automation

e8ba6460 · Armin Rauschenberger · 1f5c7406 · 1f5c7406 · e8ba6460 · e8ba6460
Commit e8ba6460 authored Jul 31, 2019 by Armin Rauschenberger
15 changed files
--- a/.Rhistory
+++ b/.Rhistory
-X
-cor(X)
-cor <- cor(X)
-diag(cor)
-cor
-sample(1:10,size=1)
-sample(1:10,size=1.5)
-sample(1:10,size=1.6)
-sample(1:10,size=1.7)
-sample(1:10,size=1.9)
-sample(1:10,size=2.0)
-y <- sign(y) * abs(y)^frame$k[j]
-hist(sign(y) * abs(y)^1)
-y <- rnorm(1000)
-hist(sign(y) * abs(y)^1)
-hist(sign(y) * abs(y)^2)
-hist(sign(y) * abs(y)^5)
-hist(sign(y) * abs(y)^0.5)
-hist(sign(y) * abs(y)^0.1)
-hist(sign(y) * abs(y)^0.1,breaks=50)
-hist(sign(y) * abs(y)^0.1,breaks=20)
-hist(sign(y) * abs(y)^0.1,breaks=10)
-hist(sign(y) * abs(y)^0,breaks=50)
-hist(sign(y) * abs(y)^Inf,breaks=50)
-hist(sign(y) * abs(y)^Inf,breaks=50,xlim=c(-2,2))
-hist(sign(y) * abs(y)^Inf,breaks=20,xlim=c(-2,2))
-hist(sign(y) * abs(y)^Inf,breaks=10,xlim=c(-2,2))
-hist(sign(y) * abs(y)^Inf,breaks=breaks,xlim=c(-2,2))
-hist(sign(y) * abs(y)^Inf,breaks=50,xlim=c(-2,2))
-hist(sign(y) * abs(y)^Inf,breaks=50,xlim=c(-2,2))
-hist(sign(y) * abs(y)^Inf,breaks=50,xlim=c(-1,1))
-hist(sign(y)*abs(y)^Inf,breaks=50,xlim=c(-1,1))
-hist(sign(y)*abs(y)^99,breaks=50,xlim=c(-1,1))
-hist(sign(y)*abs(y)^9,breaks=50,xlim=c(-1,1))
-hist(sign(y)*abs(y)^1,breaks=50,xlim=c(-1,1))
-hist(sign(y)*abs(y)^1,breaks=50,xlim=c(-1,1))
-y
-y <- rnorm(1000)
-hist(sign(y)*abs(y)^1,breaks=50)
-hist(sign(y)*abs(y)^50,breaks=50)
-hist(sign(y)*abs(y)^10,breaks=50)
-hist(sign(y)*abs(y)^0.1,breaks=50)
-hist(sign(y)*abs(y)^0.2,breaks=50)
-0^0.2
-0.0001^0.2
-(-0.0001)^0.2
-(-0.001)^0.2
-(-0.01)^0.2
-(0.01)^0.2
-(0.01)^0.05
-(0.01)^0.05
-(0.01)^0.05
-(0.01)^0.001
-(0.01)^0.000001
-?quantile
-?quantile
-?optim
-f=expression(x^2+3*x)
-D(f,'x')
-f <- expression(x^2+3*x+a)
-D(f,'x')
-f <- expression(x^2+3*x+a)
-D(f,'x')
-f <- expression(x^a+3*x)
-D(f,'x')
-f <- expression((1-pi)*z+pi*phi)
-D(f,'x')
-D(f,'pi')
-f <- expression((1-pi)*z+pi*phi)
-D(f,'pi')
-f <- expression(sum(a+b))
-D(f,'pi')
-0^1
-?ddnorm
-?dnorm
-?quantile
-hist(rnorm(10000))
-hist(rnorm(10000)^2)
-x <- rnorm(10000)^2
-hist(x)
-x <- rnorm(10000)
-hist(x)
-hist(sign(x)*abs(x)^2)
-hist(sign(x)*abs(x)^2,breaks=50)
-hist(sign(x)*abs(x)^10,breaks=50)
-hist(sign(x)*abs(x)^5,breaks=50)
-hist(sign(x)*abs(x)^2,breaks=50)
-hist(sign(x)*abs(x)^(-2),breaks=50)
-hist(sign(x)*abs(x)^(-1),breaks=50)
-hist(sign(x)*abs(x)^(-0.2),breaks=50)
-80/5
-80/30
-80/5
-hist(sign(x)*abs(x)^(-0.2),breaks=50)
-hist(sign(x)*abs(x)^(10),breaks=50)
-hist(sign(x)*abs(x)^(50),breaks=50)
-range(x)
-range(x)
-hist(sign(x)*abs(x)^(50),breaks=50)
-hist(sign(x)*abs(x)^(50),breaks=50,xlim=c(-1,1))
-hist(sign(x)*abs(x)^(50),breaks=5000,xlim=c(-1,1))
-hist(sign(x)*abs(x)^(10),breaks=5000,xlim=c(-1,1))
