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commit aa85f36
Merge: 4a05152 63c5638
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Mon Aug 9 10:11:59 2021 +0100

    Merge pull request epiforecasts#407 from epiforecasts/sshh-bot

    Make bot less bossy

commit 63c5638
Merge: a519d49 4a05152
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Aug 6 15:01:09 2021 +0100

    Merge branch 'master' into sshh-bot

commit 4a05152
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Aug 6 14:23:10 2021 +0100

    roll back to dev pkgdown

commit a519d49
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Aug 6 14:20:41 2021 +0100

    make bot less bossy

commit 66da16e
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Aug 6 12:43:15 2021 +0100

    use CRAN pkgdown

commit 0baa18c
Merge: 28d70a0 41d2258
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 15 17:42:44 2021 +0100

    Merge pull request epiforecasts#402 from epiforecasts/fix-readme-citation

    Fixes citation by rebuilding readme

commit 41d2258
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 15 10:44:02 2021 +0000

    moves doi badges around

commit fe21a13
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 15 10:39:59 2021 +0000

    fixes citation by rebuilding readme

commit 28d70a0
Merge: 2e0bb8b 63b0d55
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 15 11:23:14 2021 +0100

    Merge pull request epiforecasts#401 from epiforecasts/create-discord

    added link to discord chat in readme badge

commit 63b0d55
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Wed Jul 14 15:59:28 2021 +0100

    updated citation in README, forgot to update covidregionaldata so produced the old one on knit

commit edf7a11
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Wed Jul 14 13:25:08 2021 +0100

    added link to discord chat in readme badge

commit 2e0bb8b
Merge: 8fe326b 9f1318e
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 8 15:58:33 2021 +0100

    Merge pull request epiforecasts#396 from epiforecasts/fix-paper-author-names

    fixed Richards last name

commit 9f1318e
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Thu Jul 8 10:06:13 2021 +0100

    fixed Richards last name

commit 8fe326b
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Jul 5 11:32:57 2021 +0000

    update citation

commit d51eabc
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Jul 5 10:29:44 2021 +0000

    CRAN check

commit 7794fb0
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Jul 5 09:11:33 2021 +0000

    CRAN comments

commit 08022ac
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Jul 5 09:11:10 2021 +0000

    spelling

commit 2aa0847
Merge: b7eeeaa 5b0d347
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Sun Jul 4 17:40:32 2021 +0100

    Merge pull request epiforecasts#395 from arfon/patch-1

commit 5b0d347
Author: Arfon Smith <arfon@users.noreply.github.com>
Date:   Sat Jul 3 22:02:29 2021 +0100

    Fixing paper formatting.

commit b7eeeaa
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Jul 2 09:58:07 2021 +0100

    Remove zenodo links and reference

commit 4165c25
Merge: dea9278 a260533
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 16:41:12 2021 +0100

    Merge pull request epiforecasts#394 from epiforecasts/RichardMN-patch-1

    Spelling fix in Readme

commit a260533
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 16:40:27 2021 +0100

    Update README.md

commit 992da9e
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Thu Jul 1 17:34:50 2021 +0300

    Spelling fix in Readme

commit dea9278
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 14:11:35 2021 +0000

    lithuania in news

commit 4e1b981
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:57:05 2021 +0000

    release candidate

commit 1e095cb
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:44:42 2021 +0000

    fix paper bib

commit 1e4ebb5
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:30:46 2021 +0000

    CRAN comments

commit 0e7e837
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:25:54 2021 +0000

    tweak spelling and lint pass

commit 44fddfc
Merge: a8a97a3 2b6fb38
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:59:56 2021 +0100

    Merge pull request epiforecasts#392 from epiforecasts/final-joss-checks

    Final joss checks

commit 2b6fb38
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 12:58:32 2021 +0000

    update news

commit 78cf455
Merge: 242679f a8a97a3
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:36:36 2021 +0100

    Merge branch 'master' into final-joss-checks

commit a8a97a3
Merge: 4ad5583 bd5d30c
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Thu Jul 1 13:31:32 2021 +0100

