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qqBaseX-package.R
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qqBaseX-package.R
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library(roxygen2);library(devtools)
package.name="qqBaseX";
remove.packages(package.name);
g=getwd();
dir.create("MyPackages");
setwd("MyPackages")
if(F){
remove.packages("qqBaseX");
devtools::install_github("AndreasFischer1985/qqBaseX")
}
create=function(
name="qqBaseX",
description=list("Package"="qqBaseX","Title"="Basic functions for analyzing qualitative and quantitative data based on R's default packages.","Version"="0.1.4","Authors@R"="person(\"Andreas\", \"Fischer\", email = \"andreasfischer1985@web.de\", role = c(\"aut\", \"cre\"))","Maintainer"="'Andreas Fischer' <andreasfischer1985@web.de>","Description"="Basic functions for analyzing qualitative and quantitative data based on R's default packages.","Depends"="R (>=3.0.0)","License"="GPL-2","Encoding"="UTF-8","LazyData"="true","RoxygenNote"="6.1.0","VignetteBuilder"="knitr"),
rproj=list("Version"="1.0","RestoreWorkspace"="No","SaveWorkspace"="No","AlwaysSaveHistory"="Default","EnableCodeIndexing"="Yes","Encoding"="UTF-8","AutoAppendNewline"="Yes","StripTrailingWhitespace"="Yes","BuildType"="Package","PackageUseDevtools"="Yes","PackageInstallArgs"="--no-multiarch --with-keep.source","PackageRoxygenize"="rd,collate,namespace"),
gitignore=c(".Rproj.user"),
rbuildignore=c(paste0("^",name,"\\.Rproj$"),"^\\.Rproj\\.user$")
){
wd=getwd()
if(!dir.exists(name))dir.create(name);
setwd(name)
writeList=function(list,file)write(paste0(names(list),(unlist(lapply(list,function(x)paste0(": ",x))))),file=file)
writeList(list=description,file="DESCRIPTION")
writeList(list=rproj,file=paste0(name,".Rproj"))
write(gitignore,file=".gitignore")
write(rbuildignore,file=".RBuildignore")
setwd(wd)
};
create(package.name,
description=list(
"Package"="qqBaseX",
"Title"="Basic functions for analyzing qualitative and quantitative data based on R's default packages.",
"Version"="0.4.7",
"Authors@R"="person(\"Andreas\", \"Fischer\", email = \"andreasfischer1985@web.de\", role = c(\"aut\", \"cre\"))",
"Maintainer"="'Andreas Fischer' <andreasfischer1985@web.de>",
"Description"=
paste(
"The qqBaseX package provides basic functions for assisting all steps of analyzing qualitative and quantitative data. It was written to extend R's default packages without introducing dependencies on other packages.",
"Besides enhanced variants of standard plots and methods (e.g., bp() or dotplot()), the qqBaseX package offers a number of convenience functions - like saveDevs(), to save open graphics devices in high resolution in various formats, or cols(), to easily create color series.",
"In addition, the package includes many functions for exploring datasets (e.g., plotDF() for data.frames or plotMAT() for matrices), functions for visualizing variables (e.g., spiderplot() or flowerplot()), functions for annotating plots (e.g., boxedText()) and functions for visualizing statistical analyses (e.g., plotLM() for linear models).",
"The package also includes model-agnostic functions for quantifying the influence of individual variables on predictions (for example, af.sensitivity() and delta()).",
"In addition, the package provides functions for sourcing data via web-scraping (e.g., scrapeHTML() or extractTable()) and for preprocessing data (e.g., prepareDF() for quantitative data analysis or vecToTDM() for qualitative data analysis)."
),
"Depends"="R (>= 3.0.0)",
"License"="GPL-2",
"Encoding"="UTF-8",
"LazyData"="true",
"RoxygenNote"="6.1.0",
"VignetteBuilder"="knitr")
);
setwd(package.name)
readLines("DESCRIPTION")
####################################
# set up R-functions
####################################
if(!dir.exists("R"))dir.create("R");
setwd("R")
###########################################
# Scraping
###########################################
n <- "vgrepl"
d <- paste0( "#' Function vgrepl\n",
"#' \n#' Variant of grepl that takes a vector of patterns.\n")
f <- function(pattern,x, sumFun=NULL, ...)
{f=Vectorize(grepl,vectorize.arg="pattern");erg=f(pattern=pattern,x=x,...);
if(!is.null(sumFun))erg=sumFun(erg);erg}
vgrepl=f #c=c("d","dasd");f(c("as","d"),c)
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n <- "getHTML";
#-------------
d <- paste0( "#' Function getHTML\n",
"#' \n#' Returns HTML from an URL obained via GET-request.\n",
"#' @param url Character string speficying a valid URL.\n",
"#' @param encoding Character value specifying the encoding. Defaults to \"UTF-8\".\n",
"#' @param save Logical value specifying whether the HTML-code should be saved to a txt-file.\n",
"#' @param filename Character value specifying the filename (if save is TRUE). If NULL (default) as.numeric(Sys.time()) is applied.\n",
"#' @param closeCon Logical value specifying whether to close open connections before and after scraping. defaults to F.\n",
"#' @param method Character value specifying the method. Defaults to \"libcurl\".\n",
"#' @param silent Logical value specifying whether to skip informative messages. Defaults to T.\n",
"#' @param curlHeaders Logical value specifying whether to apply curlHeaders. Defaults to F.\n",
"#' @param headers Logical value.\n",
"#' @param browseURL Locgical value specifying wether to open the URL in a web-browser. Defaults to F.\n",
"#' @details Returns HTML from an URL obained via GET-request. Assumes UTF-8 encoding by default. Returns a character element containing HTML-code.\n",
"#' @keywords scraping\n",
"#' @export\n",
"#' @examples\n",
"#' getHTML()")
f <- function(
url="https://scholar.google.de/citations?user=-TjY7oEAAAAJ&hl=de&oi=sra",
encoding="UTF-8",
save=F,
filename=NULL,
closeCon=F,
method="libcurl",
silent=T,
curlGetHeaders=F,
browseURL=F,
...){
if(closeCon){co=as.numeric(rownames(showConnections(all=T)));for(i in co[co>2]) close(getConnection(i));}
if(!silent)message(paste0("Trying to get html from ",url))
if(is.character(url)){
if(length(grep("(^http://|^https://|^ftp://|^file://)",url))==0) url=paste0("http://",url)
if(curlGetHeaders) message(paste(curlGetHeaders(url, verify=F),collapse=""))
if(browseURL) browseURL(url)
url=url(url,method=method,...)