-hist(sign(x)*abs(x)^(10),breaks=5000000,xlim=c(-1,1))
-hist(sign(x)*abs(x)^(3),breaks=5000000,xlim=c(-1,1))
-hist(sign(x)*abs(x)^(3),1e+06,xlim=c(-1,1))
-hist(sign(x)*abs(x)^(3),10000,xlim=c(-1,1))
-hist(sign(x)*abs(x)^(3),10000,xlim=c(-1,1))
-hist(sign(x)*abs(x)^(3),10000,xlim=c(-2,2))
-range(sign(x)*abs(x)^(3))
-range(sign(x)*abs(x)^(1))
-range(sign(x)*abs(x)^(5))
-(-1)^1000
-(-1.1)^1000
-(-1)^1000
-(-0.9)^1000
-?p.adjust
-set.seed(1)
-#devtools::install_github("rauschenberger/palasso",ref="4802b1d")
-#devtools::install_github("rauschenberger/cornet",
-#                         ref="bcfdcc0",dependencies=FALSE)
-# devtools::install_github("rauschenberger/decline",ref="cb187ec",dependencies=FALSE)
-rm(list=ls(all.names=TRUE))
-.source <- .target <- "C:/Users/armin.rauschenberger/Desktop/cornet/analysis"
-# --- Preparing data. ---
-load(file.path(.source,"ppmi_2018-11-20.RData"),verbose=TRUE)
-if(any(Y[,"visit0"]!=X$"MOCA-MCATOT",na.rm=TRUE)){stop("Mismatch.")}
-if(any(rownames(Y)!=rownames(X))){stop("Mismatch.")}
-Y <- Y[,-1]
-X <- decline::curate_missing(X)
-X <- decline::curate_hidden(X)
-X <- decline::curate_levels(X)
-X <- decline::curate_constant(X)
-#--- multiple imputation ---
-set.seed(1)
-names <- colnames(X)
-colnames(X) <- paste0("x",seq_len(ncol(X)))
-X_imp <- list()
-for(i in seq_len(10)){
-X_imp[[i]] <- missRanger::missRanger(data = X, pmm.k = 3, num.trees = 100) # before without pmm.k and num.trees
-colnames(X_imp[[i]]) <- names
-}
-# --- Cross-validating models. ---
-names <- paste0(rep(c("lasso","ridge"),each=4),seq_len(4))
-loss <- fit <- pval <- list()
-for(i in seq_along(X_imp)){
-loss[[i]] <- fit[[i]] <- pval[[i]] <- list()
-cat("i =",i,"\n")
-x <- scale(decline::curate_dummies(as.data.frame(X_imp[[i]])))
-for(j in seq_along(names)){
-cat("j =",j," ")
-alpha <- 1*(substr(names[j],start=1,stop=5)=="lasso")
-index <- as.numeric(substr(names[j],start=6,stop=6))
-y <- Y[,index]
-cond <- !is.na(y)
-set.seed(i)
-loss[[i]][[names[j]]] <- cornet:::cv.cornet(y=y[cond],cutoff=25.5,
-X=x[cond,],alpha=alpha)
-set.seed(i)
-fit[[i]][[names[j]]] <- cornet::cornet(y=y[cond],cutoff=25.5,
-X=x[cond,],alpha=alpha)
-set.seed(i)
-pval[[i]][[names[j]]] <- cornet:::.test(y=y[cond],cutoff=25.5,
-X=x[cond,],alpha=alpha)
-}
-}
-save(loss,fit,pval,file=file.path(.target,"application.RData"))
-#--- interpretation ---
-load(file.path(.target,"application.RData"),verbose=TRUE)
-names <- c(paste0("lasso",1:4),paste0("ridge",1:4))
-frame <- data.frame(row.names=names)
-for(i in names){
-# proportion of data sets with deviance decrease
-dev <- as.data.frame(t(sapply(loss,function(x) x[[i]]$deviance)))
-frame[i,"dev.prop"] <- round(mean(dev$combined < dev$binomial),digits=2)
-# deviance change in percent
