-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Roxygen the package, add badges, package description file and update …
…pkgdown site.
- Loading branch information
Showing
187 changed files
with
41,088 additions
and
6,787 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,28 @@ | ||
| genlogo.R | ||
| .gitignore | ||
| ^codecov\.yml$ | ||
| ^revdep$ | ||
| ^_pkgdown\.yml$ | ||
| ^figure$ | ||
| ^pkgdown$ | ||
| ^Meta$ | ||
| NEWS | ||
| #^doc$ | ||
| #All packages | ||
| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
| ^\.gitignore$ | ||
| ^NEWS$ | ||
| #For the pkgdown website | ||
| ^docs*$ | ||
| #For the cached chunks of README.Rmd | ||
| ^cache*$ | ||
| ^README_cache*$ | ||
| #If README too big, not on CRAN but only on git | ||
| ^man/figures*$ | ||
| ^man/figures/README-chunk.*$ | ||
| ^README\.Rmd$ | ||
| ^README\.md$ | ||
| #^README\.md$ | ||
| #Specific | ||
| ^articles*$ | ||
| ^fullrespdf*$ | ||
| ^inst/animation*$ | ||
| ^articles*$ | ||
| ^\.github$ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,19 @@ | ||
| .Rproj.user | ||
| # 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/ | ||
| .Rproj.user/* | ||
| .DS_Store | ||
| *.pper | ||
| .Rproj.user/AF86C25B/pcs/source-pane.pper | ||
| .Rproj.user/AF86C25B/pcs/windowlayoutstate.pper | ||
| .DS_Store | ||
| #doc | ||
| Meta |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: plsRcox | ||
| Version: 1.7.5 | ||
| Date: 2019-04-26 | ||
| Version: 1.7.6 | ||
| Date: 2021-03-18 | ||
| Depends: R (>= 2.4.0) | ||
| biocViews: | ||
| Imports: survival, plsRglm, lars, pls, kernlab, mixOmics, risksetROC, survcomp, survAUC, rms | ||
|
|
@@ -15,7 +15,7 @@ Maintainer: Frederic Bertrand <[email protected]> | |
| Description: Provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings <doi:10.1093/bioinformatics/btu660>, Bastien, P., Bertrand, F., Meyer N., Maumy-Bertrand, M. (2015), Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data, Bioinformatics, 31(3):397-404. Cross validation criteria were studied in <arXiv:1810.02962>, Bertrand, F., Bastien, Ph. and Maumy-Bertrand, M. (2018), Cross validating extensions of kernel, sparse or regular partial least squares regression models to censored data. | ||
| License: GPL-3 | ||
| Encoding: UTF-8 | ||
| URL: http://www-irma.u-strasbg.fr/~fbertran/, https://github.com/fbertran/plsRcox | ||
| BugReports: https://github.com/fbertran/plsRcox/issues | ||
| URL: http://fbertran.github.io/plsRcox/, https://github.com/fbertran/plsRcox/ | ||
| BugReports: https://github.com/fbertran/plsRcox/issues/ | ||
| Classification/MSC: 62N01, 62N02, 62N03, 62N99 | ||
| RoxygenNote: 6.1.1 | ||
| RoxygenNote: 7.1.1 | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,119 +1,85 @@ | ||
| # imports functions | ||
| #import(boot) | ||
| import(survival) | ||
| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| S3method(DKplsRcoxmodel,default) | ||
| S3method(DKplsRcoxmodel,formula) | ||
| S3method(coxDKpls2DR,default) | ||
| S3method(coxDKpls2DR,formula) | ||
| S3method(coxDKplsDR,default) | ||
| S3method(coxDKplsDR,formula) | ||