}
html=paste(readLines(url,encoding=encoding), collapse="\n");
if(save) writeLines(
gsub("^<\n","",gsub("[ ]+"," ",paste0("<",strsplit(html,"<")[[1]]))),
paste0(ifelse(is.character(filename),filename,as.numeric(Sys.time())),".txt"))
if(closeCon){co=as.numeric(rownames(showConnections(all=T)));for(i in co[co>2]) close(getConnection(i));}
return(invisible(html))
}
getHTML=f
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n<-"scrapeHTML"
#-------------
d <- paste0( "#' Function scrapeHTML\n",
"#' \n#' Extracts Information from HTML.\n",
"#' @param html A character element containing HTML-code.\n",
"#' @param short Logical value specifying whether only lines with verbal information or link should be returned. Defaults to F.\n",
"#' @param edit Logical value specifying whether the data.frame should be plotted/edited.\n",
"#' @param save Logical value specifying whether the HTML-code should be saved to a csv-file.\n",
"#' @param plot Logical value specifying whether to plot the frequency of each HTML-tag found in the html-object.\n",
"#' @param filename Character value specifying the filename (if save is TRUE). If NULL (default) as.numeric(Sys.time()) is applied.\n",
"#' @details Extracts Information from HTML code (as returned by qqBaseX::getHTML, for example). Returns a data.frame with three columns: the first column contains html-code, the second column contains extracted verbal information, and the third column contains extracted links.\n",
"#' @keywords scraping\n",
"#' @export\n",
"#' @examples\n",
"#' scrapeHTML(getHTML())")
f <- function(
html,
short=F,
edit=T,
save=F,
plot=F,
filename=NULL){
if(length(html)>1)
if(length(dim(html))>2) stop("please provide HTML as a character vector!") else
if(length(dim(html))>1) { warning("two-dimensional input detected. Only first column is used."); html=paste(as.character(html[,1]),collapse=" ")} else html=paste(as.character(html),collapse=" ")
strings=gsub("(\n|\t)+"," ",gsub("[ ]+"," ",paste0("<",strsplit(html,"<")[[1]])))
if(plot){
s1=sort(table(gsub("(<[/]?|(>| ).*)","",strings))) # inspect all tags without parameters
bp(s1[s1>2],main2="Common Tags")
}
info=gsub("^[ ]*$","",gsub("^<[^<]*>","",strings))
links=character(length(info))
links[grep("href=[\"\'].*?[\"\']",strings)]=
gsub("[\"\'].*$","",gsub("^.*?href=[\"\']","",grep("href=[\"\'].*?[\"\']",strings,value=T)))
result=data.frame(entry=as.character(strings),info=as.character(info),links=as.character(links), stringsAsFactors=F)
if(short)result=result[nchar(as.character(result[,2]))>0|nchar(as.character(result[,3]))>0,]
if(edit)result=edit(result)
if(save) write.csv2(data.frame(result),paste0(ifelse(is.character(filename),filename,as.numeric(Sys.time())),".csv"))
return(invisible(result))
}
scrapeHTML=f
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n<-"subsetHTML"
#-------------
d <- paste0( "#' Function subsetHTML\n",
"#' \n#' Extracts a coherent subset of code from HTML-code.\n",
"#' @param html A character element containing HTML-code.\n",
"#' @param tag Character element specifying the the subsets of interest. Defaults to \"div\".\n",
"#' @param pattern Regular expression further specifying subsets of interest. If NULL (default) equals tag.\n",
"#' @param edit Logical value specifying whether the data.frame should be plotted/edited.\n",
"#' @param save Logical value specifying whether the HTML-code should be saved to a csv-file.\n",
"#' @param plot Logical value specifying whether to plot the frequency of each HTML-tag found in the html-object.\n",
"#' @param filename Character value specifying the filename (if save is TRUE). If NULL (default) as.numeric(Sys.time()) is applied.\n",
"#' @param trim Logical value specifying whether to trim text. Defaults to T.\n",
"#' @details Extracts a coherent subset of code from HTML-code (as returned by qqBaseX::getHTML, for example).\n",
"#' @keywords scraping\n",
"#' @export\n",
"#' @examples\n",
"#' subsetHTML(getHTML(\"https://jobs.meinestadt.de/nuernberg/suche?words=Wissenschaftlicher%20Mitarbeiter\",tag=\"div\",pattern=\"class=\\\"m-resultListEntries__content\\\"\"))")
f <- function (
html,
tag="div",
pattern = NULL,
edit=F,
save = F,
plot=F,
filename = NULL,
trim=T) {
if(length(html)>1)
if(length(dim(html))>2) stop("please provide HTML as a character vector!") else
if(length(dim(html))>1) { warning("two-dimensional input detected. Only first column is used."); html=paste(as.character(html[,1]),collapse=" ")} else html=paste(as.character(html),collapse=" ")
start = paste0("<",tag,"[\n\r> ]")
end = paste0("</",tag,">")
if(is.null(pattern))pattern=start
strings = gsub("[ ]+", " ", paste0("<", strsplit(html, "<")[[1]]))
if(plot){
s1=sort(table(gsub("(<[/]?|(>| ).*)","",strings))) # inspect all tags without parameters
bp(s1[s1>2],main2="Common Tags")
}
infos = gsub("^[ ]*$", "", gsub("^<[^<]*>", "", strings))
links = character(length(infos))
links[grep("href=[\"'].*?[\"']", strings)] = gsub("[\"'].*$","", gsub("^.*?href=[\"']", "", grep("href=[\"'].*?[\"']", strings, value = T)))
loc.pat = grep(pattern, strings)
loc.div1 = grep(start, strings)
loc.div2 = grep(end, strings)
result0 = character(0);result1 = character(0);result2 = character(0);result3 = character(0)
for (i1 in loc.pat) {
loc.div3 = sort(c(loc.div1[which(loc.div1 > i1)], loc.div2[which(loc.div2 > i1)]))
i2 = i1
for (i in loc.div3) { i2 = i; if (length(loc.div1[which(loc.div1 > i1 & loc.div1 <= i)]) < length(loc.div2[which(loc.div2 > i1 & loc.div2 <= i)])) break; }
string = paste(strings[i1:i2], collapse = "\n")
info = paste(infos[i1:i2], collapse = "\n")
link = paste(links[i1:i2], collapse = "\n")
text = gsub("^( )*(\n)*( )*(\n)*", "", gsub("(\n)+( )*(\n)*", "\n", gsub("<.*?>", "", string)))
