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0.9.1

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boB Rudis 1 year ago
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DESCRIPTION View File

@ -3,8 +3,8 @@ Type: Package
Encoding: UTF-8
Title: Retrieve Flu Season Data from the United States Centers for Disease Control
and Prevention ('CDC') 'FluView' Portal
Version: 0.9.0
Date: 2019-01-23
Version: 0.9.1
Date: 2020-04-01
Authors@R: c(
person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-5670-2640")),
@ -20,12 +20,12 @@ Authors@R: c(
)
Maintainer: Bob Rudis <bob@rud.is>
Description: The 'U.S.' Centers for Disease Control and Prevention (CDC) maintain
a portal <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for
a portal <https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for
accessing state, regional and national influenza statistics as well as
mortality surveillance data. The web interface makes it difficult and
time-consuming to select and retrieve influenza data. Tools are provided
to access the data provided by the portal's underlying 'API'.
URL: https://gitlab.com/hrbrmstr/cdcfluview
URL: https://git.rud.is/hrbrmstr/cdcfluview
BugReports: https://gitlab.com/hrbrmstr/cdcfluview/issues
License: MIT + file LICENSE
LazyData: true
@ -39,6 +39,7 @@ Imports:
tools,
dplyr,
jsonlite,
tibble,
stats,
utils,
sf,
@ -47,4 +48,4 @@ Imports:
readr,
MMWRweek,
units (>= 0.4-6)
RoxygenNote: 6.1.1
RoxygenNote: 7.1.0

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NAMESPACE View File

@ -40,6 +40,7 @@ importFrom(readr,read_csv)
importFrom(readr,type_convert)
importFrom(sf,st_read)
importFrom(stats,setNames)
importFrom(tibble,tibble)
importFrom(tools,file_path_sans_ext)
importFrom(utils,URLencode)
importFrom(utils,globalVariables)


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NEWS.md View File

@ -2,6 +2,7 @@
- renamed `pi_mortality` columns regarding the week to `week_*` instead of `wk_*`
for consistency with `ilinet` (#21).
- fixed CRAN check errors
# cdcfluview 0.9.0


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R/cdcfluview-package.R View File

@ -15,6 +15,7 @@
#' @importFrom purrr map map_df map_chr map_lgl discard keep
#' @importFrom readr read_csv type_convert
#' @importFrom tools file_path_sans_ext
#' @importFrom tibble tibble
#' @importFrom dplyr left_join bind_rows mutate filter data_frame %>% arrange
#' @importFrom jsonlite fromJSON
#' @importFrom stats setNames


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R/get-weekly-flu-report.r View File

@ -44,7 +44,7 @@ get_weekly_flu_report <- function() {
color <- xml2::xml_text(xml2::xml_find_all(kids, "color"), TRUE)
label <- xml2::xml_text(xml2::xml_find_all(kids, "label"), TRUE)
dplyr::data_frame(
tibble::tibble(
year = period["year"],
week_number = period["number"],
state = abbrev,


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R/mmwr-map.r View File

@ -15,7 +15,7 @@
.tmp <- lapply(1962:2050, .start_date)
mapply(function(.x, .y) {
data_frame(
tibble::tibble(
wk_start = seq(.tmp[[.x]], .tmp[[.y]], "1 week"),
wk_end = wk_start + 6,
year_wk_num = 1:length(wk_start)


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README.Rmd View File

@ -3,13 +3,13 @@ output: rmarkdown::github_document
editor_options:
chunk_output_type: console
---
```{r message=FALSE, warning=FALSE, error=FALSE, include=FALSE}
knitr::opts_chunk$set(message=FALSE, warning=FALSE, fig.retina=2)
options(width=120)
```{r pkg-knitr-opts, include=FALSE}
hrbrpkghelpr::global_opts()
```
```{r badges, results='asis', echo=FALSE, cache=FALSE}
hrbrpkghelpr::stinking_badges()
```
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](https://cran.r-project.org/package=cdcfluview)
[![Travis-CI Build Status](https://travis-ci.org/hrbrmstr/cdcfluview.svg?branch=master)](https://travis-ci.org/hrbrmstr/cdcfluview)
[![Coverage Status](https://img.shields.io/codecov/c/github/hrbrmstr/cdcfluview/master.svg)](https://codecov.io/github/hrbrmstr/cdcfluview?branch=master)
# I M P O R T A N T
@ -181,9 +181,9 @@ count(xdf, weekend, activity_level_label) %>%
```{r nat-pi-mortality}
(nat_pi <- pi_mortality("national"))
select(nat_pi, wk_end, percent_pni, baseline, threshold) %>%
gather(measure, value, -wk_end) %>%
ggplot(aes(wk_end, value)) +
select(nat_pi, week_end, percent_pni, baseline, threshold) %>%
gather(measure, value, -week_end) %>%
ggplot(aes(week_end, value)) +
geom_line(aes(group=measure, color=measure)) +
scale_y_percent() +
scale_color_ipsum(name = NULL, labels=c("Baseline", "Percent P&I", "Threshold")) +
@ -231,4 +231,4 @@ cloc::cloc_pkg_md()
## Code of Conduct
Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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README.md
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View File


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cran-comments.md View File

@ -1,30 +1,10 @@
## Test environments
* local OS X install, R 3.5.2
* local Ubuntu 16.04 R 3.5.2
* ubuntu 16.04 (on travis-ci), R current/devel
* local OS X install, R 3.6.3
* ubuntu 14.04 (on travis-ci), R 3.6.3
* win-builder (devel and release)
## R CMD check results
0 errors | 0 warnings | 1 note
* This is a maintenance update.
## Reverse dependencies
None
---
The CDC removed 2 old API endpoints so those functions have been removed.
There was a bug in the computation of "start week" that resulted in
the "ISO" day being used vs the MMWR/"epi" day being used. This
has also been fixed.
Only some examples run on CRAN due to their time consuming nature and the need
to make external network API calls. Monthly tests are performed on Travis-CI
<https://travis-ci.org/hrbrmstr/cdcfluview> and the package itself has 88%
code coverage during tests <https://codecov.io/github/hrbrmstr/cdcfluview?branch=master>.
All package functions are also evaluated on each new generation of the README.
This an update to fix tibble CRAN check warnings.

