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R folder contents for GSA package (#5)
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* Update DESCRIPTION

* Create NAMESPACE

* ud

* ud install dependencies and lint

* Update install_dependencies.R

* Update install_dependencies.R

* Update install_dependencies.R

* Update install_dependencies.R
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abdullahhamadeh authored Apr 18, 2024
1 parent b8d9a70 commit 5d7180f
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6 changes: 5 additions & 1 deletion .github/workflows/install_dependencies.R
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@@ -1 +1,5 @@
install.packages(c('testthat','rmarkdown','spelling'), repos = 'http://cran.us.r-project.org', type='win.binary')
install.packages(c('dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','ggplot2','shiny','shinyTree','shinyjs','SobolSequence','writexl','tictoc','pkgload'), repos = 'http://cran.us.r-project.org', type='win.binary')
install.packages('https://github.com/Open-Systems-Pharmacology/rClr/releases/download/v0.9.1/rClr_0.9.1.zip', repos = NULL, type = 'binary')
install.packages('https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils/releases/download/v1.4.23/ospsuite.utils_1.4.23.zip', repos = NULL, type = 'binary')
install.packages('https://github.com/Open-Systems-Pharmacology/TLF-Library/releases/download/v1.5.125/tlf_1.5.125.zip', repos = NULL, type = 'binary')
install.packages('https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases/download/v11.3.520/ospsuite_11.3.520.zip', repos = NULL, type = 'binary')
2 changes: 1 addition & 1 deletion .github/workflows/lint.yaml
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Expand Up @@ -12,7 +12,7 @@ jobs:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Checkout
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Setup
uses: r-lib/actions/setup-r@v2
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33 changes: 19 additions & 14 deletions DESCRIPTION
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@@ -1,20 +1,27 @@
Type: Package
Package: ospsuite.globalsensitivity
Title: TODO
Version: 1.0.0
Authors@R: c(
person("Open-Systems-Pharmacology Community", role = c("cph", "fnd")),
person("XXXXXXXXXXX", "XXXXXXXXXXXX", , "[email protected]", role = c("aut", "cre"))
)
Maintainer: XXXXXXXXXXX XXXXXXXXXXX <[email protected]>
Description: TODO
Title: Open Systems Pharmacology Global Sensitivity Package
Version: 0.1.0
Author: Abdullah Hamadeh (Systems In Silico Ltd.)
Maintainer: Abdullah Hamadeh <[email protected]>
Description: A global sensitivity analysis for Open Systems Pharmacology models.
License: GPL-2
URL: https://github.com/Open-Systems-Pharmacology/OSPSuite.GlobalSensitivitys,
URL: https://github.com/Open-Systems-Pharmacology/OSPSuite.GlobalSensitivity,
https://www.open-systems-pharmacology.org/OSPSuite.GlobalSensitivity/
BugReports:
https://github.com/Open-Systems-Pharmacology/OSPSuite.GlobalSensitivity/issues
Depends:
R (>= 4.1)
Depends:
ospsuite,
ggplot2,
shiny,
shinyTree,
shinyjs,
dplyr,
parallel,
SobolSequence,
writexl,
stats,
tictoc
Suggests:
knitr,
rmarkdown,
Expand All @@ -23,6 +30,4 @@ Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Collate:
'dummy.R'
RoxygenNote: 7.3.1
20 changes: 20 additions & 0 deletions NAMESPACE
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# Generated by roxygen2: do not edit by hand

export(LogNormalDistribution)
export(LogUniformDistribution)
export(NormalDistribution)
export(SADistribution)
export(SAOutput)
export(SAParameter)
export(UniformDistribution)
export(distribution)
export(generateLowryPlot)
export(generateMorrisPlot)
export(generateTornadoPlot)
export(getParameterListForUncertaintyAnalysis)
export(pltGSABarGraph)
export(runEFAST)
export(runGUI)
export(runMorris)
export(runSU)
export(runSobol)
20 changes: 20 additions & 0 deletions OSPSuite.GlobalSensitivity.Rproj
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Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX

AutoAppendNewline: Yes
StripTrailingWhitespace: Yes

BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
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