Bob Rudis <bob@rud.is>
Description: The 'U.S.' Centers for Disease Control and Prevention (CDC) maintain

5
NEWS.md

@ -1,3 +1,8 @@
#cdcfluview 0.9.1
- renamed `pi_mortality` columns regarding the week to `week_*` instead of `wk_*`
for consistency with `ilinet` (#21).
# cdcfluview 0.9.0
- fix bug in epiweek computation in ilinet() thanks to a bug report by @jturtle (#19)

2
R/aaa.R

@ -1,4 +1,4 @@
utils::globalVariables(c(".", "mmwrid", "season", "seasonid", "week_start"))
utils::globalVariables(c(".", "mmwrid", "season", "seasonid", "week_start", "wk_start", "wk_end", "year_wk_num"))
# CDC U.S. region names to ID map
.region_map <- c(national=3, hhs=1, census=2, state=5)

8
R/pi-mortality.r

@ -37,6 +37,8 @@
#' the function is smart enough to retrieve by season ID vs convert that
#' to a year.
#' @note Queries for "state" and "region" are not necessarily as "instantaneous" as other API endpoints and can near or over 30s retrieval delays.
#'
#' For consistency with \code{\link{ilinet}} columns indicating the week now contain 'week' instead of the previously abbreviation 'wk'.
#' @references
#' - [Pneumonia and Influenza Mortality Surveillance Portal](https://gis.cdc.gov/grasp/fluview/mortality.html)
#' @export
@ -144,6 +146,12 @@ pi_mortality <- function(coverage_area=c("national", "state", "region"), years=N
xdf$number_pneumonia <- to_num(xdf$number_pneumonia)
xdf$all_deaths <- to_num(xdf$all_deaths)
xdf$Total_PnI <- to_num(xdf$Total_PnI)
xdf <- xdf %>%
dplyr::rename(
week_start = wk_start,
week_end = wk_end,
year_week_num = year_wk_num
)
xdf <- .mcga(xdf)
xdf

2
man/pi_mortality.Rd

@ -48,6 +48,8 @@ calculated at the national and regional level and by age group.
}
\note{
Queries for "state" and "region" are not necessarily as "instantaneous" as other API endpoints and can near or over 30s retrieval delays.
For consistency with \code{\link{ilinet}} columns indicating the week now contain 'week' instead of the previously abbreviation 'wk'.
}
\examples{
\dontrun{

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