-dec <- (dev$combined-dev$binomial)/dev$binomial
-frame[i,"dev.min"] <- round(100*min(dec),digits=1)
-frame[i,"dev.max"] <- round(100*max(dec),digits=1)
-# proportion of data sets with AUC increase
-auc <- as.data.frame(t(sapply(loss,function(x) x[[i]]$auc)))
-frame[i,"auc.prop"] <- round(mean(auc$combined > auc$binomial),digits=2)
-# quantiles weight parameter
-q <- round(quantile(sapply(fit,function(x) x[[i]]$pi.min),probs=c(0,0.5,1)),digits=2)
-frame[i,"pi.min"] <- q[1]
-frame[i,"pi.med"] <- q[2]
-frame[i,"pi.max"] <- q[3]
-# quantiles scale parameter
-q <- round(quantile(sapply(fit,function(x) x[[i]]$sigma.min),probs=c(0,0.5,1)),digits=2)
-frame[i,"sd.min"] <- q[1]
-frame[i,"sd.med"] <- q[2]
-frame[i,"sd.max"] <- q[3]
-# significance based on multi-split
-pvalue <- sapply(pval,function(x) median(unlist(x[[i]])))
-frame[i,"pval.min"] <- signif(min(pvalue),digits=2)
-frame[i,"pval.max"] <- signif(max(pvalue),digits=2)
-frame[i,"pval.prop"] <- round(mean(pvalue<0.05),digits=2)
-}
-frame
-writeLines(text=capture.output(utils::sessionInfo()),
-con=file.path(.target,"info_app.txt"))
-?auc
-?pROC::auc
-response <- rep(c(0,1),times=c(50,50))
-predictor <- runif(100)
-auc(response,predictor)
-pROC::auc(response,predictor)
-pROC::auc(response,predictor)
-response <- rep(c(0,1),times=c(95,5))
-pROC::auc(response,predictor)
-pROC::auc(response,predictor)
-pROC::auc(response,predictor)
-pROC::auc(response,predictor)
-response <- rep(c(0,1),times=c(95,5))
-response <- rep(c(0,1),times=c(95,5)); predictor <- runif(100)
-pROC::auc(response,predictor)
-response <- rep(c(0,1),times=c(95,5)); predictor <- runif(100)
-pROC::auc(response,predictor)
-response <- rep(c(0,1),times=c(95,5)); predictor <- runif(100)
-pROC::auc(response,predictor)
-response <- rep(c(0,1),times=c(95,5)); predictor <- runif(100)
-pROC::auc(response,predictor)
-response <- rep(c(0,1),times=c(95,5)); predictor <- 0
-pROC::auc(response,predictor)
-response <- rep(c(0,1),times=c(95,5)); predictor <- rep(0,times=100)
-pROC::auc(response,predictor)
-response <- rep(c(0,1),times=c(95,5)); predictor <- rep(1,times=100)
-pROC::auc(response,predictor)
-?missRanger
-?missRanger::missRanger
-install.packages(c("assertthat", "backports", "callr", "cli", "clipr", "curl", "devtools", "digest", "evaluate", "foreach", "fs", "git2r", "glmnet", "highr", "iterators", "knitr", "markdown", "mime", "openssl", "palasso", "parsedate", "pillar", "pkgbuild", "processx", "purrr", "rcmdcheck", "Rcpp", "rematch2", "remotes", "rhub", "rlang", "rmarkdown", "rsconnect", "rstudioapi", "rversions", "sys", "testthat", "tibble", "tinytex", "usethis", "whoami", "xfun", "xml2"))
-##############
-### cornet ###
-##############
-#--- generate toydata ----------------------------------------------------------