if(trim==T){
result0 = c(result0, gsub("[\n]+","\n",qqBaseX::trim(string)))
result1 = c(result1, gsub("[\n]+","\n",qqBaseX::trim(text)))
result2 = c(result2, gsub("[\n]+","\n",qqBaseX::trim(info)))
result3 = c(result3, gsub("[\n]+","\n",qqBaseX::trim(link)))
} else {
result0 = c(result0, (string))
result1 = c(result1, (text))
result2 = c(result2, (info))
result3 = c(result3, (link))
}
}
result=data.frame(entry=result0, info=result2, links=result3, stringsAsFactors=F) #text=result1
result=result[grep(paste0("^",start),result[,1]),]
if(edit) result=edit(result)
if (save){
write.csv2(data.frame(result),paste0(ifelse(is.character(filename),filename,as.numeric(Sys.time())),".csv"))
}
return(invisible(result))
}
subsetHTML=f
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n<-"extractTable"
#-------------
d <- paste0( "#' Function extractTable\n",
"#' \n#' Extracts table as data.frames from multiple lines of text.\n",
"#' @param x A character element containing all the text toextract the table from (or a character vector containing one text-line per element).\n",
"#' @param reg.up Regular expression spefifying the top of the table. Defaults to NULL.\n",
"#' @param reg.down Regular expression spefifying the bottom of the table. Defaults to NULL.\n",
"#' @param reg.left Regular expression spefifying the bottom of the table. Defaults to \"^\".\n",
"#' @param reg.right Regular expression spefifying the bottom of the table. Defaults to \"$\"\n",
"#' @param reg.fix Regular expression spefifying the bottom of the table. Defaults to NULL.\n",
"#' @param header Logical value that specifies, whether to treat first row and column as row- and column-names. Defaults to F.\n",
"#' @param trim Logical value that specifies, whether to trim entries. Defaults to T.\n",
"#' @param convert Logical value that specifies, whether to convert table to numeric (after correcting for notation in case correctNotation is set to T). Please use with care, if table contains non-numeric information. Defaults to T.\n",
"#' @param correctNotation Logical value that specifies, whether to correct for the fact that entries use commata instead of dots. Erases all dots in all entries and subsequently replaces commata by dots. Defaults to F.\n",
"#' @details Extracts table as data.frames from multiple lines of text. Columns are assumed to be separated by whitespaces that are placed at the same position in each line. Please make sure that headers don't span multiple columns or rows.\n",
"#' @keywords scraping\n",
"#' @export\n")
f=function(
x,
reg.up=NULL,
reg.down=NULL,
reg.left="^",
reg.right="$",
reg.fix=NULL,
header=F,
trim=T,
convert=F,
correctNotation=F){
if(length(x)==1) x=strsplit(x,"(\r\n|\r|\n)")[[1]]
trimIt=function(x)gsub("(^[ ]+|[ ]+$)","",x);
if(!is.null(reg.up)){
lines=(grep(reg.up,x)[1]):(grep(reg.down,x)[1]-1)
x=x[lines]
rows=(unlist(gregexpr(reg.left,x[1]))[1]):(unlist(gregexpr(reg.right,x[1]))[1])
x=substr(x,min(rows),max(rows));
}
cells=x[nchar(x)>0&!(grepl("^[ ]+$",x))] #streiche leere zeilen
t=data.frame(sapply(cells,function(y)paste0(y,paste(rep(" ",max(nchar(cells))-nchar(y)),collapse=""))))
t2=strsplit(as.character(t[,1]),"")
d1=data.frame(t2[[1]]);for(i in 2:length(t2))d1=data.frame(d1,t2[[i]])
t2=t(d1)
w=c(which(colSums(t2==" ")==max(colSums(t2==" "))),dim(t2)[2])
e=list();
for(i in 1:length(w))e[[i]]=apply(data.frame(t2[,ifelse(i==1,1,w[i-1]):w[i]]),1,function(x)paste(x,collapse=""))
erg=data.frame(e[[1]]);
for(i in 2:length(w))erg=apply(data.frame(erg,e[[i]]),2,as.character)
if(header){
colnames(erg)=trim(as.character(erg[1,]))
rownames(erg)=trim(as.character(erg[,1]))
erg=erg[-1,-1]
} else { colnames(erg)=1:dim(erg)[2];rownames(erg)=1:dim(erg)[1];}
erg=erg[,!colSums(erg==" ")==max(colSums(erg==" "))];
rn=rownames(erg);
if(correctNotation)erg=apply(erg,2,function(x)gsub("[%.]","",x)) #erase % and dots
if(correctNotation)erg=apply(erg,2,function(x)gsub("[,]",".",x)) #change comm to dots
if(!is.null(reg.fix))erg=gsub(reg.fix,"",erg)
if(convert){erg=apply(erg,2,as.numeric);rownames(erg)=rn}
if(trim)return(trimIt(erg)) else return(erg)
}
extractTable=f
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n <- "scrapeJDDM"
d <- paste0(
"#' Function scrapeJDDM\n",
"#' \n#' Downloads and returns data and metadata from the database of the Journal of Dynamic Decision Making.\n",
"#' @param plot Logical value specifying wether to plot data on reads and downloads.\n",
"#' @param urls Character vector specifying the URLs of the individual issues to scrape.\n",
"#' @param url2 Character value specifying the URL of global journal statistics.\n",
"#' @param plot Logical value specifying wether to plot data on reads and downloads.\n",
"#' @details Downloads and returns data and metadata from the database of the Journal of Dynamic Decision Making.\n",
"#' @keywords scraping\n",
"#' @export\n",
"#' @examples\n",
"#' s=scrapeJDDM();"
);
f<-function(
plot=T,
urls=paste0("https://journals.ub.uni-heidelberg.de/index.php/jddm/issue/view/",c(3269,2836,2269,3694,4432)),
url2="https://journals.ub.uni-heidelberg.de/cgi-bin/oastats.cgi?repo=ojs;from_date=2015-09-29%2021:39:27;id=jddm:"
){
article.ids = character(0)
all.authors = character(0)
authors = character(0)
years = character(0)
article.labels = character(0)
for (url in urls) {
html0 = gsub("(\t|\n)", "", paste(readLines(url, encoding = "UTF-8"),
collapse = "\n"))
links = matchAll(html0, "https://journals.ub.uni-heidelberg.de/index.php/jddm/article/view/[0-9/]*\\\">PDF")[[1]][,
1]
article.ids = c(article.ids, gsub("(.*view/|\\\">PDF)",
"", links))
all.authors = c(all.authors, gsub("</div>.*", "", strsplit(html0,
"(\"authors\\\">)")[[1]])[-1])
authors = paste0(gsub(",.*", "", all.authors), " et al.")