    Merge pull request epiforecasts#388 from RichardMN:source-fields

    Add source text and url fields to classes

commit bd5d30c
Merge: 40d0b9d 4ad5583
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 12:29:38 2021 +0000

    merge master, fix merge, et al

commit 4ad5583
Merge: 9df009d 6dc82c0
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Thu Jul 1 13:24:18 2021 +0100

    Merge pull request epiforecasts#393 from epiforecasts:devcontainer

    Devcontainer

commit 6dc82c0
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 12:23:59 2021 +0000

    update prec-commit

commit 49deed2
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 11:56:19 2021 +0000

    docker build working

commit ae46da4
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 11:05:19 2021 +0100

    Update check-full.yaml

commit c030f17
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 09:58:13 2021 +0000

    update naming and add docthis

commit 4a07fd1
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 09:53:32 2021 +0000

    switch to devcontainer

commit 242679f
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Thu Jul 1 08:24:21 2021 +0100

    updated versioning and made title case

commit 40d0b9d
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Tue Jun 29 19:33:11 2021 +0300

    Add source fields for country and global sources.

commit c60fb7e
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Tue Jun 29 12:13:20 2021 +0100

    updated version to description and news, also made recomended changes

commit 84aa59e
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Mon Jun 28 16:04:26 2021 +0100

    updated news

commit 611bfc7
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Mon Jun 28 16:02:28 2021 +0100

    updated citation, left doi blank as not sure what this will be...

commit 2f2c015
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Mon Jun 28 15:48:20 2021 +0100

    updated title to be same as the paper, author list looks the same as paper

commit 9df009d
Merge: 337f0b1 4f5ee09
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Mon Jun 28 14:30:28 2021 +0100

    Merge pull request epiforecasts#390 from RichardMN/fix-render-available-datasets-389

    Fixed glitch in rendering available datasets file - fixes epiforecasts#389

commit 337f0b1
Merge: bf4b680 07b7e39
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Mon Jun 28 14:27:57 2021 +0100

    Merge pull request epiforecasts#383 from epiforecasts/hexisticker

    made draft hexsticker

commit 07b7e39
Merge: de74f9b bf4b680
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Mon Jun 28 13:26:22 2021 +0100

    Merge branch 'master' into hexisticker

commit de74f9b
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Mon Jun 28 13:25:45 2021 +0100

    made recomended changes, removed old logos and placed hexsticker in correct location

commit 1de2205
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sat Jun 26 22:56:21 2021 +0300

    Render documentation, generate available datasets file, lint

commit bb115ca
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sat Jun 26 22:21:55 2021 +0300

    Fixed handling of NULL in summary table, completed country data

commit 4f5ee09
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sat Jun 26 21:53:43 2021 +0300

    Fixed glitch in rendering available datasets file, added Switzerland test data

commit df7993b
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Thu Jun 24 22:21:28 2021 +0300

    Build documentation

commit 00fd919
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Thu Jun 24 22:11:42 2021 +0300

    Adjusted summary method, began adding source text and url fields

commit 7cd6f05
Merge: 06a7eb4 ea6a48e
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Wed Jun 23 21:08:06 2021 +0300

    Merge pull request epiforecasts#386 from RichardMN/hexisticker-regions

    Hexisticker - with region colouring using natural earth data and mapshaper for geometry manipulation

commit ea6a48e
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Wed Jun 23 20:31:08 2021 +0300

    Change outlines to be lines, reorder display, remove commented code

commit ce0214d
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Tue Jun 22 21:27:05 2021 +0300

    Outlines added to supported countries, palette adjusted, code reorganised slightly.

commit 2815431
Merge: 5a11397 3b18401
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Tue Jun 22 20:59:40 2021 +0300

    Merge remote-tracking branch 'upstream/master' into hexisticker-regions

commit 5a11397
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Mon Jun 21 18:36:31 2021 +0300

    Fixed separation of countries with level 1 and level 2 data

commit 628a22f
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sun Jun 20 13:59:13 2021 +0300

