Fixes #25

CRAN-RELEASE

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

DESCRIPTION

@@ -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: 0.9.1
-Date: 2020-04-01
+Version: 0.9.2
+Date: 2020-10-13
 Authors@R: c(
     person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"), 
            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
     time-consuming to select and retrieve influenza data. Tools are provided 
     to access the data provided by the portal's underlying 'API'.
-URL: https://git.rud.is/hrbrmstr/cdcfluview
-BugReports: https://gitlab.com/hrbrmstr/cdcfluview/issues
+URL: https://github.com/hrbrmstr/cdcfluview
+BugReports: https://github.com/hrbrmstr/cdcfluview/issues
 License: MIT + file LICENSE
 LazyData: true
 Suggests:
     testthat,
     covr
 Depends:
-    R (>= 3.2.0)
+    R (>= 3.5.0)
 Imports:
     httr,
+    progress,
     tools,
     dplyr,
     jsonlite,
@@ -48,4 +49,4 @@ Imports:
     readr,
     MMWRweek,
     units (>= 0.4-6)
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1

NAMESPACE

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

NEWS.md

@@ -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_*`
   for consistency with `ilinet` (#21).

R/agd-ipt.r

@@ -41,7 +41,7 @@ age_group_distribution <- function(years = NULL) {
   typ_names <- c("virusid", "vir_description", "vir_label", "vir_startmmwrid", "vir_endmmwrid",
                  "vir_displayorder", "vir_colorname", "vir_color_hexvalue", "vir_labtypeid",
                  "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$Season, sea_names)
   age_df <- stats::setNames(xdat$Age, age_names)
@@ -54,7 +54,7 @@ age_group_distribution <- function(years = NULL) {
   class(vir_df) <- c("tbl_df", "tbl", "data.frame")
 
   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")
 
   vir_df <- vir_df[,vir_df_cols]

R/cdcfluview-package.R

@@ -1,7 +1,7 @@
 #' 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
-#' <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
 #' Mortality Surveillance Data. The Flash interface makes it difficult and
 #' time-consuming to select and retrieve influenza data. This package
@@ -11,7 +11,7 @@
 #' @name cdcfluview
 #' @docType package
 #' @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 readr read_csv type_convert
 #' @importFrom tools file_path_sans_ext

R/get-flu-data.r

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

R/get-weekly-flu-report.r

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

README.Rmd

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

README.md

@@ -42,7 +42,7 @@ Control and Prevention (‘CDC’) ‘FluView’ Portal
 ## Description
 
 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
 Surveillance Data. The Flash interface makes it difficult and
 time-consuming to select and retrieve influenza data. This package
@@ -107,10 +107,12 @@ back-ported to the master branch when necessary.
 ``` r
 # CRAN
 install.packages("cdcfluview")
-# master branch
-devtools::install_git("https://sr.ht/~hrbrmstr/cdcfluview")
-devtools::install_git("https://gitlab.com/hrbrmstr/cdcfluview")
-devtools::install_github("hrbrmstr/cdcfluview")
+
+# main branch
+remotes::install_git("https://git.rud.is/hrbrmstr/cdcfluview.git")
+remotes::install_git("https://sr.ht/~hrbrmstr/cdcfluview")
+remotes::install_git("https://gitlab.com/hrbrmstr/cdcfluview")
+remotes::install_github("hrbrmstr/cdcfluview")
 ```
 
 ## Usage
@@ -120,9 +122,9 @@ library(cdcfluview)
 library(hrbrthemes)
 library(tidyverse)
 
-# current verison
+# current versoon
 packageVersion("cdcfluview")
-## [1] '0.9.1'
+## [1] '0.9.2'
 ```
 
 ### 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…
 ## $ 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,…
-## $ 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_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…

cran-comments.md

@@ -1,10 +1,12 @@
 ## Test environments
-* local OS X install, R 3.6.3
-* ubuntu 14.04 (on travis-ci), R 3.6.3
-* win-builder (devel and release)
+* local R installation, R 4.0.3
+* ubuntu 16.04 (on travis-ci), R 4.0.3
+* win-builder (devel)
 
 ## 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

man/cdcfluview.Rd

@@ -6,7 +6,7 @@
 \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
-\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
 Mortality Surveillance Data. The Flash interface makes it difficult and
 time-consuming to select and retrieve influenza data. This package