authors[grep("Fischer(.*)Holt(.*)Funke", all.authors)] = "Editoral"
years = c(years, rep(gsub("(.*[(]|[)])", "", matchOne(html0,
"<title>Vol [0-9]* \\([0-9]*\\)"))[, 1], length(links)))
}
article.labels = paste0(authors, " (", years, ")")
names(article.labels) = article.ids
html = list()
for (i in 1:length(article.ids)) {
html[as.character(article.ids[i])] = paste(readLines(paste0(url2,
gsub("/.*", "", article.ids[i]), ";lang=ende;overlay=1"),
encoding = "UTF-8"), collapse = "\n")
message(article.ids[i])
}
html = unlist(html)
current.year = as.numeric(gsub("-.*", "", (Sys.Date())))
span = current.year - 2015 + 1
results = list()
for (i in 1:length(html)) {
months = paste(paste0(">", c("Jan", "Feb", "Mar", "Apr",
"May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov",
"Dec"), "<"), collapse = "|")
df = data.frame(c("Intro", matchAll(html[i], months)[[1]]),
strsplit(as.character(html[i]), months))
df[, 2] = gsub("<table class=\\\"stats\\\"><tr><th>20[0-9][0-9]</th>",
"", df[, 2])
numbers = sapply(matchAll(df[, 2], ">[0-9]+<"), function(x) as.numeric(gsub("[<>]",
"", c(x[1:2]))))[, -1]
if (is.null(dim(numbers)))
numbers = as.matrix(numbers)
colnames(numbers) = gsub("[<>]", "", df[-1, 1])
rownames(numbers) = c("Downloads", "Frontdoor")
mo = dim(numbers)[2]
numbers = cbind(numbers, matrix(NA, nrow = 2, ncol = 24 -
mo))
colnames(numbers) = paste(colnames(numbers), c(rep(current.year,
12), rep(current.year - 1, 12)))
st = matchAll(df[, 2], ">[0-9]+<")
prior = as.numeric(gsub("[<>]", "", st[[length(st)]][-c(1:2),
1]))
prior = c(prior, rep(NA, 2 * (as.numeric(gsub("-.*",
"", (Sys.Date()))) - 2014) - length(prior)))
numbers = cbind(numbers, t(data.frame(prior[seq(1, length(prior),
2)], prior[seq(1, length(prior), 2) + 1])))
colnames(numbers)[25:(24 + span)] = as.numeric(gsub("-.*",
"", (Sys.Date()))):2015
results[[as.character(article.ids[i])]] = numbers
}
m = matrix(ncol = (24 + span))
for (i in 1:length(results)) m = rbind(m, results[[i]])
m = m[-1, ]
rownames(m) = paste(rownames(m), rep(article.ids, each = 2))
if (as.numeric(gsub("(^[0-9]*-|-[0-9]*$)", "", Sys.Date())) <
12) {
shift = which(!is.na(m[, 1]))
m[shift, 13:24] = m[shift, 1:12]
m[shift, 1:12] = NA
m = m[, first(which(dim(m)[1] != colSums(is.na(m)))):dim(m)[2]]
}
names(article.labels) = article.ids
current.year = as.numeric(gsub("-.*", "", (Sys.Date())))
years.JDDM = (as.numeric(gsub("-.*", "", (Sys.Date()))) -
2014)
entryNo = 2 * 12 + years.JDDM - 2
downloads = m[seq(1, dim(m)[1], 2), dim(m)[2]:1]
frontdoor = m[seq(1, dim(m)[1], 2) + 1, dim(m)[2]:1]
downloads.per.year = m[seq(1, dim(m)[1], 2), dim(m)[2]:1][,
1:years.JDDM]
frontdoor.per.year = m[seq(1, dim(m)[1], 2) + 1, dim(m)[2]:1][,
1:years.JDDM]
frontdoor.per.year[is.na(frontdoor.per.year)] = 0
downloads.per.year[is.na(downloads.per.year)] = 0
df = data.frame(article.ids, article.labels, all.authors,
authors, years, download.link = paste0("https://journals.ub.uni-heidelberg.de/index.php/jddm/article/download/",
article.ids), downloads, frontdoor)
if (F) {
if (any(rowSums(is.na(downloads[, (current.year - 2013):dim(downloads)[2]])) >
11) | any(rowSums(is.na(frontdoor[, (current.year -
2013):dim(frontdoor)[2]])) > 11))
warning("only a subset of papers is returned. please try again next month")
df = df[(rowSums(is.na(downloads[, (current.year - 2013):dim(downloads)[2]])) <
12 & rowSums(is.na(frontdoor[, (current.year - 2013):dim(frontdoor)[2]])) <
12), ]
}
if (plot) {
downloads2 = downloads[, colnames(downloads) != as.character(current.year -
1) & colnames(downloads) != as.character(current.year)]
rownames(downloads2) = article.labels
downloads2 = downloads2[order(rowSums(downloads2, na.rm = T),
decreasing = T)[1:min(dim(downloads2)[1], 25)], ]
dev.new(width = 10, height = 7)
plotMAT(downloads2, main = "Cumulation of Downloads",
cumsum = T)
frontdoor2 = frontdoor[, colnames(frontdoor) != as.character(current.year -
1) & colnames(frontdoor) != as.character(current.year)]
rownames(frontdoor2) = article.labels
frontdoor2 = frontdoor2[order(rowSums(frontdoor2, na.rm = T),
decreasing = T)[1:min(dim(frontdoor2)[1], 25)], ]
dev.new(width = 10, height = 7)
plotMAT(frontdoor2, main = "Cumulation of Reads", cumsum = T)
}
return(df)
}
scrapeJDDM=f;
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
#g1=getHTML("https://statistik.ub.uni-heidelberg.de/oa_statistik/doc_id/period/showmonth/?doc_id=ojs:jddm:69298")
#g2=getHTML("https://statistik.ub.uni-heidelberg.de/oa_statistik/doc_id/country/?doc_id=ojs:jddm:69298")
#g3=getHTML("https://journals.ub.uni-heidelberg.de/cgi-bin/oastats.cgi?repo=ojs;from_date=2015-09-29%2021:39:27;id=jddm:69298;lang=ende;overlay=1")
#strsplit(g1,"\\{")
###########################################
# Plotting
###########################################
n="saveDevs"
d <- paste0(
"#' Function saveDevs\n",
"#' \n#' Saves each element of dev.list() to a graphical device such as pdf, png or similar.\n",
"#' @param filename Character vector containing file names.\n",
"#' @param width Width of the devices. If NA (default), width of the devices is left unchanged.\n",
"#' @param height Height of the devices. If NA (default), height of the devices is left unchanged.\n",
"#' @param dev Graphical device (currently, pdf, win.metafile, png, bmp, jpg and tiff are supported).\n",
"#' @param units Parameter passed to dev.copy. Defaults to \"in\". Is ignored if dev==pdf.\n",
"#' @param res Resolution (dots per inch) of the devices. Defaults to 300. Is ignored if dev==pdf.\n",
"#' @param mess Logical value specifying if a message should be printed after saving the devices. Defaults to T.\n",
"#' @param close Logical value specifying whether to close devices after saving them.\n",
"#' @details Saves each element of dev.list() to a graphical device such as pdf, png or similar.\n",
"#' @keywords plotting\n",
"#' @export\n",
"#' @examples\n",
"#' saveDevs();"
);
f <- function (
filename = NA,
width = NA,
height = NA,
dev = png,
units = "in",
res = 300,
mess = T,
close = F,
...){
n = deparse(substitute(dev))
n[n == "win.metafile"] = "emf"
l = dev.list()
if (length(l)==0) {warning("No device open.");return(invisible());}
if (length(filename) != length(l)) filename = rep(filename[1], length(l))
if (length(width) != length(l)) width = rep(width[1], length(l))
if (length(height) != length(l)) height = rep(height[1], length(l))
filename[is.na(filename)]=""
if(sum(table(match(filename, levels(as.factor(filename))))>1)>0)filename=paste(filename,1:length(filename))
if(filename[1]=="" & length(filename)==1) filename="Plot"
filename[grepl(paste0("[.]",n,"$"),filename)==F] = paste0(filename[grepl(paste0("[.]",n,"$"),filename)==F], ".", n)
for (i in 1:length(l)) {
d = l[i]
dev.set(d)
width1 = width[i]
height1 = height[i]
filename1 = filename[i]
if (is.na(width1))width1 = (dev.size()[1])
if (is.na(height1))height1 = (dev.size()[2])
if (length(grep("(bmp|png|jpg|tiff)", n)) > 0) dev.copy(dev, filename1,
width = width1, height = height1, units = units,res = res, ...)
