refacto : pruned trisk core model

.Rbuildignore

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+^LICENSE\.md$

.github/.gitignore

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+*.html

.github/CONTRIBUTING.md

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+As a developer you'll need to set two enviornmental variables (e.g.
+in .Renviron):
+
+```
+# Where to save project agnostic files?
+# For example, see 2DII's Dropbox at
+# PortCheck/00_Data/07_AnalysisInputs/ST_INPUTS_MASTER
+ST_DATA_PATH=/a/path
+
+# Where to save project specific inputs and outputs?
+# For example, for bonds (fastest) see 2DII's Dropbox at 
+# PortCheck_v2/10_Projects/ST_TESTING_BONDS
+ST_PROJECT_FOLDER_INPUT=/another/path/inputs
+ST_PROJECT_FOLDER_OUTPUT=/another/path/outputs
+```
+

.github/workflows/check-standard.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    timeout-minutes: 30
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/pr-check-file-encodings.yaml

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+name: check file encodings in PR
+on: [pull_request]
+jobs:
+  file-encoding:
+    name: file encooding check
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+      - name: run the checkout action
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: list all changed files
+        run: |
+          files=$(git diff --name-only origin/$GITHUB_BASE_REF...${{ github.sha }})
+          IFS=$'\n'; files=($files); unset IFS;  # split the string into an array
+          file --mime "${files[@]}"
+      - name: list all changed files with the wrong encoding
+        run: |
+          files=$(git diff --name-only origin/$GITHUB_BASE_REF...${{ github.sha }})
+          IFS=$'\n'; files=($files); unset IFS;  # split the string into an array
+          ! file --mime "${files[@]}" | grep -v "charset=utf-8\|charset=us-ascii\|charset=binary\| (No such file or directory)$"

.github/workflows/pr-commands.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: Rscript -e 'roxygen2::roxygenise()'
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: Rscript -e 'install.packages("styler")'
+
+      - name: Style
+        run: Rscript -e 'styler::style_pkg()'
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/render-readme.yaml

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+on:
+  push:
+    paths:
+      - README.Rmd
+
+name: Render README
+
+jobs:
+  render:
+    name: Render README
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v1
+      - name: Install rmarkdown, remotes, and the local package
+        run: |
+          install.packages("remotes")
+          remotes::install_local(".")
+          remotes::install_cran("rmarkdown")
+        shell: Rscript {0}
+      - name: Render README
+        run: Rscript -e 'rmarkdown::render("README.Rmd")'
+      - name: Commit results
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+### MacOS specific ###
+# Folder view configuration files
+# Mac files
+.DS_STORE
+**/.DS_STORE
+Desktop.ini
+*.icloud
+.Rproj.user
+docs
+tests/testthat/_snaps/run_trisk*
+tests/testthat/_snaps/run_lrisk*
+workspace/
+.vscode
+inst/doc

DESCRIPTION

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+Package: trisk.model
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: The package provides functions and workflows for conducting
+    financial stress tests of listed equity, corporate bond and corporate
+    loan portfolios.  It specifically focuses on climate change related
+    risks, such as transition/policy risk, litigation risk and physical
+    risk. The methodologies developed by 2DII focus on forward looking
+    approaches and asset based analyses where possible. Some external
+    stress tests are also featured.  This package is currently in the beta
+    stage and not finalised yet. Changes to the methodology will still be
+    made that can and will impact the outcomes of the analysis.  
+License: GPL (>= 3)
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Depends:
+    R (>= 3.4)
+Imports: 
+    dplyr,
+    fs,
+    glue,
+    magrittr,
+    purrr,
+    readr,
+    rlang,
+    tibble,
+    tidyr,
+    uuid,
+    zoo
+Suggests: 
+    rmarkdown,
+    r2dii.plot,
+    testthat (>= 3.0.0),
+    spelling,
+    knitr
+Config/testthat/edition: 3