-set.seed(1)
-#toydata <- NULL
-#save(toydata,file=file.path("C:/Users/armin.rauschenberger/Desktop/package/cornet/data/toydata.R"))
-#--- compile package -----------------------------------------------------------
-rm(list=ls())
-name <- "cornet"
-#load("D:/cornet/package/toydata.RData")
-pkg <- "C:/Users/armin.rauschenberger/Desktop/cornet/cornet"
-setwd(dir=pkg)
-devtools::as.package(x=pkg,create=FALSE)
-devtools::load_all(path=pkg)
-#usethis::use_data(toydata,overwrite=TRUE)
-devtools::document(pkg=pkg)
-unlink(file.path(pkg,"vignettes","figure"),recursive=TRUE)
-#all <- dir(file.path(pkg,"vignettes"))
-#delete <- "..."
-#sapply(delete,function(x) file.remove(file.path(pkg,"vignettes",x)))
-setwd(dir=pkg)
-unlink(file.path(pkg,"docs"),recursive=TRUE)
-pkgdown::build_site(pkg=pkg)
-file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-devtools::check(pkg=pkg,quiet=FALSE,manual=TRUE)
-devtools::install(pkg=pkg,upgrade=FALSE)
-##############
-### mixnet ###
-##############
-#--- generate toydata ----------------------------------------------------------
-set.seed(1)
-#toydata <- NULL
-#save(toydata,file=file.path("C:/Users/armin.rauschenberger/Desktop/package/cornet/data/toydata.R"))
-#--- compile package -----------------------------------------------------------
-rm(list=ls())
-name <- "mixnet"
-#load("D:/cornet/package/toydata.RData")
-pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(dir=pkg)
-devtools::as.package(x=pkg,create=FALSE)
-devtools::load_all(path=pkg)
-#usethis::use_data(toydata,overwrite=TRUE)
-devtools::document(pkg=pkg)
-unlink(file.path(pkg,"vignettes","figure"),recursive=TRUE)
-setwd(dir=pkg)
-unlink(file.path(pkg,"docs"),recursive=TRUE)
-pkgdown::build_site(pkg=pkg)
-file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-devtools::check(pkg=pkg,quiet=FALSE,manual=TRUE)
-devtools::install(pkg=pkg,upgrade=FALSE)
-cornet::.check
-cornet:::.check
-file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-#--- generate toydata ----------------------------------------------------------
-set.seed(1)
-#toydata <- NULL
-#save(toydata,file=file.path("C:/Users/armin.rauschenberger/Desktop/package/cornet/data/toydata.R"))
-#--- compile package -----------------------------------------------------------
-rm(list=ls())
-name <- "mixnet"
-#load("D:/cornet/package/toydata.RData")
-pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(dir=pkg)
-devtools::as.package(x=pkg,create=FALSE)
-devtools::load_all(path=pkg)
-#usethis::use_data(toydata,overwrite=TRUE)
-devtools::document(pkg=pkg)
-unlink(file.path(pkg,"vignettes","figure"),recursive=TRUE)
-setwd(dir=pkg)
-unlink(file.path(pkg,"docs"),recursive=TRUE)
-pkgdown::build_site(pkg=pkg)
-file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-devtools::check(pkg=pkg,quiet=FALSE,manual=TRUE)