else if (length(grep("(pdf|emf)", n)) > 0)
dev.copy(dev, filename1, width = width1, height = height1, ...)
else dev.copy(dev, filename1, width = width1, height = height1, ...)
dev.off()
}
if (close) graphics.off()
if (mess) message(ifelse(length(l) > 1, paste0(length(l), " devices saved to\n", getwd()), paste0(length(l), " device saved to\n", getwd())))
}
saveDevs=f
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n="plotXY"
#-------------
d <- paste0( "#' Function plotXY\n",
"#' \n#' Plots bivariate correlation based on two numeric vectors.\n",
"#' @param x Numeric vector.\n",
"#' @param y Numeric vector of the same length as x.\n",
"#' @param complexity Numeric value specifying the amount of nonlinearity modelled. Defaults to 0 (i.e., a linear model).\n",
"#' @param rep.nnet Numeric value specifying the number of nnet-objects to choose the best model from.\n",
"#' @param attrModel Logical value specifying whether to add the model as an attribute to the object returned.\n",
"#' @param na.rm Logical value indicating whether missing values should be skipped. Defaults to T.\n",
"#' @param color1 Color of points in the scattergram. Defaults to rgb(0,0,0,.7).\n",
"#' @param color2 Color of the regression line. Defaults to rgb(0,0,1).\n",
"#' @param color3 Color of the prediction interval. Defaults to rgb(0,0,1,.2).\n",
"#' @param ... additional parameters passed to the plot function.\n",
"#' @details Plots scattergram and bivariate correlation based on two numeric vectors.\n",
"#' @keywords plotting\n",
"#' @export\n",
"#' @examples\n",
"#' plotXY()")
f<- function (
x = NULL,
y = NULL,
complexity = 0,
rep.nnet = 10,
attrModel = T,
na.rm = T,
color1 = rgb(0, 0, 0, 0.7),
color2 = rgb(0, 0, 1),
color3 = rgb(0, 0, 1, 0.2),
xlab = "x",
ylab = "y",
axes = T,
add = F,
main = NA,
sub = NA,
pch = 16,
lwd = 2,
cex = 0.7,
cex.sub = 0.7,
generalize = F,
main1 = NULL,
main2 = NULL,
main3 = NULL,
mar=NA,
adj.main1 = 0,
adj.main2 = 0,
adj.main3 = 0,
col.main1 = "black",
col.main2 = "black",
col.main3 = "black",
cex.main1 = 1.2,
cex.main2 = 1.2,
cex.main3 = 1.2,
font.main1 = 1,
font.main2 = 2,
font.main3 = 4,
...)
{
if (is.null(sub))
sub = ifelse(complexity == 0, "Shaded area represents 95%-confidence interval.",
"Shaded area represents 95%-prediction interval.")
if (is.null(x) & is.null(y)) {
x = rnorm(100)
y = rnorm(100)
}
mar0 = NULL
if (is.numeric(mar)) {
mar0 = par("mar")
par(mar = mar)
}
data = data.frame(x, y)
if (na.rm == T) data = data[complete.cases(data), ]
data0 = data
data = data.frame(scale(data))
colnames(data) = colnames(data0)
nnet = NULL
lm = NULL
if (complexity>0)
if (length(grep("^quantqual$", (installed.packages()[, "Package"]))) == 0) {
complexity=0;
warning("complexity set to 0 because quantqual-package is not installed.\nYou may install it via devtools::install_github(\"AndreasFischer1985/quantqual\")")
}
if (complexity > 0) {
if (!generalize)
nnet = quantqual::nnets(data, "y", size = complexity, linout = T, rep.nnet = rep.nnet)[[1]]
else nnet = quantqual::af.nnet(data, "y", size = complexity, decay = NULL, linout = T, rep.nnet = rep.nnet)
xTrain = data[colnames(data) != "y"]
yTrain = data["y"]
p = quantqual::predintNNET(nnet, xTrain, yTrain, main = main, sub = sub,
color1 = color1, color2 = color2, color3 = color3,
xlab = xlab, ylab = ylab, axes = axes, plot = F)
p = p[order(data[, 1]), ]
len = dim(p)[1]
in1 = sort(data[, 1])
ou1 = p[, 1]
inner = p[, 2]
outer = p[, 3]
}
else {
l1 = lm(data[, 2] ~ data[, 1])
lm = l1
co1 = confint(l1)
len = 100
in1 = seq(min(data[, 1]), max(data[, 1]), length.out = len)
ou1 = in1 * coef(l1)[2] + coef(l1)[1]
ou2 = data.frame(in1 * co1[2, 1] + co1[1, 1], in1 * co1[2,
2] + co1[1, 2], in1 * co1[2, 1] + co1[1, 2], in1 *
co1[2, 2] + co1[1, 1])
inner = apply(ou2, 1, min)
outer = apply(ou2, 1, max)
}
unscale = function(x, m, s) x * s + m
in1 = unscale(in1, mean(data0[, 1], na.rm = T), sd(data0[, 1], na.rm = T))
ou1 = unscale(ou1, mean(data0[, 2], na.rm = T), sd(data0[, 2], na.rm = T))
inner = unscale(inner, mean(data0[, 2], na.rm = T), sd(data0[, 2], na.rm = T))
outer = unscale(outer, mean(data0[, 2], na.rm = T), sd(data0[, 2], na.rm = T))
if (add == F) plot(data0[, 1], data0[, 2], xlab = xlab, ylab = ylab, main = main, type = "n", axes = axes, ...)
