@ -1,28 +1,40 @@ | |||
#' Retrieve CDC U.S. Coverage Map | |||
#' Retrieve CDC U.S. Basemaps | |||
#' | |||
#' The CDC FluView application uses a composite basemap of coverage areas | |||
#' within the United States that elides and scales Alaska, Hawaii and | |||
#' Puerto Rico and provides elided and scaled breakouts for New York City | |||
#' and the District of Columbia.\cr | |||
#' The CDC FluView application uses a composite basemaps of coverage areas | |||
#' within the United States that elides and scales Alaska, Hawaii, | |||
#' Puerto Rico & the Virgin Islands and some further provide elided and scaled | |||
#' breakouts for New York City and the District of Columbia.\cr | |||
#' \cr | |||
#' The basemap provides polygon identifiers by: | |||
#' \cr | |||
#' - `STATE_FIPS` | |||
#' - `STATE_ABBR` | |||
#' - `STATE_NAME` | |||
#' - `HHS_Region` | |||
#' - `FIPSTXT`) | |||
#' \cr | |||
#' This function retrieves the shapefile, projects to EPSG:5069 and | |||
#' This function retrieves the given shapefile, projects to EPSG:5069 and | |||
#' returns it as an `sf` (simple features) object. | |||
#' | |||
#' @md | |||
#' @export | |||
#' @param basemap select the CDC basemap. One of: | |||
#' - "`national`": outline of the U.S. + AK, HI, PR + VI | |||
#' - "`hhs`": outline of the U.S. + HHS Region Outlines + AK, HI, PR + VI | |||
#' - "`census`": outline of the U.S. + Census Region Outlines + AK, HI, PR + VI | |||
#' - "`states`": outline of the U.S. + State Outlines + AK, HI, PR + VI | |||
#' - "`spread`": outline of the U.S. + State Outlines + AK, HI, PR + VI & Guam | |||
#' - "`surv`": outline of the U.S. + State Outlines + AK, HI, PR + VI | |||
#' @note These are just the basemaps. You need to pair it with the data you wish to visualize. | |||
#' @examples \dontrun{ | |||
#' plot(cdc_coverage_map()) | |||
#' plot(cdc_basemap("national")) | |||
#' } | |||
cdc_coverage_map <- function() { | |||
xsf <- sf::st_read(.cdc_basemap, quiet=TRUE, stringsAsFactors=FALSE) | |||
cdc_basemap <- function(basemap = c("national", "hhs", "census", "states", "spread", "surv")) { | |||
switch( | |||
basemap, | |||
national = .national_outline, | |||
hhs = .hhs_subregions_basemap, | |||
census = .census_divisions_basemap, | |||
states = .states_basemap, | |||
spread = .spread_basemap, | |||
surv = .surv_basemap | |||
) -> selected_map | |||
xsf <- sf::st_read(selected_map, quiet=TRUE, stringsAsFactors=FALSE) | |||
sf::st_crs(xsf) <- 4326 | |||
sf::st_transform(xsf, 5069) | |||
} |
@ -1,10 +1,10 @@ | |||
% Generated by roxygen2: do not edit by hand | |||
% Please edit documentation in R/agd-ipt.r | |||
\name{agd_ipt} | |||
\alias{agd_ipt} | |||
\name{age_group_distribution} | |||
\alias{age_group_distribution} | |||
\title{Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories} | |||
\usage{ | |||
agd_ipt() | |||
age_group_distribution() | |||
} | |||
\description{ | |||
Retrieves the age group distribution of influenza positive tests that are reported by |
@ -0,0 +1,37 @@ | |||
% Generated by roxygen2: do not edit by hand | |||
% Please edit documentation in R/coverage-map.r | |||
\name{cdc_basemap} | |||
\alias{cdc_basemap} | |||
\title{Retrieve CDC U.S. Basemaps} | |||
\usage{ | |||
cdc_basemap(basemap = c("national", "hhs", "census", "states", "spread", | |||
"surv")) | |||
} | |||
\arguments{ | |||
\item{basemap}{select the CDC basemap. One of: | |||
\itemize{ | |||
\item "\code{national}": outline of the U.S. + AK, HI, PR + VI | |||
\item "\code{hhs}": outline of the U.S. + HHS Region Outlines + AK, HI, PR + VI | |||
\item "\code{census}": outline of the U.S. + Census Region Outlines + AK, HI, PR + VI | |||
\item "\code{states}": outline of the U.S. + State Outlines + AK, HI, PR + VI | |||
