0.9.1

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: 0.9.0
+Version: 0.9.1
-Date: 2019-01-23
+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

NAMESPACE

@@ -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)

NEWS.md

@@ -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
 

R/cdcfluview-package.R

@@ -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

R/get-weekly-flu-report.r

@@ -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,

R/mmwr-map.r

@@ -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)

README.Rmd

@@ -3,13 +3,13 @@ output: rmarkdown::github_document
 editor_options: 
   chunk_output_type: console
 ---
-```{r message=FALSE, warning=FALSE, error=FALSE, include=FALSE}
+```{r pkg-knitr-opts, include=FALSE}
-knitr::opts_chunk$set(message=FALSE, warning=FALSE, fig.retina=2)
+hrbrpkghelpr::global_opts()
-options(width=120)
+```
+
+```{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) %>% 
+select(nat_pi, week_end, percent_pni, baseline, threshold) %>% 
-  gather(measure, value, -wk_end) %>% 
+  gather(measure, value, -week_end) %>% 
-  ggplot(aes(wk_end, value)) + 
+  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.

cran-comments.md

@@ -1,30 +1,10 @@
 ## Test environments
-
+* local OS X install, R 3.6.3
-* local OS X install, R 3.5.2
+* ubuntu 14.04 (on travis-ci), R 3.6.3
-* local Ubuntu 16.04 R 3.5.2
-* ubuntu 16.04 (on travis-ci), R current/devel
 * win-builder (devel and release)
 
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note
 
-* This is a maintenance update.
+This an update to fix tibble CRAN check warnings.
-
-## 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.

man/cdc_basemap.Rd

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

man/cdcfluview.Rd

@@ -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

man/census_regions.Rd

@@ -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)
 }

man/get_flu_data.Rd

@@ -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,
+get_flu_data(
-  data_source = "ilinet", years = as.numeric(format(Sys.Date(),
+  region = "hhs",
-  "\%Y")))
+  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}",

man/get_hosp_data.Rd

@@ -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",
+get_hosp_data(
-  years = as.numeric(format(Sys.Date(), "\%Y")) - 1)
+  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

man/hhs_regions.Rd

@@ -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)
 }

man/hospitalizations.Rd

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

man/mmwrid_map.Rd

@@ -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>).

man/pi_mortality.Rd

@@ -4,8 +4,7 @@
 \alias{pi_mortality}
 \title{Pneumonia and Influenza Mortality Surveillance}
 \usage{
-pi_mortality(coverage_area = c("national", "state", "region"),
+pi_mortality(coverage_area = c("national", "state", "region"), years = NULL)
-  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

man/who_nrevss.Rd

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