From 88035e27130828b75aed7a422c59c82f9f6dc800 Mon Sep 17 00:00:00 2001 From: Richard Martin-Nielsen Date: Thu, 2 Dec 2021 19:07:46 +0200 Subject: [PATCH] Squashed commit of the following: commit 04009e7157970b5abe68acb1d8aa07242e82d8b0 Merge: d1630f56 68200f9b Author: Sam Abbott Date: Wed Dec 1 14:27:05 2021 +0000 Merge pull request #443 from epiforecasts/feature-boostrap-5-in-docs Switch to bootstrap 5 for pkgdown commit 68200f9bf7a9f359ce3757ebc00ab233766dc624 Author: Sam Abbott Date: Wed Dec 1 13:52:07 2021 +0000 switch to bootstrap 5 for pkgdown commit d1630f564618840e3ea6941fbebfdba43d1fbe3e Merge: 71d7b1f1 ddbdb8e8 Author: Sam Abbott Date: Wed Dec 1 13:48:12 2021 +0000 Merge pull request #442 from epiforecasts/fix-logo Fix giant logo by specifying width instead of height commit ddbdb8e8301c76facdb7da662ed533df3c811f1d Merge: a19643ff 71d7b1f1 Author: Sam Abbott Date: Wed Dec 1 13:47:52 2021 +0000 Merge branch 'master' into fix-logo commit a19643ff780775a8a3bfc6c4b7813000038fc9af Author: Hugo Gruson Date: Wed Dec 1 14:30:11 2021 +0100 Fix giant logo by specifying width instead of height fix #440 commit 71d7b1f129ae397eb528dd75757de8d4c4fa8afb Merge: 2e5cabc1 fb10488e Author: Sam Abbott Date: Wed Dec 1 10:21:14 2021 +0000 Merge pull request #438 from epiforecasts/rm-joss-action Remove action re-building JOSS paper commit fb10488e23a87ab4ee55fd2c5965ac80e44a35ca Author: Hugo Gruson Date: Tue Nov 30 19:09:00 2021 +0100 Remove action re-building JOSS paper commit 2e5cabc18dae7d6d24d728c49f19e4c92759981b Author: Sam Abbott Date: Mon Nov 29 13:43:29 2021 +0000 Update NEWS.md commit d1350d9a88572e0a33804e886fffa24eef69ba41 Merge: 8c77b825 782256cd Author: Sam Abbott Date: Mon Nov 29 13:41:00 2021 +0000 Merge pull request #436 from epiforecasts/fix-germany fix Germany case/death data commit 782256cdbe98d8246376a80392ea3e7fad5de038 Author: Sebastian Funk Date: Mon Nov 29 07:40:01 2021 +0000 add missing sum commit 4c7cb8c0d74205e664399b38a780cd62de768667 Author: Sebastian Funk Date: Mon Nov 29 07:19:09 2021 +0000 fix Germany case/death data commit 8c77b825d0607e8a836a4f525b39a11ce1a01af0 Author: Sam Abbott Date: Tue Oct 12 10:20:55 2021 +0100 Check package once a week vs daily commit b5b9cbf7b2aa19d5490294f417f3badaeb3a2bb0 Merge: c782b57b 91d0f0c8 Author: Sam Abbott Date: Thu Sep 30 13:01:56 2021 +0100 Merge pull request #428 from RichardMN/update-Vietnam-url-and-docs Update vietnam url and docs commit 91d0f0c807804ba7cbe78d09b68b5e3a92613f5e Author: Richard Martin-Nielsen Date: Thu Sep 30 09:12:37 2021 +0300 Rebuilt all country data table and Vietnam documentation commit 1d6c02485db643a681ac2d57c80ed0250a6108e1 Author: Tri Luu Date: Thu Sep 30 09:38:37 2021 +0700 Update stable API URL of