\item "\code{spread}": outline of the U.S. + State Outlines + AK, HI, PR + VI & Guam | |||
\item "\code{surv}": outline of the U.S. + State Outlines + AK, HI, PR + VI | |||
}} | |||
} | |||
\description{ | |||
The CDC FluView application uses a composite basemaps of coverage areas | |||
within the United States that elides and scales Alaska, Hawaii, | |||
Puerto Rico & the Virgin Islands and some further provide elided and scaled | |||
breakouts for New York City and the District of Columbia.\cr | |||
\cr | |||
This function retrieves the given shapefile, projects to EPSG:5069 and | |||
returns it as an \code{sf} (simple features) object. | |||
} | |||
\note{ | |||
These are just the basemaps. You need to pair it with the data you wish to visualize. | |||
} | |||
\examples{ | |||
\dontrun{ | |||
plot(cdc_basemap("national")) | |||
} | |||
} |
@ -1,32 +0,0 @@ | |||
% Generated by roxygen2: do not edit by hand | |||
% Please edit documentation in R/coverage-map.r | |||
\name{cdc_coverage_map} | |||
\alias{cdc_coverage_map} | |||
\title{Retrieve CDC U.S. Coverage Map} | |||
\usage{ | |||
cdc_coverage_map() | |||
} | |||
\description{ | |||
The CDC FluView application uses a composite basemap of coverage areas | |||
within the United States that elides and scales Alaska, Hawaii and | |||
Puerto Rico and provides elided and scaled breakouts for New York City | |||
and the District of Columbia.\cr | |||
\cr | |||
The basemap provides polygon identifiers by: | |||
\cr | |||
\itemize{ | |||
\item \code{STATE_FIPS} | |||
\item \code{STATE_ABBR} | |||
\item \code{STATE_NAME} | |||
\item \code{HHS_Region} | |||
\item \code{FIPSTXT}) | |||
\cr | |||
This function retrieves the shapefile, projects to EPSG:5069 and | |||
returns it as an \code{sf} (simple features) object. | |||
} | |||
} | |||
\examples{ | |||
\dontrun{ | |||
plot(cdc_coverage_map()) | |||
} | |||
} |
@ -1,26 +1,44 @@ | |||
context("basic functionality") | |||
test_that("we can do something", { | |||
skip_on_cran() | |||
expect_that(agd_ipt(), is_a("data.frame")) | |||
expect_that(geographic_spread(), is_a("data.frame")) | |||
expect_that(surveillance_areas(), is_a("data.frame")) | |||
expect_that(state_data_providers(), is_a("data.frame")) | |||
expect_that(hospitalizations("flusurv"), is_a("data.frame")) | |||
expect_that(hospitalizations("eip"), is_a("data.frame")) | |||
expect_that(hospitalizations("eip", "Colorado"), is_a("data.frame")) | |||
expect_that(hospitalizations("ihsp"), is_a("data.frame")) | |||
expect_that(hospitalizations("ihsp", "Oklahoma"), is_a("data.frame")) | |||
expect_that(ilinet("national"), is_a("data.frame")) | |||
expect_that(ilinet("hhs"), is_a("data.frame")) | |||
expect_that(ilinet("census"), is_a("data.frame")) | |||
expect_that(ilinet("state"), is_a("data.frame")) | |||
expect_that(ili_weekly_activity_indicators(2017), is_a("data.frame")) | |||
expect_that(pi_mortality("national"), is_a("data.frame")) | |||
expect_that(pi_mortality("state"), is_a("data.frame")) | |||
expect_that(pi_mortality("region"), is_a("data.frame")) | |||
expect_that(state_data_providers(), is_a("data.frame")) | |||
expect_that(surveillance_areas(), is_a("data.frame")) | |||
expect_that(who_nrevss("national"), is_a("list")) | |||
expect_that(who_nrevss("hhs"), is_a("list")) | |||
expect_that(who_nrevss("census"), is_a("list")) | |||
expect_that(who_nrevss("state"), is_a("list")) | |||
expect_that(cdc_coverage_map(), is_a("sf")) | |||
expect_that(cdc_basemap("national"), is_a("sf")) | |||
expect_that(cdc_basemap("hhs"), is_a("sf")) | |||
expect_that(cdc_basemap("census"), is_a("sf")) | |||
expect_that(cdc_basemap("states"), is_a("sf")) | |||
expect_that(cdc_basemap("spread"), is_a("sf")) | |||
expect_that(cdc_basemap("surv"), is_a("sf")) | |||
}) |