-?palasso:::.folds
-palasso::.folds
-palasso:::.folds
-cornet:::.check
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-?usethis::use_build_ignore
-file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-pkg
-set.seed(1)
-rm(list=ls())
-name <- "mixnet"
-pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(dir=pkg)
-devtools::as.package(x=pkg,create=FALSE)
-devtools::load_all(path=pkg)
-#usethis::use_data(toydata,overwrite=TRUE)
-devtools::document(pkg=pkg)
-?unlink
-unlink(file.path(pkg,"vignettes","figure"),recursive=TRUE)
-setwd(dir=pkg)
-unlink(file.path(pkg,"docs"),recursive=TRUE)
-pkgdown::build_site(pkg=pkg)
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-devtools::check(pkg=pkg,quiet=FALSE,manual=TRUE)
-devtools::spell_check(pkg=pkg)
-devtools::check_rhub(pkg=pkg)
-#pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(pkg)
-pkg
-system("git remote set-url origin https://rauschenberger:Eu57Rom!@github.com/rauschenberger/mixnet.git")
-system("git remote -v")
-system("git add --all")
-system("git commit -m \"automation\"")
-system("git push origin master") # GitHub
-#install.packages("plsgenomics")
-data(Ecoli,package="plsgenomics")
-install.packages("plsgenomics")
-install.packages("BiocManager")
-BiocManager::install("mixOmics")
-##############
-### mixnet ###
-##############
-#--- generate toydata ----------------------------------------------------------
-set.seed(1)
-#toydata <- NULL
-#save(toydata,file=file.path("C:/Users/armin.rauschenberger/Desktop/package/cornet/data/toydata.R"))
-#--- compile package -----------------------------------------------------------
-rm(list=ls())
-name <- "mixnet"
-#load("D:/cornet/package/toydata.RData")
-pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(dir=pkg)
-devtools::as.package(x=pkg,create=FALSE)
-devtools::load_all(path=pkg)
-#usethis::use_data(toydata,overwrite=TRUE)
-devtools::document(pkg=pkg)
-unlink(file.path(pkg,"vignettes","figure"),recursive=TRUE)
-setwd(dir=pkg)
-unlink(file.path(pkg,"docs"),recursive=TRUE)
-pkgdown::build_site(pkg=pkg)
-#file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-#usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-devtools::check(pkg=pkg,quiet=FALSE,manual=TRUE)
-devtools::install(pkg=pkg,upgrade=FALSE)
-#install.packages("plsgenomics")
-data(Ecoli,package="plsgenomics")
-X <- Ecoli$CONNECdata
-Y <- Ecoli$GEdata
-loss <- mixnet:::cv.mixnet(Y=Y,X=X)
-loss
-loss["meta",]<loss["base",]
-mean(loss["meta",]<loss["base",])
-mean(loss["meta",]<loss["base",])
-#install.packages("BiocManager")
-#BiocManager::install("mixOmics")
-data(liver.toxicity,package="mixOmics")
-X <- liver.toxicity$gene
-Y <- liver.toxicity$clinic
-Y$Cholesterol.mg.dL. <- -Y$Cholesterol.mg.dL.