if (add == F) if (!is.null(sub)) title(sub = sub, cex.sub = cex.sub)
polygon(c(in1, in1[length(in1):1]), c(inner, outer[length(outer):1]), col = color3[1], border = NA)
if(length(data0[, 1])!=length(color1))color1=color1[1]
points(data0[, 1], data0[, 2], pch = pch, col = color1)
lines(in1, ou1, , col = color2[1], lwd = lwd)
dat = data.frame(predictor = in1, prediction = ou1, lower.bound = inner, upper.bound = outer)
if (attrModel)
if (!is.null(nnet)) attr(dat, "model") = nnet
else attr(dat, "model") = lm
if (!is.null(main1))
title(main1, line = 1, adj = adj.main1, cex.main = cex.main1, col = col.main1, font.main = font.main1)
if (!is.null(main2))
title(main2, line = 2, adj = adj.main2, cex.main = cex.main2, col = col.main2, font.main = font.main2)
if (!is.null(main3))
title(main3, line = 3, adj = adj.main3, cex.main = cex.main3, col = col.main3, font.main = font.main3)
if (is.numeric(mar)) par(mar = mar0)
return(invisible(dat))
}
plotXY=f
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n <- "cols"
#------------
d <- paste0(
"#' Function cols\n",
"#' \n#' Returns a vector of colors of a certain length.\n",
"#' @param num Number of colors to return or a numeric vector containing indices of colors. Defaults to 1.\n",
"#' @param col2 Character vector specifying the darker color of the specturm to be returned.\n",
"#' @param col1 Character vector specifying the lighter color of the specturm to be returned.\n",
"#' @details Returns a vector of colors of a certain length. If col1 and col2 are NULL (default) a rainbow palette is returned. If col2 is specified, col1 is set to \"white\". If col1 is specified, col2 is set to \"black\". In addition to regular color labels, the cols-function accepts some pre-defined color-labels (such as \"jddm\" or \"jddmLight\" for the Logo-colors of the Journal of Dynamic Decision Making). If num is a numeric vector, the color palette will have max(num) colors, the number of colors returned equals length(num), and num itself is applied as a vector of indices for the color palette returned. \n",
"#' @keywords plotting\n",
"#' @export\n",
"#' @examples\n",
"#' bp(1:10,col=cols(10,\"jddm\"))"
);
f<-function(num=1,col2=NULL,col1=NULL){
if(is.null(num))num=1
if(length(num)>1){num=num[1];warning("Please provide a single number for num (or set col1 and col2 to NULL). Only first element is used.");}
if(length(col1)>1){col1=col1[1];warning("Please provide a single color name for col1. Only first element is used.");}
if(length(col2)>1){col2=col2[1];warning("Please provide a single color name for col2. Only first element is used.");}
if(!is.numeric(num)&is.null(col1)&is.null(col2)){col1=num;col2=num;num=1}
if(is.numeric(num)&is.null(col1)&is.null(col2))if(length(num)>1){num[num<1]=1;return(rainbow(max(num))[num]);} else return(rainbow(num))
if(is.null(col1))col1="white";
if(is.null(col2))col2="black"
x="jddm";y=rgb(135/255,44/255,40/255); if(col1==x)col1=y;if(col2==x)col2=y;
x="jddmLight";y=rgb(118/255,119/255,118/255);if(col1==x)col1=y;if(col2==x)col2=y;
x="fbb";y=rgb(0/255,84/255,122/255); if(col1==x)col1=y;if(col2==x)col2=y;
x="fbbLight";y=rgb(217/255,231/255,239/255); if(col1==x)col1=y;if(col2==x)col2=y;
x="bst";y=rgb(0/255,50/255,100/255); if(col1==x)col1=y;if(col2==x)col2=y;
x="ba";y=rgb(226/255,0/255,26/255); if(col1==x)col1=y;if(col2==x)col2=y;
if(length(num)>1){num[num<1]=1;return(colorRampPalette(c(col1,col2))(max(num))[num]);}
if(num==1)return(col2)
return(colorRampPalette(c(col1,col2))(num));
}
cols=f
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n<-"cols2"
#------------
d <- paste0(
"#' Function cols2\n",
"#' \n#' Returns a vector of transparent colors based on a vector of colors.\n",
"#' @param col Character vector specifying the colors to be transformed.\n",
"#' @param transparency Numberic value specifying the transparency of the colors to be returned. Defaults to .3\n",
"#' @details Returns a vector of transparent colors based on a vector of colors.\n",
"#' @keywords plotting\n",
"#' @export\n",
"#' @examples\n",
"#' cols2(cols(10,\"jddm\")))"
);
f<-function(col,transparency=.7){
if(length(transparency)!=1)transparency=F
if(is.na(transparency)|!is.numeric(transparency))transparency=F
if(transparency<0)transparency=F
ifelse(transparency==F,
list(sapply(col,function(x)qqBaseX::cols(3,x,"white")[2])),
list(apply(col2rgb(col),2,function(x)rgb(x[1]/255,x[2]/255,x[3]/255,1-transparency))))[[1]]
}
cols2=f;
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n="decollide"
#-------------
d <- paste0(
"#' Function decollide\n",
"#' \n#' Returns a matrix with coordinates and text for plotting texts without collisions.\n",
"#' @param x Numeric vector containing x-coordinates of text elements.\n",
"#' @param y Numeric vector containing x-coordinates of text elements.\n",
"#' @param text Character vector containing text-elements to be plotted.\n",
"#' @param jitter Logical value specifying whether to add a small random component after each step.\n",
"#' @param cex Numeric value specifying the relative font size of the text. Defaults to 1.\n",
"#' @param frame Numeric value specifying the relative font size of an invisible frame around the text. Defaults to 1.5\n",
"#' @param lock.x Logical value specifying whether to skip shifts on the x-axis. Defaults to F.\n",
"#' @param lock.y Logical value specifying whether to skip shifts on the y-axis. Defaults to F.\n",
"#' @param verbose Logical value specifying whether to give information on the process after each step.\n",