Vietnam --- .github/workflows/check-full.yaml | 2 +- .github/workflows/draft-pdf.yml | 23 ----------------------- NEWS.md | 4 ++++ R/Germany.R | 8 ++++---- R/Vietnam.R | 12 ++++++------ README.Rmd | 2 +- README.md | 24 ++++++++++++------------ _pkgdown.yml | 1 + data/all_country_data.rda | Bin 3011 -> 3010 bytes man/Vietnam.Rd | 2 +- 10 files changed, 30 insertions(+), 48 deletions(-) delete mode 100644 .github/workflows/draft-pdf.yml diff --git a/.github/workflows/check-full.yaml b/.github/workflows/check-full.yaml index 8e759ccf..e51ccf81 100644 --- a/.github/workflows/check-full.yaml +++ b/.github/workflows/check-full.yaml @@ -7,7 +7,7 @@ name: R-CMD-check branches: - master schedule: - - cron: '0 0 * * *' + - cron: '0 0 * * 1' pull_request: branches: - '*' diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml deleted file mode 100644 index 5b7b614c..00000000 --- a/.github/workflows/draft-pdf.yml +++ /dev/null @@ -1,23 +0,0 @@ -on: [push] - -jobs: - paper: - runs-on: ubuntu-latest - name: Paper Draft - steps: - - name: Checkout - uses: actions/checkout@v2 - - name: Build draft PDF - uses: openjournals/openjournals-draft-action@master - with: - journal: joss - # This should be the path to the paper within your repo. - paper-path: inst/paper/paper.md - - name: Upload - uses: actions/upload-artifact@v1 - with: - name: paper - # This is the output path where Pandoc will write the compiled - # PDF. Note, this should be the same directory as the input - # paper.md - path: inst/paper/paper.pdf diff --git a/NEWS.md b/NEWS.md index efcbe4cf..17b3e22f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -11,6 +11,10 @@ This release is currently under development * Updated the package logo to include the newly supported data sets. +## Bug fixes + +- Fixed a bug in the data sourced from Germany so that instead of treating it as a line list of individuals it is treated as a relatively finely resolved count data which needs to be summed up (by @sbfnk). + # covidregionaldata 0.9.2 This release adds support for the Covid19 Data Hub which includes Google and Apple mobility data amongst a large range of other data sets, data from the European Commission's Joint Research Centre which is at both the regional and national level, and individual sources for regional data from several countries. Package updates have been made in line with a software review at the [Journal of Open Source Software](https://github.com/openjournals/joss-reviews/issues/3290). Finally, this release exposes more of the testing infrastructure to users and adds a package hexsticker. diff --git a/R/Germany.R b/R/Germany.R index a4108765..3108357a 100644 --- a/R/Germany.R +++ b/R/Germany.R @@ -94,8 +94,8 @@ Germany <- R6::R6Class("Germany", .data$date ) %>% summarise( - cases_new = as.numeric(sum(.data$cases_new > 0)), - deaths_new = as.numeric(sum(.data$deaths_new > 0)) + cases_new = as.numeric(sum(.data$cases_new)), + deaths_new = as.numeric(sum(.data$deaths_new)) ) %>% ungroup() }, @@ -116,8 +116,8 @@ Germany <- R6::R6Class("Germany", .data$level_2_region, .data$date ) %>% summarise( - cases_new = as.numeric(sum(.data$cases_new > 0)), - deaths_new = as.numeric(sum(.data$deaths_new > 0)) + cases_new = as.numeric(sum(.data$cases_new)), + deaths_new = as.numeric(sum(.data$deaths_new)) ) %>% ungroup() } diff --git a/R/Vietnam.R b/R/Vietnam.R index ebc35abb..12758396 100644 --- a/R/Vietnam.R +++ b/R/Vietnam.R @@ -4,7 +4,7 @@ #' @description Information for downloading, cleaning #' and processing covid-19 region data for Vietnam. #' -#' @source \url{https://covid.ncsc.gov.vn} +#' @source \url{https://covid19.ncsc.gov.vn} #' @export #' @concept dataset #' @family subnational @@ -29,10 +29,10 @@ Vietnam <- R6::R6Class("Vietnam", #' @field common_data_urls List of named links to raw data. common_data_urls = list( # nolint start - "case_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=case_by_time", - "death_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=death_by_time", - "recovered_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=recovered_by_time", - "provinces" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces" + "case_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=case_by_time", + "death_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=death_by_time", + "recovered_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=recovered_by_time", + "provinces" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces" # nolint end ), #' @field source_data_cols existing columns within the raw data @@ -44,7 +44,7 @@ Vietnam <- R6::R6Class("Vietnam", "Public COVID-19 for Vietnam, curated by NCSC's COVID-19 team", #' @field source_url Website address for explanation/introduction of the #' data - source_url = "https://covid.ncsc.gov.vn", + source_url = "https://covid19.ncsc.gov.vn", #' @description Set up a table of region codes for clean data #' @importFrom tibble tibble diff --git a/README.Rmd b/README.Rmd index 6dac1dd8..a42bda15 100644 --- a/README.Rmd +++ b/README.Rmd @@ -11,7 +11,7 @@ knitr::opts_chunk$set( ) ``` -# Subnational data for the COVID-19 outbreak +# Subnational data for the COVID-19 outbreak [![R-CMD-check](https://github.com/epiforecasts/covidregionaldata/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/covidregionaldata/actions) [![Codecov test coverage](https://codecov.io/gh/epiforecasts/covidregionaldata/branch/master/graph/badge.svg)](https://codecov.io/gh/epiforecasts/covidregionaldata?branch=master) [![Data