-loss <- mixnet:::cv.mixnet(Y=Y,X=X)
-mean(loss["meta",]<loss["base",])
-loss
-mean(loss["meta",]<=loss["base",])
-sum(loss["meta",]<=loss["base",])/sum(loss["meta",]<=loss["base",])
-sum(loss["meta",]<=loss["base",])/sum(loss["meta",]<=loss["base",])
-sum(loss["meta",]<=loss["base",])/sum(loss["base",]<=loss["none",])
-loss
-#install.packages("plsgenomics")
-data(Ecoli,package="plsgenomics")
-X <- Ecoli$CONNECdata
-Y <- Ecoli$GEdata
-loss <- mixnet:::cv.mixnet(Y=Y,X=X)
-rowMeans(loss)
-mean(loss["meta",]<=loss["base",])
-data(Ecoli,package="plsgenomics")
-X <- Ecoli$CONNECdata
-Y <- Ecoli$GEdata
-loss <- mixnet:::cv.mixnet(Y=Y,X=X)
-mean(loss["meta",]<=loss["base",])
-##############
-### mixnet ###
-##############
-#--- generate toydata ----------------------------------------------------------
-set.seed(1)
-#toydata <- NULL
-#save(toydata,file=file.path("C:/Users/armin.rauschenberger/Desktop/package/cornet/data/toydata.R"))
-#--- compile package -----------------------------------------------------------
-rm(list=ls())
-name <- "mixnet"
-#load("D:/cornet/package/toydata.RData")
-pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(dir=pkg)
-devtools::as.package(x=pkg,create=FALSE)
-devtools::load_all(path=pkg)
-#usethis::use_data(toydata,overwrite=TRUE)
-devtools::document(pkg=pkg)
-unlink(file.path(pkg,"vignettes","figure"),recursive=TRUE)
-setwd(dir=pkg)
-unlink(file.path(pkg,"docs"),recursive=TRUE)
-pkgdown::build_site(pkg=pkg)
-#file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-#usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-devtools::check(pkg=pkg,quiet=FALSE,manual=TRUE)
-devtools::install(pkg=pkg,upgrade=FALSE)
-#devtools::build(pkg=pkg)
-#devtools::build(pkg=pkg,binary=TRUE) # only for zip file
-#.rs.restartR()
-#pkg <- "C:/Users/armin.rauschenberger/Desktop/cornet/cornet"
-#version <- substring(text=readLines(file.path(pkg,"DESCRIPTION"))[[2]],first=10)
-#archive <- paste0("C:/Users/armin.rauschenberger/Desktop/cornet/cornet_",version,".zip")
-#utils::install.packages(archive,repos=NULL)
-#--- upload package ------------------------------------------------------------
-#pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(pkg)
-system("git remote set-url origin https://rauschenberger:Eu57Rom!@github.com/rauschenberger/mixnet.git")
-system("git remote -v")
-system("git add --all")
-system("git commit -m \"automation\"")
-system("git push origin master") # GitHub
-##############
-### mixnet ###
-##############
-#--- generate toydata ----------------------------------------------------------
-set.seed(1)
-#toydata <- NULL
-#save(toydata,file=file.path("C:/Users/armin.rauschenberger/Desktop/package/cornet/data/toydata.R"))
-#--- compile package -----------------------------------------------------------
-rm(list=ls())
-name <- "mixnet"
-#load("D:/cornet/package/toydata.RData")
-pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(dir=pkg)
-devtools::as.package(x=pkg,create=FALSE)
-devtools::load_all(path=pkg)
-#usethis::use_data(toydata,overwrite=TRUE)
-devtools::document(pkg=pkg)
-unlink(file.path(pkg,"vignettes","figure"),recursive=TRUE)
-setwd(dir=pkg)
-unlink(file.path(pkg,"docs"),recursive=TRUE)
-pkgdown::build_site(pkg=pkg)
-#file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-#usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-devtools::check(pkg=pkg,quiet=FALSE,manual=TRUE)
-devtools::install(pkg=pkg,upgrade=FALSE)
-#devtools::build(pkg=pkg)
-#devtools::build(pkg=pkg,binary=TRUE) # only for zip file
-#.rs.restartR()