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man/cdc_basemap.Rd View File

@ -4,8 +4,9 @@
\alias{cdc_basemap}
\title{Retrieve CDC U.S. Basemaps}
\usage{
cdc_basemap(basemap = c("national", "hhs", "census", "states", "spread",
"surv"))
cdc_basemap(
basemap = c("national", "hhs", "census", "states", "spread", "surv")
)
}
\arguments{
\item{basemap}{select the CDC basemap. One of:


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man/cdcfluview.Rd View File

@ -3,7 +3,6 @@
\docType{package}
\name{cdcfluview}
\alias{cdcfluview}
\alias{cdcfluview-package}
\title{Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal}
\description{
The U.S. Centers for Disease Control (CDC) maintains a portal


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man/census_regions.Rd View File

@ -4,7 +4,9 @@
\name{census_regions}
\alias{census_regions}
\title{Census Region Table}
\format{A data frame with 51 rows and 2 variables}
\format{
A data frame with 51 rows and 2 variables
}
\usage{
data(census_regions)
}


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man/get_flu_data.Rd View File

@ -4,9 +4,12 @@
\alias{get_flu_data}
\title{Retrieves state, regional or national influenza statistics from the CDC (deprecated)}
\usage{
get_flu_data(region = "hhs", sub_region = 1:10,
data_source = "ilinet", years = as.numeric(format(Sys.Date(),
"\%Y")))
get_flu_data(
region = "hhs",
sub_region = 1:10,
data_source = "ilinet",
years = as.numeric(format(Sys.Date(), "\%Y"))
)
}
\arguments{
\item{region}{one of "\code{hhs}", "\code{census}", "\code{national}",


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man/get_hosp_data.Rd View File

@ -4,8 +4,11 @@
\alias{get_hosp_data}
\title{Retrieves influenza hospitalization statistics from the CDC (deprecated)}
\usage{
get_hosp_data(area = "flusurvnet", age_group = "overall",
years = as.numeric(format(Sys.Date(), "\%Y")) - 1)
get_hosp_data(
area = "flusurvnet",
age_group = "overall",
years = as.numeric(format(Sys.Date(), "\%Y")) - 1
)
}
\arguments{
\item{area}{one of "\code{flusurvnet}", "\code{eip}", "\code{ihsp}", or two


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man/hhs_regions.Rd View File

@ -4,7 +4,9 @@
\name{hhs_regions}
\alias{hhs_regions}
\title{HHS Region Table}
\format{A data frame with 59 rows and 4 variables}
\format{
A data frame with 59 rows and 4 variables
}
\usage{
data(hhs_regions)
}


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man/hospitalizations.Rd View File

@ -4,8 +4,11 @@
\alias{hospitalizations}
\title{Laboratory-Confirmed Influenza Hospitalizations}
\usage{
hospitalizations(surveillance_area = c("flusurv", "eip", "ihsp"),
region = "all", years = NULL)
hospitalizations(
surveillance_area = c("flusurv", "eip", "ihsp"),
region = "all",
years = NULL
)
}
\arguments{
\item{surveillance_area}{one of "\code{flusurv}", "\code{eip}", or "\code{ihsp}"}


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man/mmwrid_map.Rd View File

@ -4,7 +4,9 @@
\name{mmwrid_map}
\alias{mmwrid_map}
\title{MMWR ID to Calendar Mappings}
\format{A data frame with 4,592 rows and 4 columns}
\format{
A data frame with 4,592 rows and 4 columns
}
\description{
The CDC uses a unique "Morbidity and Mortality Weekly Report" identifier
for each week that starts at 1 (Ref: < https://www.cdc.gov/mmwr/preview/mmwrhtml/su6004a9.htm>).


+ 2
- 3
man/pi_mortality.Rd View File

@ -4,8 +4,7 @@
\alias{pi_mortality}
\title{Pneumonia and Influenza Mortality Surveillance}
\usage{
pi_mortality(coverage_area = c("national", "state", "region"),
years = NULL)
pi_mortality(coverage_area = c("national", "state", "region"), years = NULL)
}
\arguments{
\item{coverage_area}{coverage area for data (national, state or region)}
@ -29,7 +28,7 @@ NCHS Mortality Surveillance System data are presented by the week the death occu
at the national, state, and HHS Region levels. Data on the percentage of deaths due
to P&I on a national level are released two weeks after the week of death to allow
for collection of enough data to produce a stable percentage. States and HHS regions
with less than 20% of the expected total deaths (average number of total deaths
with less than 20\% of the expected total deaths (average number of total deaths
reported by week during 2008-2012) will be marked as insufficient data. Collection
of complete data is not expected at the time of initial report, and a reliable
percentage of deaths due to P&I is not anticipated at the U.S. Department of Health


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man/who_nrevss.Rd View File

@ -4,8 +4,7 @@
\alias{who_nrevss}
\title{Retrieve WHO/NREVSS Surveillance Data}
\usage{
who_nrevss(region = c("national", "hhs", "census", "state"),
years = NULL)
who_nrevss(region = c("national", "hhs", "census", "state"), years = NULL)
}
\arguments{
\item{region}{one of "\code{national}", "\code{hhs}", "\code{census}", or "\code{state}"}


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