| S3method(coxDKsplsDR,default) | ||
| S3method(coxDKsplsDR,formula) | ||
| S3method(coxpls,default) | ||
| S3method(coxpls,formula) | ||
| S3method(coxpls2,default) | ||
| S3method(coxpls2,formula) | ||
| S3method(coxpls2DR,default) | ||
| S3method(coxpls2DR,formula) | ||
| S3method(coxpls3,default) | ||
| S3method(coxpls3,formula) | ||
| S3method(coxpls3DR,default) | ||
| S3method(coxpls3DR,formula) | ||
| S3method(coxplsDR,default) | ||
| S3method(coxplsDR,formula) | ||
| S3method(coxsplsDR,default) | ||
| S3method(coxsplsDR,formula) | ||
| S3method(larsDR_coxph,default) | ||
| S3method(larsDR_coxph,formula) | ||
| S3method(plsRcoxmodel,default) | ||
| S3method(plsRcoxmodel,formula) | ||
| S3method(predict,plsRcoxmodel) | ||
| S3method(print,plsRcoxmodel) | ||
| S3method(print,summary.plsRcoxmodel) | ||
| S3method(summary,plsRcoxmodel) | ||
| export(DKplsRcox) | ||
| export(DKplsRcoxmodel) | ||
| export(DR_coxph) | ||
| export(coxDKpls2DR) | ||
| export(coxDKplsDR) | ||
| export(coxDKsplsDR) | ||
| export(coxpls) | ||
| export(coxpls2) | ||
| export(coxpls2DR) | ||
| export(coxpls3) | ||
| export(coxpls3DR) | ||
| export(coxplsDR) | ||
| export(coxsplsDR) | ||
| export(cv.autoplsRcox) | ||
| export(cv.coxDKplsDR) | ||
| export(cv.coxDKsplsDR) | ||
| export(cv.coxpls) | ||
| export(cv.coxplsDR) | ||
| export(cv.coxsplsDR) | ||
| export(cv.larsDR) | ||
| export(cv.plsRcox) | ||
| export(larsDR_coxph) | ||
| export(plsRcox) | ||
| export(plsRcoxmodel) | ||
| import(kernlab) | ||
| import(lars) | ||
| import(mixOmics) | ||
| import(pls) | ||
| import(plsRglm) | ||
| import(mixOmics) | ||
| import(risksetROC) | ||
| import(survcomp) | ||
| import(survAUC) | ||
| import(rms) | ||
|
|
||
| importFrom("grDevices", "dev.new") | ||
| importFrom("graphics", "abline", "axis", "layout", "segments") | ||
| importFrom("stats", "as.formula", "complete.cases", "contrasts", | ||
| "extractAIC", "is.empty.model", "median", "model.matrix", | ||
| "model.response", "model.weights", "residuals", "uniroot", | ||
| "var", "weighted.mean") | ||
| importFrom("utils", "head") | ||
|
|
||
|
|
||
| # functions | ||
| export(DR_coxph ) | ||
| export(larsDR_coxph ) | ||
| export(larsDR_coxph.default) | ||
| export(larsDR_coxph.formula) | ||
| export(coxpls ) | ||
| export(coxpls.default ) | ||
| export(coxpls.formula ) | ||
| export(coxpls2 ) | ||
| export(coxpls2.default ) | ||
| export(coxpls2.formula ) | ||
| export(coxpls3 ) | ||
| export(coxpls3.default ) | ||
| export(coxpls3.formula ) | ||
| export(coxplsDR ) | ||
| export(coxplsDR.default ) | ||
| export(coxplsDR.formula ) | ||
| export(coxpls2DR ) | ||
| export(coxpls2DR.default ) | ||
| export(coxpls2DR.formula ) | ||
| export(coxpls3DR ) | ||
| export(coxpls3DR.default ) | ||
| export(coxpls3DR.formula ) | ||
| export(coxsplsDR ) | ||
| export(coxsplsDR.default ) | ||
| export(coxsplsDR.formula ) | ||
| export(coxDKplsDR ) | ||
| export(coxDKplsDR.default ) | ||
| export(coxDKplsDR.formula ) | ||
| export(coxDKpls2DR ) | ||
| export(coxDKpls2DR.default ) | ||
| export(coxDKpls2DR.formula ) | ||