status](https://img.shields.io/badge/Data-status-lightblue.svg?style=flat)](https://epiforecasts.io/covidregionaldata/articles/supported-countries.html) [![metacran downloads](http://cranlogs.r-pkg.org/badges/grand-total/covidregionaldata?color=ff69b4)](https://cran.r-project.org/package=covidregionaldata) diff --git a/README.md b/README.md index b452cac6..537bfece 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -# Subnational data for the COVID-19 outbreak +# Subnational data for the COVID-19 outbreak [![R-CMD-check](https://github.com/epiforecasts/covidregionaldata/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/covidregionaldata/actions) [![Codecov test @@ -118,18 +118,18 @@ nots <- get_national_data() #> Processing data nots #> # A tibble: 142,911 × 15 -#> date un_region who_region country iso_code cases_new cases_total -#> -#> 1 2020-01-03 Asia EMRO Afghanistan AF 0 0 -#> 2 2020-01-03 Europe EURO Albania AL 0 0 -#> 3 2020-01-03 Africa AFRO Algeria DZ 0 0 -#> 4 2020-01-03 Oceania WPRO American Samoa AS 0 0 -#> 5 2020-01-03 Europe EURO Andorra AD 0 0 -#> 6 2020-01-03 Africa AFRO Angola AO 0 0 -#> 7 2020-01-03 Americas AMRO Anguilla AI 0 0 +#> date un_region who_region country iso_code cases_new cases_total +#> +#> 1 2020-01-03 Asia EMRO Afghanistan AF 0 0 +#> 2 2020-01-03 Europe EURO Albania AL 0 0 +#> 3 2020-01-03 Africa AFRO Algeria DZ 0 0 +#> 4 2020-01-03 Oceania WPRO American Samoa AS 0 0 +#> 5 2020-01-03 Europe EURO Andorra AD 0 0 +#> 6 2020-01-03 Africa AFRO Angola AO 0 0 +#> 7 2020-01-03 Americas AMRO Anguilla AI 0 0 #> 8 2020-01-03 Americas AMRO Antigua & Barbuda AG 0 0 -#> 9 2020-01-03 Americas AMRO Argentina AR 0 0 -#> 10 2020-01-03 Asia EURO Armenia AM 0 0 +#> 9 2020-01-03 Americas AMRO Argentina AR 0 0 +#> 10 2020-01-03 Asia EURO Armenia AM 0 0 #> # … with 142,901 more rows, and 8 more variables: deaths_new , #> # deaths_total , recovered_new , recovered_total , #> # hosp_new , hosp_total , tested_new , tested_total diff --git a/_pkgdown.yml b/_pkgdown.yml index 881c72f3..27a7fa1e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,5 +1,6 @@ url: epiforecasts.io/covidregionaldata/ template: + bootstrap: 5 params: bootswatch: lumen docsearch: diff --git a/data/all_country_data.rda b/data/all_country_data.rda index d89f20b72ca2ae935868025d54b7b42352b4bf12..0d177cf3b295c98fd3073a6bff41fed06d6b0b9d 100644 GIT binary patch delta 2989 zcmV;e3sUsM7s3}2LRx4!F+o`-Q&~VT@;v|tOpy^Jf4iE2L4ewUmVri-R!}Xd4HN+h zB$`YhO{tOSQ_(VdXwjtg8fiSE(H5pn8ollho9Dn?in+(AtDl@Mug$JfQUe z0001J00000001%>02}}S000000g%uD000000006_NRuS>CL>JMJdpJb28XG#fCJRg zpa1{>1ONtr0Fl2He=-6FiIY+4o|#V~dY+PIlQM^>$n`dp^+)QD)eqF3rh19$U}$6n zf6@}co_iZr44EW{9zcCg^C|q+nvmVg5(h&ehwtF08~SDEBmk5{AQ0}naRbu_m62Rt zzPwKoKoGJ@c0r1-lkoL(`bj0pVZ|63q-cqVNsO!p{H*7Se^PvCf1fo^JXdA7et*?