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cdcfluview
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Fixes #25

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boB Rudis 4 years ago
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c2b16f4911
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1f5996af24
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12 changed files with 48 additions and 36 deletions
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  1. 4
      CRAN-RELEASE
  2. 13
      DESCRIPTION
  3. 1
      NAMESPACE
  4. 7
      NEWS.md
  5. 4
      R/agd-ipt.r
  6. 4
      R/cdcfluview-package.R
  7. 4
      R/get-flu-data.r
  8. 4
      R/get-weekly-flu-report.r
  9. 12
      README.Rmd
  10. 17
      README.md
  11. 12
      cran-comments.md
  12. 2
      man/cdcfluview.Rd

4
CRAN-RELEASE
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@ -1,2 +1,2 @@
This package was submitted to CRAN on 2019-01-24. This package was submitted to CRAN on 2020-04-02.
Once it is accepted, delete this file and tag the release (commit 2b6698f1c2). Once it is accepted, delete this file and tag the release (commit c2b16f4911).

13
DESCRIPTION
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@ -3,8 +3,8 @@ Type: Package
Encoding: UTF-8 Encoding: UTF-8
Title: Retrieve Flu Season Data from the United States Centers for Disease Control Title: Retrieve Flu Season Data from the United States Centers for Disease Control
and Prevention ('CDC') 'FluView' Portal and Prevention ('CDC') 'FluView' Portal
Version: 0.9.1 Version: 0.9.2
Date: 2020-04-01 Date: 2020-10-13
Authors@R: c( Authors@R: c(
person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"), person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-5670-2640")), comment = c(ORCID = "0000-0001-5670-2640")),
@ -25,17 +25,18 @@ Description: The 'U.S.' Centers for Disease Control and Prevention (CDC) maintai
mortality surveillance data. The web interface makes it difficult and mortality surveillance data. The web interface makes it difficult and
time-consuming to select and retrieve influenza data. Tools are provided time-consuming to select and retrieve influenza data. Tools are provided
to access the data provided by the portal's underlying 'API'. to access the data provided by the portal's underlying 'API'.
URL: https://git.rud.is/hrbrmstr/cdcfluview URL: https://github.com/hrbrmstr/cdcfluview
BugReports: https://gitlab.com/hrbrmstr/cdcfluview/issues BugReports: https://github.com/hrbrmstr/cdcfluview/issues
License: MIT + file LICENSE License: MIT + file LICENSE
LazyData: true LazyData: true
Suggests: Suggests:
testthat, testthat,
covr covr
Depends: Depends:
R (>= 3.2.0) R (>= 3.5.0)
Imports: Imports:
httr, httr,
progress,
tools, tools,
dplyr, dplyr,
jsonlite, jsonlite,
@ -48,4 +49,4 @@ Imports:
readr, readr,
MMWRweek, MMWRweek,
units (>= 0.4-6) units (>= 0.4-6)
RoxygenNote: 7.1.0 RoxygenNote: 7.1.1

1
NAMESPACE
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@ -20,6 +20,7 @@ export(surveillance_areas)
export(who_nrevss) export(who_nrevss)
import(MMWRweek) import(MMWRweek)
import(httr) import(httr)
import(progress)
import(units) import(units)
import(xml2) import(xml2)
importFrom(dplyr,"%>%") importFrom(dplyr,"%>%")

7
NEWS.md
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@ -1,4 +1,9 @@
#cdcfluview 0.9.1 # cdcfluview 0.9.2
- Underlying hidden API changed (h/t @Ian-McGovern — #25 & CRAN & Travis) for `age_group_distribution()` so
this has been fixed and the warnings for `dplyr::progress_estimated()` were also fixed.
# cdcfluview 0.9.1
- renamed `pi_mortality` columns regarding the week to `week_*` instead of `wk_*` - renamed `pi_mortality` columns regarding the week to `week_*` instead of `wk_*`
for consistency with `ilinet` (#21). for consistency with `ilinet` (#21).

