9 Documenting the package and adding README and pkgdown website
We finish by running commands that will document the package.
litr::document() # <-- use instead of devtools::document()## ℹ Updating cssr documentation
## ℹ Loading cssr
## Writing 'NAMESPACE'
## Writing 'checkB.Rd'
## Writing 'checkClusters.Rd'
## Writing 'checkCssClustersInput.Rd'
## Writing 'checkCssInputs.Rd'
## Writing 'checkCssLassoInputs.Rd'
## Writing 'checkCssLoopOutput.Rd'
## Writing 'checkCutoff.Rd'
## Writing 'checkFormCssDesignInputs.Rd'
## Writing 'checkFormatClustersInput.Rd'
## Writing 'checkGenClusteredDataInputs.Rd'
## Writing 'checkGetClusterSelMatrixInput.Rd'
## Writing 'checkGetCssPredsInputs.Rd'
## Writing 'checkGetSelectedClustersOutput.Rd'
## Writing 'checkGetXglmnetInputs.Rd'
## Writing 'checkMaxNumClusts.Rd'
## Writing 'checkMinNumClusts.Rd'
## Writing 'checkNewXProvided.Rd'
## Writing 'checkPropFeatsRemove.Rd'
## Writing 'checkSamplingType.Rd'
## Writing 'checkSelectedClusters.Rd'
## Writing 'checkWeighting.Rd'
## Writing 'checkXInputResults.Rd'
## Writing 'checkY.Rd'
## Writing 'clusterRepLasso.Rd'
## Writing 'corFunction.Rd'
## Writing 'createSubsamples.Rd'
## Writing 'css.Rd'
## Writing 'cssLasso.Rd'
## Writing 'cssLoop.Rd'
## Writing 'cssPredict.Rd'
## Writing 'cssSelect.Rd'
## Writing 'cssr-package.Rd'
## Writing 'formCssDesign.Rd'
## Writing 'formatClusters.Rd'
## Writing 'genClusteredData.Rd'
## Writing 'genMuXZSd.Rd'
## Writing 'getAllClustWeights.Rd'
## Writing 'getClustWeights.Rd'
## Writing 'getClusterSelMatrix.Rd'
## Writing 'getClusterSelsFromGlmnet.Rd'
## Writing 'getCssDesign.Rd'
## Writing 'getCssPreds.Rd'
## Writing 'getCssSelections.Rd'
## Writing 'getLassoLambda.Rd'
## Writing 'getModelSize.Rd'
## Writing 'getPrototypes.Rd'
## Writing 'getSelMatrix.Rd'
## Writing 'getSelectedClusters.Rd'
## Writing 'getSelectedSets.Rd'
## Writing 'getSelectionPrototypes.Rd'
## Writing 'getSubsamps.Rd'
## Writing 'getXglmnet.Rd'
## Writing 'identifyPrototype.Rd'
## Writing 'makeCoefficients.Rd'
## Writing 'makeCovarianceMatrix.Rd'
## Writing 'print.cssr.Rd'
## Writing 'printCssDf.Rd'
## Writing 'processClusterLassoInputs.Rd'
## Writing 'protolasso.Rd'9.1 Add README
litr::add_readme("../source-files/README.Rmd")## ✔ Writing 'README.Rmd'
## ✔ Adding '^README\\.Rmd$' to '.Rbuildignore'
## ✔ Creating '.git/hooks/'
## ✔ Writing '.git/hooks/pre-commit'Let’s move the two images that we refer to in the README into man/figures. This is based on the “Images and figures” section of the man page for pkgdown::build_home_index().