    Update README.md

commit a6beb0a
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sun Jun 20 13:57:58 2021 +0300

    Add link to regional maps

commit 88f7116
Merge: 57d20c9 a137ddf
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sun Jun 20 13:56:19 2021 +0300

    Merge branch 'hexisticker-regions' of https://github.com/RichardMN/covidregionaldata into hexisticker-regions

commit 57d20c9
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sun Jun 20 13:32:12 2021 +0300

    Initial work to show regions for countries where we have regional data

commit a137ddf
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sun Jun 20 13:32:12 2021 +0300

    Initial work to show regions for countries where we have regional data

commit 06a7eb4
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Fri Jun 18 09:29:56 2021 +0100

    altered borders to make regional data clearer

commit fa13d32
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Thu Jun 17 13:31:19 2021 +0100

    updated designs

commit 2d91ab1
Merge: 96ee5ad f952cfc
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Jun 16 17:20:51 2021 +0100

    Merge branch 'master' into hexisticker

commit 96ee5ad
Merge: 63f7765 0564367
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Wed Jun 16 13:32:36 2021 +0100

    Merge branch 'master' into hexisticker

commit 63f7765
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Wed Jun 16 13:28:45 2021 +0100

    made draft hexsticker
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@RichardMN
RichardMN committed Sep 12, 2021
1 parent bf4b680 commit 661bef3
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -27,3 +27,4 @@ SMG.md
^.*.pdf$
^inst/paper$
^inst/examples$
^\.devcontainer$
47 changes: 47 additions & 0 deletions .devcontainer/Dockerfile
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# R version: latest, ... ,4.0.1 , 4.0.0
ARG VARIANT="latest"
FROM rocker/verse:${VARIANT}

# Use the [Option] comment to specify true/false arguments that should appear in VS Code UX
#
# [Option] Install zsh
ARG INSTALL_ZSH="true"
# [Option] Upgrade OS packages to their latest versions
ARG UPGRADE_PACKAGES="false"

# Install needed packages and setup non-root user. Use a separate RUN statement to add your own dependencies.
ARG USERNAME=vscode
ARG USER_UID=1100
ARG USER_GID=$USER_UID
COPY .devcontainer/library-scripts/*.sh /tmp/library-scripts/
RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
&& /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \
&& usermod -a -G staff ${USERNAME} \
&& apt-get -y install \
python3-pip \
libgit2-dev \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libxt-dev \
&& apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts

RUN python3 -m pip --no-cache-dir install radian pre-commit
RUN install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \
devtools \
languageserver \
precommit \
git2r \
&& rm -rf /tmp/downloaded_packages


RUN apt-get update \
&& export DEBIAN_FRONTEND=noninteractive \
&& apt-get -y install --no-install-recommends libgdal-dev libudunits2-dev

# install dependencies
COPY DESCRIPTION /tmp/package/DESCRIPTION
RUN Rscript -e "devtools::install_dev_deps('/tmp/package')"

# add docthis
RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")'
43 changes: 43 additions & 0 deletions .devcontainer/devcontainer.json
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// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
// https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/r
{
"name": "covidregionaldata",
"build": {
"dockerfile": "Dockerfile",
// Update VARIANT to pick a specific R version: latest, ... ,4.0.1 , 4.0.0
"args": { "VARIANT": "latest" },
"context": ".."
},

// Set *default* container specific settings.json values on container create.
"settings": {
"r.rterm.linux": "/usr/local/bin/radian",
"r.bracketedPaste": true,
"r.sessionWatcher": true,
"[r]": {
"editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?"
}
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": [
"ikuyadeu.r",
"reditorsupport.r-lsp",
"shan.code-settings-sync"
],

// Use 'forwardPorts' to make a list of ports inside the container available locally.
// "forwardPorts": [],

// Use 'postCreateCommand' to run commands after the container is created.
// "postCreateCommand": "R --version",

// Uncomment to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker.
// "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],

// Uncomment when using a ptrace-based debugger like C++, Go, and Rust
// "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ],

// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
"remoteUser": "vscode"
}
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