Nothing
## ---- prompt=TRUE--------------------------------------------------------
library(scmamp)
data(data_gh_2008)
head(data.gh.2008)
data(data_gh_2010)
head(data.gh.2010)
data(data_blum_2015)
head(data.blum.2015)
## ---- eval=FALSE, prompt=TRUE--------------------------------------------
# data.raw <- readComparisonFile(file="results.dat", alg.cols=c('Alg_1', 'Alg_2', 'Alg_3'),
# skip=5, sep=";")
## ---- prompt=TRUE--------------------------------------------------------
data.dir <- system.file("loading_tests",package="scmamp")
file.path <- paste(data.dir, "rgg_complete_comparison.out", sep="/")
data.raw <- readComparisonFile(file=file.path, alg.cols=3:10, col.names=NULL)
head(data.raw)
## ---- prompt=TRUE--------------------------------------------------------
dir <- paste(system.file("loading_tests",package="scmamp"),
"comparison_files", sep="/")
list.files(dir)
## ---- prompt=TRUE--------------------------------------------------------
fname.pattern <- "rgg_size_([0-9]*)_r_([0-9]*.[0-9]*)\\.out"
## ---- prompt=TRUE--------------------------------------------------------
var.names <- c("Size", "Radius")
## ---- prompt=TRUE--------------------------------------------------------
alg.names <- c("FruitFly", "Shukla", "Ikeda", "Turau", "Rand1", "Rand2", "FrogCOL", "FrogMIS")
## ---- prompt=TRUE--------------------------------------------------------
rm("data.raw")
data.raw <- readComparisonDir (directory=dir, alg.cols=alg.names, col.names=NULL,
names=var.names, fname.pattern=fname.pattern)
head(data.raw)
## ---- prompt=TRUE--------------------------------------------------------
dir <- system.file("loading_tests", package="scmamp")
file <- paste(dir, "rgg_complete_experiment.out", sep="/")
content <- read.csv(file)
content[c(1,901,181),]
## ---- prompt=TRUE, cache=TRUE--------------------------------------------
rm("data.raw")
data.raw <- readExperimentFile (file=file, alg.col="Algorithm", value.col="Evaluation")
head(data.raw)
## ---- prompt=TRUE, cache=TRUE--------------------------------------------
rm("data.raw")
dir <- paste(system.file("loading_tests", package="scmamp"),
"experiment_files", sep="/")
list.files(dir)[1:10]
pattern <- "rgg_size_([0-9]*)_r_(0.[0-9]*)_([a-z, A-Z, 1, 2]*).out"
var.names <- c("Size", "Radius", "Algorithm")
data.raw <- readExperimentDir (directory=dir, names=var.names, fname.pattern=pattern,
alg.var.name='Algorithm', value.col=1, col.names="Evaluation")
head(data.raw)
## ---- echo=-1------------------------------------------------------------
summarizeData(data=data.raw, fun=median, group.by=c("Size"), ignore=c("Radius"))
## ------------------------------------------------------------------------
data.filtered <- filterData(data=data.raw,
condition="Size == 100 & Rand1 <= Rand2",
remove.cols="Size")
dim(data.filtered)
dim(data.raw)
## ------------------------------------------------------------------------
summarizeData(data.filtered, group.by=c("Radius"))
## ---- warning=FALSE , cache=TRUE , echo=-1-------------------------------
test <- "wilcoxon"
group.by <- c("Size","Radius")
alg.cols <- 3:10
result <- postHocTest(data=data.raw, algorithms=alg.cols, group.by=group.by,
test=test, control="max", correct="holland")
## ------------------------------------------------------------------------
summ <- result$summary
pval <- result$corrected.pval
bold <- is.na(pval)
mark <- pval > 0.05
mark[, (1:2)] <- FALSE
mark[is.na(mark)] <- FALSE
digits <- c(0, 3, rep(2, 8))
writeTabular(table=summ, format="f", bold=bold, mark=mark, mark.char="+",
hrule=c(0, 10, 20, 30), vrule = c(2, 4), digits=digits,
print.row.names=FALSE)
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