"#' @param cex Numeric value specifying the maximum number of steps. Defaults to 100.\n",
"#' @details Returns a matrix with coordinates and text for plotting texts without collisions. Iteratively shifts text elements until all collisions are eliminated or the maximum number of repetitions is reached.\n",
"#' @keywords plotting\n",
"#' @export\n",
"#' @examples\n",
"#' set.seed(0);decollide(x=rnorm(10),y=rnorm(10),text=paste0(1:10,\":\",round(rnorm(10),3)),cex=1,font=1,plot=T)"
);
f<-function(x,y,text,jitter=F,cex=1,font=1,frame=1.5,plot=F,lock.x=F,lock.y=F,verbose=F,repetitions=100){
x0=x;y0=y;
if(plot){xrange=max(x)-min(x);yrange=max(y)-min(y);plot(x,y,type="n",xlim=c(min(x)-xrange/2,max(x)+xrange/2),ylim=c(min(y)-yrange/2,max(y)+yrange/2));text(x,y,text,font=font,cex=cex);}else
xrange=par("usr")[2]-par("usr")[1];yrange=par("usr")[4]-par("usr")[3];
sw=strwidth(text,font=font,cex=cex*frame,units="user");
sh=strheight(text,font=font,cex=cex*frame,units="user");
co=cbind(x-sw/2,x+sw/2,y-sh/2,y+sh/2)
m=matrix(0,nrow=dim(co)[1],ncol=dim(co)[1])
for(i in 1:repetitions){
for(i in 1:dim(co)[1])for(j in 1:dim(co)[1])if(i!=j){
col=co[j,1]<=co[i,2]&co[j,2]>=co[i,1]&((co[j,3]<=co[i,4]&co[j,4]>=co[i,3])|(co[j,4]>=co[i,3]&co[j,3]<=co[i,4]))
m[i,j]=col;
if(col){
if(x[i]>=x[j]&!lock.x) x[i]=x[i]+xrange/100;
if(x[i]<x[j]&!lock.x) x[i]=x[i]-xrange/100;
if(y[i]>=y[j]&!lock.y) y[i]=y[i]+yrange/100;
if(y[i]<y[j]&!lock.x) y[i]=y[i]-yrange/100;
if(jitter){
co=cbind(x-sw/2,x+sw/2,y-sh/2,y+sh/2)
col=co[j,1]<co[i,2]&co[j,2]>co[i,1]&((co[j,3]<co[i,4]&co[j,4]>co[i,3])|(co[j,4]>co[i,3]&co[j,3]<co[i,4]))
if(col){
if(abs(x[i]-x[j])>=0&!lock.x) x[i]=x[i]+ifelse(jitter,rnorm(1,sd=sd(x)/100),0);
if(abs(y[i]-y[j])>=0&!lock.y) y[i]=y[i]+ifelse(jitter,rnorm(1,sd=sd(y)/100),0);
}
}
}
co=cbind(x-sw/2,x+sw/2,y-sh/2,y+sh/2)
};if(verbose)message(sum(m)/2); if(plot){plot(x,y,type="n",xlim=c(min(x)-xrange/2,max(x)+xrange/2),ylim=c(min(y)-yrange/2,max(y)+yrange/2));text(x,y,text,font=font,cex=cex);}
if(sum(m)/2==0)break;
}
return(data.frame(x,y,text))
}
decollide=f;
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n="mar"
d <- paste0(
"#' Function mar\n",
"#' \n#' Returns margins of plots given numeric vectors to add and/or multiply, and/or a set of labels for each axis.\n",
"#' @param mar Numeric vector containing default margins. Defaults to c(5.1, 4.1, 4.1, 2.1).\n",
"#' @param mar1 Numeric vector to be multiplied with mar. Defaults to c(1,1,1,1).\n",
"#' @param mar0 Numeric vector to be added to the product of mar and mar1. Defaults to c(0,0,0,0).\n",
"#' @param labels1 Character vector containing labels for axis 1 (bottom).\n",
"#' @param labels2 Character vector containing labels for axis 2 (left).\n",
"#' @param labels3 Character vector containing labels for axis 3 (up).\n",
"#' @param labels4 Character vector containing labels for axis 4 (right).\n",
"#' @param set Logical value specifying whether to set the margins after determining them. Defaults to T\n",
"#' @details Returns margins of plots given numeric vectors to add and/or multiply, and/or a set of labels for each axis.\n",
"#' @keywords plotting\n",
"#' @export\n",
"#' @examples\n",
"#' mar();"
);
f=function(mar=c( 5.1,4.1,4.1,2.1), mar1=c(1,1,1,1), mar0=c(0,0,0,0), labels1=NULL, labels2=NULL, labels3=NULL, labels4=NULL, labelFactor=3,set=T){
if(is.null(mar))if(length(dev.list())>0) {mar=par("mar")} else mar=c( 5.1,4.1,4.1,2.1)
if(!is.null(labels1)) mar[1]=mar[1]+max(strwidth(labels1,units="inches")*labelFactor,na.rm=T)
if(!is.null(labels2)) mar[2]=mar[2]+max(strwidth(labels2,units="inches")*labelFactor,na.rm=T)
if(!is.null(labels3)) mar[3]=mar[3]+max(strwidth(labels3,units="inches")*labelFactor,na.rm=T)
if(!is.null(labels4)) mar[4]=mar[4]+max(strwidth(labels4,units="inches")*labelFactor,na.rm=T)
mar=mar*mar1
mar=mar+mar0
if(set!=F) par("mar"=mar)
return(invisible(mar))
}
mar=f
write(paste0(d,"\n\n",n," <- ",paste(deparse(f),collapse="\n")),file=paste0(n,".r"))
n <- "bp"
#------------
d <- paste0(
"#' Function bp\n",
"#' \n#' Custom barplot with labeled bars.\n",
"#' @param x Numeric vector, matrix or data.frame containing the values to be displayed.\n",
"#' @param sd Numeric vector, matrix or data.frame of same format as x containing standard deviations.\n",
"#' @param cex Size of axis fonts. Defaults to 1.\n",
"#' @param beside Logical value indicating if bars should be placed next to each other. Defaults to T.\n",
"#' @param horiz Logical value indicating if bars should be placed horizontal. Defaults to F.\n",
"#' @param breakLabels Logical value indicating if labels of bars should be tranformed by qqBaseX::labelbreaker. Defaults to F.\n",
"#' @param add.numbers Logical value indicating if numbers should be placed above bars. Defaults to F.\n",
"#' @param ndigits Numeric value specifying the number of digits to be plotted (if add.numbers==T). Defaults to 2.\n",
"#' @param ncex Size of fonts. If NA (default) is set to cex.\n",
"#' @param nsrt Numeric value specifying the rotation of the numbers (between 0 and 360 degrees). Defaults to 0.\n",
"#' @param npos Numeric value specifying the position of numbers. If NA (default) it is determined automatically.\n",
"#' @param ncol Vector containing the color of bars. Defaults to \"black\".\n",
"#' @param sdcol Vector containing the color of arrows. Defaults to \"grey\".\n",
"#' @param grid Logical value indicating whether to plot a grid. Defaults to T.\n",
"#' @param plot Logical value indicating whether to plot the barplot. Defaults to T.\n",