4
R/agd-ipt.r
View File

@ -41,7 +41,7 @@ age_group_distribution <- function(years = NULL) {
typ_names <- c("virusid", "vir_description", "vir_label", "vir_startmmwrid", "vir_endmmwrid", typ_names <- c("virusid", "vir_description", "vir_label", "vir_startmmwrid", "vir_endmmwrid",
"vir_displayorder", "vir_colorname", "vir_color_hexvalue", "vir_labtypeid", "vir_displayorder", "vir_colorname", "vir_color_hexvalue", "vir_labtypeid",
"vir_sortid") "vir_sortid")
vir_names <- c("virusid", "ageid", "count", "mmwrid", "seasonid", "publishyearweekid", "loaddatetime") vir_names <- c("virusid", "ageid", "count", "mmwrid", "seasonid")
sea_df <- stats::setNames(xdat$Season, sea_names) sea_df <- stats::setNames(xdat$Season, sea_names)
age_df <- stats::setNames(xdat$Age, age_names) age_df <- stats::setNames(xdat$Age, age_names)
@ -54,7 +54,7 @@ age_group_distribution <- function(years = NULL) {
class(vir_df) <- c("tbl_df", "tbl", "data.frame") class(vir_df) <- c("tbl_df", "tbl", "data.frame")
vir_df_cols <- c("sea_label", "age_label", "vir_label", "count", "mmwrid", "seasonid", vir_df_cols <- c("sea_label", "age_label", "vir_label", "count", "mmwrid", "seasonid",
"publishyearweekid", "sea_description", "sea_startweek", "sea_description", "sea_startweek",
"sea_endweek", "vir_description", "vir_startmmwrid", "vir_endmmwrid") "sea_endweek", "vir_description", "vir_startmmwrid", "vir_endmmwrid")
vir_df <- vir_df[,vir_df_cols] vir_df <- vir_df[,vir_df_cols]

4
R/cdcfluview-package.R
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@ -1,7 +1,7 @@
#' Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal #' Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal
#' #'
#' The U.S. Centers for Disease Control (CDC) maintains a portal #' The U.S. Centers for Disease Control (CDC) maintains a portal
#' <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for #' <https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for
#' accessing state, regional and national influenza statistics as well as #' accessing state, regional and national influenza statistics as well as
#' Mortality Surveillance Data. The Flash interface makes it difficult and #' Mortality Surveillance Data. The Flash interface makes it difficult and
#' time-consuming to select and retrieve influenza data. This package #' time-consuming to select and retrieve influenza data. This package
@ -11,7 +11,7 @@
#' @name cdcfluview #' @name cdcfluview
#' @docType package #' @docType package
#' @author Bob Rudis (bob@@rud.is) #' @author Bob Rudis (bob@@rud.is)
#' @import httr MMWRweek xml2 units #' @import httr MMWRweek xml2 units progress
#' @importFrom purrr map map_df map_chr map_lgl discard keep #' @importFrom purrr map map_df map_chr map_lgl discard keep
#' @importFrom readr read_csv type_convert #' @importFrom readr read_csv type_convert
#' @importFrom tools file_path_sans_ext #' @importFrom tools file_path_sans_ext

4
R/get-flu-data.r
View File

@ -142,9 +142,9 @@ get_flu_data <- function(region="hhs", sub_region=1:10,
files <- unzip(out_file, exdir=out_dir, overwrite=TRUE) files <- unzip(out_file, exdir=out_dir, overwrite=TRUE)
pb <- dplyr::progress_estimated(length(files)) pb <- progress::progress_bar$new(total = length(files))
lapply(files, function(x) { lapply(files, function(x) {
pb$tick()$print() pb$tick()
ct <- ifelse(grepl("who", x, ignore.case=TRUE), 1, 1) ct <- ifelse(grepl("who", x, ignore.case=TRUE), 1, 1)
suppressMessages(readr::read_csv(x, skip=ct)) suppressMessages(readr::read_csv(x, skip=ct))
}) -> file_list }) -> file_list

4
R/get-weekly-flu-report.r
View File

@ -27,12 +27,12 @@ get_weekly_flu_report <- function() {
# for each period extract the state information and # for each period extract the state information and
# shove it all into a data frame # shove it all into a data frame
pb <- dplyr::progress_estimated(length(periods)) pb <- progress::progress_bar$new(total = length(periods))
suppressWarnings(suppressMessages( suppressWarnings(suppressMessages(
purrr::map_df(periods, function(period) { purrr::map_df(periods, function(period) {
pb$tick()$print() pb$tick()
tp <- sprintf("//timeperiod[@number='%s' and @year='%s']", tp <- sprintf("//timeperiod[@number='%s' and @year='%s']",
period["number"], period["year"]) period["number"], period["year"])