| export(coxDKsplsDR ) | ||
| export(coxDKsplsDR.default ) | ||
| export(coxDKsplsDR.formula ) | ||
| export(cv.autoplsRcox ) | ||
| export(cv.coxDKplsDR ) | ||
| export(cv.coxDKsplsDR ) | ||
| export(cv.coxpls ) | ||
| export(cv.coxplsDR ) | ||
| export(cv.coxsplsDR ) | ||
| export(cv.larsDR ) | ||
| export(cv.plsRcox ) | ||
| export(DKplsRcox ) | ||
| export(DKplsRcoxmodel.default ) | ||
| export(DKplsRcoxmodel.formula ) | ||
| #export(bootplscox ) | ||
| #export(coefs.plsRcox ) | ||
| #export(kfolds2CVinfos_cox ) | ||
| #export(permcoefs.plsRcox ) | ||
| #export(PLS_cox_kfoldcv ) | ||
| #export(PLS_cox_kfoldcv_formula ) | ||
| #export(PLS_cox_wvc ) | ||
| export(plsRcox ) | ||
| export(plsRcoxmodel.default ) | ||
| export(plsRcoxmodel.formula ) | ||
| export(predict.plsRcoxmodel ) | ||
| export(print.plsRcoxmodel ) | ||
| export(print.summary.plsRcoxmodel) | ||
| #export(simul_data_UniYX_cox ) | ||
| export(summary.plsRcoxmodel ) | ||
| #export(tilt.bootplscox ) | ||
|
|
||
|
|
||
| S3method("plsRcoxmodel", "default") | ||
| S3method("plsRcoxmodel", "formula") | ||
| S3method("DKplsRcoxmodel", "default") | ||
| S3method("DKplsRcoxmodel", "formula") | ||
|
|
||
| ## S3 methods for generics in base | ||
| S3method("predict", "plsRcoxmodel") | ||
| S3method("print", "plsRcoxmodel") | ||
| S3method("summary", "plsRcoxmodel") | ||
| S3method("print", "summary.plsRcoxmodel") | ||
| S3method("coxDKplsDR", "formula") | ||
| S3method("coxDKplsDR", "default") | ||
| S3method("coxDKpls2DR", "formula") | ||
| S3method("coxDKpls2DR", "default") | ||
| S3method("coxDKsplsDR", "formula") | ||
| S3method("coxDKsplsDR", "default") | ||
| S3method("coxplsDR", "formula") | ||
| S3method("coxplsDR", "default") | ||
| S3method("coxpls2DR", "formula") | ||
| S3method("coxpls2DR", "default") | ||
| S3method("coxpls3DR", "formula") | ||
| S3method("coxpls3DR", "default") | ||
| S3method("coxsplsDR", "formula") | ||
| S3method("coxsplsDR", "default") | ||
| S3method("larsDR_coxph", "formula") | ||
| S3method("larsDR_coxph", "default") | ||
| S3method("coxpls", "formula") | ||
| S3method("coxpls", "default") | ||
| S3method("coxpls2", "formula") | ||
| S3method("coxpls2", "default") | ||
| S3method("coxpls3", "formula") | ||
| S3method("coxpls3", "default") | ||
|
|
||
| import(survAUC) | ||
| import(survcomp) | ||
| import(survival) | ||
| importFrom(grDevices,dev.new) | ||
| importFrom(graphics,abline) | ||
| importFrom(graphics,axis) | ||
| importFrom(graphics,layout) | ||
| importFrom(graphics,segments) | ||
| importFrom(stats,as.formula) | ||
| importFrom(stats,complete.cases) | ||
| importFrom(stats,contrasts) | ||
| importFrom(stats,extractAIC) | ||
| importFrom(stats,is.empty.model) | ||
| importFrom(stats,median) | ||
| importFrom(stats,model.matrix) | ||
| importFrom(stats,model.response) | ||
| importFrom(stats,model.weights) | ||
| importFrom(stats,residuals) | ||
| importFrom(stats,uniroot) | ||
| importFrom(stats,var) | ||
| importFrom(stats,weighted.mean) | ||
| importFrom(utils,head) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.