-#pkg <- "C:/Users/armin.rauschenberger/Desktop/cornet/cornet"
-#version <- substring(text=readLines(file.path(pkg,"DESCRIPTION"))[[2]],first=10)
-#archive <- paste0("C:/Users/armin.rauschenberger/Desktop/cornet/cornet_",version,".zip")
-#utils::install.packages(archive,repos=NULL)
-#--- upload package ------------------------------------------------------------
-#pkg <- "C:/Users/armin.rauschenberger/Desktop/mixnet/mixnet"
-setwd(pkg)
-system("git remote set-url origin https://rauschenberger:Eu57Rom!@github.com/rauschenberger/mixnet.git")
-system("git remote -v")
-system("git add --all")
-system("git commit -m \"automation\"")
-system("git push origin master") # GitHub
-set.seed(1)
-#toydata <- NULL
-#save(toydata,file=file.path("C:/Users/armin.rauschenberger/Desktop/package/cornet/data/toydata.R"))
-#--- compile package -----------------------------------------------------------
-rm(list=ls())
-name <- "joinet"
-#load("D:/cornet/package/toydata.RData")
-pkg <- "C:/Users/armin.rauschenberger/Desktop/joinet/joinet"
-setwd(dir=pkg)
-devtools::as.package(x=pkg,create=FALSE)
-devtools::load_all(path=pkg)
-#usethis::use_data(toydata,overwrite=TRUE)
-devtools::document(pkg=pkg)
-unlink(file.path(pkg,"vignettes","figure"),recursive=TRUE)
-setwd(dir=pkg)
-unlink(file.path(pkg,"docs"),recursive=TRUE)
-pkgdown::build_site(pkg=pkg)
-#file.remove(file.path(pkg,c(".Rbuildignore",".Rhistory")))
-#usethis::use_build_ignore(files=c("Readme.Rmd",".travis.yml","_pkgdown.yml","docs","cran-comments.md","appveyor.yml",".Rhistory"))
-devtools::check(pkg=pkg,quiet=FALSE,manual=TRUE)
-devtools::install(pkg=pkg,upgrade=FALSE)
--- a/NEWS.md
+++ b/NEWS.md
-## mixnet 0.0.1 (2019-06-01)
+## joinet 0.0.1 (2019-07-31)

 * first submission
\ No newline at end of file
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -9,10 +9,10 @@ authors:
 home:
   links:
   - text: "Download package"
-     href: https://github.com/rauschenberger/mixnet
+     href: https://github.com/rauschenberger/joinet

 navbar:
-  title: "mixnet"
+  title: "joinet"
  left:
    - text: "functions"
      href: reference/index.html
@@ -24,17 +24,17 @@ navbar:
      href: news/index.html
  right:
    - icon: fa-github
-      href: https://github.com/rauschenberger/mixnet
+      href: https://github.com/rauschenberger/joinet
    - icon: fa-download
-      href: https://cran.r-project.org/package=mixnet
+      href: https://cran.r-project.org/package=joinet

 reference:
  - title: "User functions"
    contents:
-      - mixnet
-      - predict.mixnet
-      - coef.mixnet
-      - weights.mixnet
+      - joinet
+      - predict.joinet
+      - coef.joinet
+      - weights.joinet
  - title: "Internal functions"
    contents:
-      - cv.mixnet
+      - cv.joinet
--- a/docs/articles/article.html
+++ b/docs/articles/article.html
@@ -51,13 +51,13 @@
      </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/rauschenberger/mixnet">
+  <a href="https://github.com/rauschenberger/joinet">
    <span class="fa fa-github"></span>
     
  </a>
 </li>
 <li>
-  <a href="https://cran.r-project.org/package=mixnet">
+  <a href="https://cran.r-project.org/package=joinet">
    <span class="fa fa-download"></span>
     
  </a>

--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -82,13 +82,13 @@
      
      <ul class="nav navbar-nav navbar-right">
        <li>
-  <a href="https://github.com/rauschenberger/mixnet">
+  <a href="https://github.com/rauschenberger/joinet">
    <span class="fa fa-github"></span>
     
  </a>
 </li>