Nothing
## ----include=FALSE-------------------------------------------------------
library(knitr)
knitr::opts_chunk$set(fig.width=7, fig.height=7, comment="")
## ------------------------------------------------------------------------
library(repo)
rp <- repo_open(tempdir(), force=T)
## ------------------------------------------------------------------------
rp$attach("index.Rmd", "Source code for Repo vignette")
rp$options(src="index.Rmd")
## ---- eval=F-------------------------------------------------------------
# myiris <- scale(as.matrix(iris[,1:4]))
## ---- eval=F-------------------------------------------------------------
# rp$put(myiris)
## ------------------------------------------------------------------------
## chunk "myiris" {
myiris <- scale(as.matrix(iris[,1:4]))
rp$put(
obj = myiris,
name = "myiris",
description = paste(
"A normalized version of the iris dataset coming with R.",
"Normalization is made with the scale function",
"with default parameters."
),
tags = c("dataset", "iris", "repodemo")
)
## }
## ------------------------------------------------------------------------
rp$chunk("myiris")
## ------------------------------------------------------------------------
rp$rm("myiris")
rp$build("myiris", "index.Rmd")
## ------------------------------------------------------------------------
rp$put(iris$Species, "irisLabels",
tags = c("labels", "iris", "repodemo"))
## ------------------------------------------------------------------------
irispca <- princomp(myiris)
iris2d <- irispca$scores[,c(1,2)]
plot(iris2d, main="2D visualization of the Iris dataset",
col=rp$get("irisLabels"))
## ------------------------------------------------------------------------
fpath <- file.path(rp$root(), "iris2D.pdf")
pdf(fpath)
plot(iris2d, main="2D visualization of the Iris dataset",
col=rp$get("irisLabels"))
invisible(dev.off())
rp$attach(fpath, "Iris 2D visualization obtained with PCA.",
c("visualization", "iris", "repodemo"),
to="myiris")
## ---- eval=FALSE---------------------------------------------------------
# rp$sys("iris2D.pdf", "evince")
## ------------------------------------------------------------------------
kiris <- kmeans(myiris, 5)$cluster
rp$put(kiris, "iris_5clu", "Kmeans clustering of the Iris data, k=5.",
c("metadata", "iris", "kmeans", "clustering", "repodemo"),
depends="myiris")
## ------------------------------------------------------------------------
plot(iris2d, main="Iris dataset kmeans clustering", col=kiris)
## ------------------------------------------------------------------------
fpath <- file.path(rp$root(), "iris2Dclu.pdf")
pdf(fpath)
plot(iris2d, main="Iris dataset kmeans clustering", col=kiris)
invisible(dev.off())
rp$attach(fpath, "Iris K-means clustering.",
c("visualization", "iris", "clustering", "kmeans", "repodemo"),
to="iris_5clu")
## ------------------------------------------------------------------------
res <- table(rp$get("irisLabels"), kiris)
rp$put(res, "iris_cluVsSpecies",
paste("Contingency table of the kmeans clustering versus the",
"original labels of the Iris dataset."),
c("result", "iris","validation", "clustering", "repodemo", "hide"),
src="index.Rmd", depends=c("myiris", "irisLabels", "iris_5clu"))
## ------------------------------------------------------------------------
rp$info()
## ------------------------------------------------------------------------
rp ## resolves to print(rp)
## ------------------------------------------------------------------------
print(rp, all=T)
## ------------------------------------------------------------------------
print(rp, tags="clustering", all=T)
## ------------------------------------------------------------------------
rp$print(show="st")
## ------------------------------------------------------------------------
rp$find("clu", all=T)
## ------------------------------------------------------------------------
rp$pies()
## ------------------------------------------------------------------------
rp$check()
## ------------------------------------------------------------------------
depgraph <- rp$dependencies(plot=F)
library(knitr)
kable(depgraph)
## ------------------------------------------------------------------------
if(require("igraph", NULL, T, F))
rp$dependencies()
## ------------------------------------------------------------------------
if(require("igraph"))
rp$dependencies(generated=F)
## ------------------------------------------------------------------------
x <- rp$get("myiris")
## ------------------------------------------------------------------------
rm("myiris")
rp$load("myiris")
"myiris" %in% ls()
## ------------------------------------------------------------------------
rp$info("myiris")
## ------------------------------------------------------------------------
kiris2 <- kmeans(myiris, 5)$cluster
rp$put(kiris2, "iris_5clu",
"Kmeans clustering of the Iris data, k=5. Today's version!",
depends="myiris", replace="addversion")
## ------------------------------------------------------------------------
rp
## ------------------------------------------------------------------------
rp$info("iris_5clu")
## ------------------------------------------------------------------------
rp$info("iris_5clu#1")
## ------------------------------------------------------------------------
## First run
system.time(rp$lazydo(
{
Sys.sleep(.5)
result <- "This took half a second to compute"
}
))
## Second run
system.time(rp$lazydo(
{
Sys.sleep(.5)
result <- "This took half a second to compute"
}
))
## ------------------------------------------------------------------------
rp$put("Local content", "item1",
"This points to big data you may want to download",
"tag", URL="http://exampleURL/repo")
print(rp$get("item1"))
## ---- eval=F-------------------------------------------------------------
# rp$pull("item1", replace=T)
## ---- include=F----------------------------------------------------------
rp$set("item1", obj="Remote content")
## ------------------------------------------------------------------------
print(rp$get("item1"))
## ------------------------------------------------------------------------
h <- rp$handlers()
names(h)
## ------------------------------------------------------------------------
print(h$iris_cluVsSpecies())
## ------------------------------------------------------------------------
h$iris_cluVsSpecies("tag", "onenewtag")
h$iris_cluVsSpecies("info")
## ------------------------------------------------------------------------
h <- repo_open(rp$root())$handlers()
## ------------------------------------------------------------------------
h$repo
## ------------------------------------------------------------------------
h <- h$repo$handlers()
## ---- eval=FALSE---------------------------------------------------------
# help(repo)
## ---- eval=FALSE---------------------------------------------------------
# help(repo_func)
## ---- include=F----------------------------------------------------------
## cleaning the tempdir causes CRAN checks to fail on some platforms,
## so it is now left behind
##
## unlink(rp$root(), recursive=T)
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