fs::dir_create("man/figures")
fs::file_copy("../source-files/stability-selection-diagram.png", "man/figures")
fs::file_copy("../source-files/sel_props.png", "man/figures")9.2 Add pkdgown site
litr::add_pkgdown("../source-files/_pkgdown.yml")## ✔ Adding '^_pkgdown\\.yml$', '^docs$', '^pkgdown$' to '.Rbuildignore'## Warning in tools::parse_Rd(path, macros = macros, encoding = "UTF-8"):
## ./man/cssLoop.Rd:10: unknown macro '\item'## Warning in tools::parse_Rd(path, macros = macros, encoding = "UTF-8"):
## ./man/cssLoop.Rd:12: unknown macro '\item'## Warning in tools::parse_Rd(path, macros = macros, encoding = "UTF-8"):
## ./man/getSelMatrix.Rd:45: unknown macro '\item'## Warning in tools::parse_Rd(path, macros = macros, encoding = "UTF-8"):
## ./man/getSelMatrix.Rd:47: unknown macro '\item'## -- Installing package into temporary library -----------------------------------
## == Building pkgdown site =======================================================
## Reading from: '/Users/jacobbien/Documents/GitHub/cssr-project/cssr'
## Writing to: '/Users/jacobbien/Documents/GitHub/cssr-project/docs'
## -- Initialising site -----------------------------------------------------------
## -- Building home ---------------------------------------------------------------
## Reading 'LICENSE.md'
## Writing '404.html'
## -- Building function reference -------------------------------------------------
## Writing 'reference/index.html'
## Reading 'man/checkB.Rd'
## Reading 'man/checkClusters.Rd'
## Reading 'man/checkCssClustersInput.Rd'
## Reading 'man/checkCssInputs.Rd'
## Reading 'man/checkCssLassoInputs.Rd'
## Reading 'man/checkCssLoopOutput.Rd'
## Reading 'man/checkCutoff.Rd'
## Reading 'man/checkFormCssDesignInputs.Rd'
## Reading 'man/checkFormatClustersInput.Rd'
## Reading 'man/checkGenClusteredDataInputs.Rd'
## Reading 'man/checkGetClusterSelMatrixInput.Rd'
## Reading 'man/checkGetCssPredsInputs.Rd'
## Reading 'man/checkGetSelectedClustersOutput.Rd'
## Reading 'man/checkGetXglmnetInputs.Rd'
## Reading 'man/checkMaxNumClusts.Rd'
## Reading 'man/checkMinNumClusts.Rd'
## Reading 'man/checkNewXProvided.Rd'
## Reading 'man/checkPropFeatsRemove.Rd'
## Reading 'man/checkSamplingType.Rd'
## Reading 'man/checkSelectedClusters.Rd'
## Reading 'man/checkWeighting.Rd'
## Reading 'man/checkXInputResults.Rd'
## Reading 'man/checkY.Rd'
## Reading 'man/clusterRepLasso.Rd'
## Reading 'man/corFunction.Rd'
## Reading 'man/createSubsamples.Rd'
## Reading 'man/css.Rd'
## Reading 'man/cssLasso.Rd'
## Reading 'man/cssLoop.Rd'
## Unknown tag: UNKNOWN/tag
## Unknown tag: UNKNOWN/tag
## Reading 'man/cssPredict.Rd'
## Reading 'man/cssSelect.Rd'
## Reading 'man/cssr-package.Rd'
## Reading 'man/formCssDesign.Rd'
## Reading 'man/formatClusters.Rd'
## Reading 'man/genClusteredData.Rd'
## Reading 'man/genMuXZSd.Rd'
## Reading 'man/getAllClustWeights.Rd'
## Reading 'man/getClustWeights.Rd'
## Reading 'man/getClusterSelMatrix.Rd'
## Reading 'man/getClusterSelsFromGlmnet.Rd'
## Reading 'man/getCssDesign.Rd'
## Reading 'man/getCssPreds.Rd'
## Reading 'man/getCssSelections.Rd'
## Reading 'man/getLassoLambda.Rd'
## Reading 'man/getModelSize.Rd'
## Reading 'man/getPrototypes.Rd'
## Reading 'man/getSelMatrix.Rd'
## Unknown tag: UNKNOWN/tag
## Unknown tag: UNKNOWN/tag
## Reading 'man/getSelectedClusters.Rd'
## Reading 'man/getSelectedSets.Rd'
## Reading 'man/getSelectionPrototypes.Rd'
## Reading 'man/getSubsamps.Rd'
## Reading 'man/getXglmnet.Rd'
## Reading 'man/identifyPrototype.Rd'
## Reading 'man/makeCoefficients.Rd'
## Reading 'man/makeCovarianceMatrix.Rd'
## Reading 'man/print.cssr.Rd'
## Reading 'man/printCssDf.Rd'
## Reading 'man/processClusterLassoInputs.Rd'
## Reading 'man/protolasso.Rd'
## Writing 'sitemap.xml'
## -- Building search index -------------------------------------------------------
## == DONE ========================================================================