12
README.Rmd
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@ -72,10 +72,12 @@ All development happens in branches now with only critical fixes being back-port
```{r eval=FALSE} ```{r eval=FALSE}
# CRAN # CRAN
install.packages("cdcfluview") install.packages("cdcfluview")
# master branch
devtools::install_git("https://sr.ht/~hrbrmstr/cdcfluview") # main branch
devtools::install_git("https://gitlab.com/hrbrmstr/cdcfluview") remotes::install_git("https://git.rud.is/hrbrmstr/cdcfluview.git")
devtools::install_github("hrbrmstr/cdcfluview") remotes::install_git("https://sr.ht/~hrbrmstr/cdcfluview")
remotes::install_git("https://gitlab.com/hrbrmstr/cdcfluview")
remotes::install_github("hrbrmstr/cdcfluview")
``` ```
## Usage ## Usage
@ -85,7 +87,7 @@ library(cdcfluview)
library(hrbrthemes) library(hrbrthemes)
library(tidyverse) library(tidyverse)
# current verison # current version
packageVersion("cdcfluview") packageVersion("cdcfluview")
``` ```

17
README.md
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@ -42,7 +42,7 @@ Control and Prevention (‘CDC’) ‘FluView’ Portal
## Description ## Description
The U.S. Centers for Disease Control (CDC) maintains a portal The U.S. Centers for Disease Control (CDC) maintains a portal
<http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing <https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing
state, regional and national influenza statistics as well as Mortality state, regional and national influenza statistics as well as Mortality
Surveillance Data. The Flash interface makes it difficult and Surveillance Data. The Flash interface makes it difficult and
time-consuming to select and retrieve influenza data. This package time-consuming to select and retrieve influenza data. This package
@ -107,10 +107,12 @@ back-ported to the master branch when necessary.
``` r ``` r
# CRAN # CRAN
install.packages("cdcfluview") install.packages("cdcfluview")
# master branch
devtools::install_git("https://sr.ht/~hrbrmstr/cdcfluview") # main branch
devtools::install_git("https://gitlab.com/hrbrmstr/cdcfluview") remotes::install_git("https://git.rud.is/hrbrmstr/cdcfluview.git")
devtools::install_github("hrbrmstr/cdcfluview") remotes::install_git("https://sr.ht/~hrbrmstr/cdcfluview")
remotes::install_git("https://gitlab.com/hrbrmstr/cdcfluview")
remotes::install_github("hrbrmstr/cdcfluview")
``` ```
## Usage ## Usage
@ -120,9 +122,9 @@ library(cdcfluview)
library(hrbrthemes) library(hrbrthemes)
library(tidyverse) library(tidyverse)
# current verison # current versoon
packageVersion("cdcfluview") packageVersion("cdcfluview")
## [1] '0.9.1' ## [1] '0.9.2'
``` ```
### Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories ### Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories
@ -137,7 +139,6 @@ glimpse(age_group_distribution(years=2015))
## $ count <int> 0, 1, 0, 1, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 3, 2, 2, 3, 3, 3, 0, 0, 2, 0, 1, 1, 0, 0… ## $ count <int> 0, 1, 0, 1, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 3, 2, 2, 3, 3, 3, 0, 0, 2, 0, 1, 1, 0, 0…
## $ mmwrid <int> 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2… ## $ mmwrid <int> 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2…
## $ seasonid <int> 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,… ## $ seasonid <int> 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,…
## $ publishyearweekid <int> 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3038, 3…
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "… ## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "…
## $ sea_startweek <int> 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2… ## $ sea_startweek <int> 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2…
## $ sea_endweek <int> 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2… ## $ sea_endweek <int> 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2…

12
cran-comments.md
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@ -1,10 +1,12 @@
## Test environments ## Test environments
* local OS X install, R 3.6.3 * local R installation, R 4.0.3
* ubuntu 14.04 (on travis-ci), R 3.6.3 * ubuntu 16.04 (on travis-ci), R 4.0.3
* win-builder (devel and release) * win-builder (devel)
## R CMD check results ## R CMD check results
0 errors | 0 warnings | 1 note 0 errors | 0 warnings | 0 notes
This an update to fix tibble CRAN check warnings. * This is a maintanance/bug-fix release
* Fixed CRAN check error for age_group_distribution function
* Fixed dplyr warning

2
man/cdcfluview.Rd
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@ -6,7 +6,7 @@
\title{Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal} \title{Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal}
\description{ \description{
The U.S. Centers for Disease Control (CDC) maintains a portal The U.S. Centers for Disease Control (CDC) maintains a portal
\url{http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html} for \url{https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html} for
accessing state, regional and national influenza statistics as well as accessing state, regional and national influenza statistics as well as
Mortality Surveillance Data. The Flash interface makes it difficult and Mortality Surveillance Data. The Flash interface makes it difficult and
time-consuming to select and retrieve influenza data. This package time-consuming to select and retrieve influenza data. This package

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