$ zjY7gxazc{~9(1vdff6bpc)~`491Qn1X&Nsk6c`#%I?%~bwnOoj=ad^+M=Q0+F@8R95NqV1PwNTjzZ&co;2cxL6KSkmi2mdj+d* zLnnOzo!aCDHVF}&$!JOALW8>d?UCrg0jhcVLEVQEoK$fbEpwHd;?8H%EsTW1~uU`iq{`XzMrzFb8zcTs`?e3&bu2NFQn~g8C z9kEe_{-y?}hIH27w6)07eLGX8H9=G=u}yPc<{P%i+|{Gp)wTCuJKqkE4vhMoc$_Y- znh6yt)L?b8s<>z|T2G<_+`o>0gc4rem+`-E z$(%IIp`=ckb_z=_*_WHEamfbjuCOLl zcB)}SMmN|QY_{THsk#X4-^Zt{e4(gg%(;v;e`6!0HfK~8*L3d7sIVrbS z%boe$98LQVS!@@SF$lEK)x3iuTgR%(mJmdXYrgY%=kA#L?SfX?WMz4;moozCj)uc= ze{Q@3Lp($xcb5_gy<-H%1%U{B7YH(mv7CS zK=o#yf6tK|7#@ba@6DtIbq|w%_Vjumz&RB7esT_`4Y4ZhD{C)spME7}jX^WfISOaZSXge< znz5*2IumSUp&(+J4KdgcXe3Z{e;=p%cX#+<%6OVJpVfTLH-(veH7I|yUIJ-oL!$8(1fN3-)(jh>T)XJ-p6*Msyrw%r&QDXa>Eerv6e^AIIxGn7g z-aSUM+C55wpt*z8bj!)i8;cMd47>zySXl;f*m-qWc&qkZTzQy?VPe8Ji>X*uTj}$iWY;O*;)K3! zk_^yZR=)A?ie-Dz*o3i+f5g2COCcy2S|Cvz=Ml_>i9t39eO;G&d?zrl9n~0D>9*j& zg$!SffsikHc1{VQ2Z+>mK`@`wU{nIcWwG2iBYTTR&mB#{L0GE{BEAi!1XHis^Ajj) zejY;sfHHi3?wX2a2+lT0{_|n)W~xzEgx5bt$RCxBzSxa9+V1!re?!m=TZGW>7DA$e z+C>Hs6*$zC;)WaGY>sQVY+jejt^;VXC!pO;Yh9m86hL?>l(g5lv!Fm|86;$pQi{P{ zf}km9?ZmFoV+Px7&};^)gO+_#GYI+x=%Tj@sxlEniMZQse~(?i4iAri>-I*!$79#{ zahx9~Mo(4_ZLinPutomNb9KAF%eA5Jgx;ma-0Ox76&T4Kwi%FLdvds=LE#h~&dK0k zq?Rri7r^hy)2U78qcfc{349cxQi>RbiBoibA)9XSGOIBlDNUCTjUv7RV)$}$x!n)Q z=W=omq&fM_f7lOLtfhj2s3N znPQ?ce+z?akf5-I8qkzpTP#o5B^tO=AXP3PzJ1!fg&d$LRus*wLK_lb?y+e+$%)$Q2D|h=5)$?zSthg#n3EKQD|j z4{rmAB&A@khPm2ZY-%GD20&CP#N%5*dJDf&(u)MJLI2T?LE+86Q-N58(T{=B1jyVV z|E~$)-`~T)W^|83nA39<+vyynh)~EnMCwUP*oq47KV2iLc3d360T+mU4qg8PoL6N^ ze_QC!#~sjB&Gi;U`5y4oGV?%1o0`Hgce3oFs>Y55@wJ`e%ootwm_90bbz12{X zsJaYrLR}V~7s0$XNV%3Y5s^TNJ+Rtxf6^SJkf8vwRD`j9`f0$L0O3^oJ6ncBLbdw_ z7GO>UP!mGYahXTNwX~cUR0j%qsYnG>3EHB?$kznTh4vWjypSu^C3tP^iFdRS+(qNnWPY7(ZQ#M{R{y)lC8AG;Hn{u*71hgOhjKQ^_8ho~BPzPf@0g4FezsjF|zWOqx9rrU~f*pp^h72{cbs+JGLWfB*mh z0000005l$;0ZIS@U;rV2XaE2cO)vle00004z$8eK=`=E_`lp#sB?fI#=`wmAspx7C zQ%9%)f2Ky%4FJGKm}&qr8~^|S00001kk9}C0000000KmU0RSe3K~1UZVlf(;8fau` zpbUnZGCd{}On_(r9yEm@vdnivDAGw9s0VT9Y9H#{I7rJ&;tjOIAEC~`nElyyi2x-S zOal($y%;@^YbGcSy~TCoGXO%Fnu=tGyMwFif85&HB$j#{SAi)MWb%Z@Rs(icbHyn> zG(E0rpN=c4+&_QvwnkxLDY+p@griTJvB<*RMX_6xF|;N2UoA6qUvpMXLo95w?wTu` zEZVkQ)+y=3Os##ag=nF6TJ<$oIg=dx<-a|a&FX|GxVfJ*!T)!SEA7S<_FjCT*2+0u zf2Ki;!_}8TE=;n`N zWl1vrYEMFiW2+30ReuxzJseWnU#YRclp=V_rBQh6s7 z2u4PPu|6(FB!VK4MR8C_$g~O9%S?;4>e8KQ!~{UwZ8l*r%&RP@e{1Hw z)y;S5J1081dv~nxYQANz_16$wMo;HvM9k)b6p&FsO%u*$4*q-#vn9}8bux;V=NPw> z=YaF?;h*6Imx{~yU$5WK4KpZK=?$y4BwN$rHwIL^eWfN_#F8-g!zw9E<1!aoh5L)J zQdxHXTEFIMdsjNDSo%!w#2Hi*MErKISf}mh4c%p*u6IZx+p-Uj^f8t&xo3eh0 zC|n>=q)V~dNU?%iVKWF_Ai!HR2nIy3STQ#Y6BrlDVk(+g0VN2vKSoLp6Ov`z)8=mK zWgf!pd}Q~`LRxrjh#osr+2F)RRtM161Ls`
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