"#' @param main Character vector with one element containing the barplot's title. Defaults to NULL\n",
"#' @param sub Character vector with one element containing the barplot's subtitle. Defaults to NULL\n",
"#' @param xlim.factor Numeric value for adding extra space to the right of the barplot (if a legend is provided). Defaults to 1.5\n",
"#' @param xlim Numeric vector containing xlim.\n",
"#' @param las Numeric value specifying the rotation of the y-axis (0 for 90 percent rotation, 1 for 0 percent rotation). Defaults to 1.\n",
"#' @param srt Numeric value specifying the rotation of the x-axis (between 0 and 360 degrees). Defaults to 45.\n",
"#' @param names.arg Character vector containing names of bars. If NULL (default) colnames of x will be applied as names.arg.\n",
"#' @param legend.text Legend text. Set to NA or to F to supress legend. If NULL (default) rownames of x will be applied as legend.text.\n",
"#' @param optimize.legend Logical or character value. If T (Default), the legend is shifted to the right if overlapping with bars (as long as no args.legend are provided). If a position is provided instead (\"bottom\", \"bottomleft\", \"left\",\"topleft\",\"top\",\"topright\",\"right\",\"bottomright\") the legend will be placed and shifted accordingly. Adding a \"1\" at the end of a position (e.g., \"top1\") results in the legend being drawn horizontally instead of vertically.\n",
"#' @param args.legend List with arguments to pass to legend(). Defaults to list(bg = \"white\").\n",
"#' @param density Vector giving the density of shading lines, in lines per inch, for the bars or bar components. The default value of NULL means that no shading lines are drawn. Non-positive values of density also inhibit the drawing of shading lines.\n",
"#' @param angle Slope of shading lines, given as an angle in degrees (counter-clockwise), for the bars or bar components.\n",
"#' @param col Vector containing the color of bars. If NULL (default) colors are generated based on the rainbow-palette.\n",
"#' @param grid.col Character or rgb value containing the color of grid lines. Defaults to \"grey\".\n",
"#' @param axes Logical value indicating whether to plot axes. Defaults to T.\n",
"#' @param add Logical value indicating whether to plot the barplot to the current device. Defaults to F.\n",
"#' @param adj Numeric value between 0 and 1, indicating where to plot main title and axis labels - if any - between left (0) and right (1). Defaults to 0.5\n",
"#' @param default.labels Logical value, indicating whether to use traditional barplot-labels (which, e.g., hide in case of overlap) instead of bp-style labels. Defaults to F.\n",
"#' @param xlab Character value representing the label to be drawn next to the x-axis. Defaults to NA.\n",
"#' @param ylab Character value representing the label to be drawn next to the y-axis. Defaults to NA.\n",
"#' @param border Color of the bars' border. Defaults to NA.\n",
"#' @param grid.mode Numeric value specifying when to plot the grid. 0 for grid in the background, 1 for grid in the foreground. Defaults to 0.\n",
"#' @param ... Additional graphical parameters for barplot.\n",
"#' @details Plots a barplot and adds labels and numbers to bars. Optionally allows for plotting standard deviations around each bar.\n",
"#' @keywords plotting\n",
"#' @export\n",
"#' @examples\n",
"#' bp(data.frame(group1=c(variable1=1,variable2=2),group2=c(variable1=3,variable2=4)),horiz=T,main=\"Example\")"
);
f <- function (x = NULL, sd = NULL, cex = 1, beside = T, horiz = F, breakLabels = F,
add.numbers = F, ndigits = 2, ncex = NA, nsrt = 0, npos = NA,
ncol = "black", sdcol="grey", grid = T, plot = T, main = NULL, sub = NULL,
xlim.factor = 1.5, las = 1, srt = 45, xlim = NULL, ylim = NULL, names.arg = NULL,
legend.text = NULL, optimize.legend=T, args.legend = NULL, density = NULL,
angle = 45, col = NULL, grid.col = "grey", axes = T, add = F,
adj = 0.5, default.labels = F, xlab = NA, ylab = NA, border = NA,
grid.mode = 0, main1 = NULL, main2 = NULL, main3 = NULL,
adj.main1 = 0, adj.main2 = 0, adj.main3 = 0, col.main1 = "black",
col.main2 = "black", col.main3 = "black", cex.main1 = 1.2,
cex.main2 = 1.2, cex.main3 = 1.2, font.main1 = 1, font.main2 = 2,
font.main3 = 4, omitZeros = T, mar = NA, automar=F, ...)
{
addChars = ifelse(is.character(add.numbers), add.numbers, "")
mar0 = NULL
if (is.character(add.numbers)) add.numbers = T
if (is.null(ncex)) ncex = cex
else if (is.na(ncex)) ncex = cex
if (!is.null(npos))
if (is.na(npos))
if (beside == T)
npos = ifelse(horiz == T, 4, 3)
else npos = NULL
if (is.null(x)) x = data.frame(test1 = c(1, 2, 3), test2 = c(2, 3, 4))
else if (is.table(x)) {
y = matrix(sapply(x, as.numeric), nrow = dim(x)[1])
if (length(dim(x)) == 1) {
rownames(y) = names(x)
}
else {
rownames(y) = rownames(x)
colnames(y) = colnames(x)
}
x = y
}
el = list(...)
x = as.matrix(x)
if (is.character(x))
stop("Please provide numeric data!")
x2 = ifelse(dim(x)[2] == 1 & beside==T, list(x[, 1]), list(x))[[1]]
if (!is.null(sd)) {
sd = ifelse(dim(x)[2] == 1, list(as.matrix(sd)[, 1]), list(as.matrix(sd)))[[1]]
}
if (is.null(rownames(x)))
rownames(x) = 1:dim(x)[1]
if (is.null(colnames(x)))
colnames(x) = 1:dim(x)[2]
if (is.matrix(x2)) {
rownames(x2) = rownames(x)
colnames(x2) = colnames(x)
}
else names(x2) = rownames(x)
width = unlist(ifelse(length(el[["width"]]) > 0, el["width"], list(1))[[1]])
space = unlist(ifelse(length(el[["space"]]) > 0, el["space"], ifelse(beside & dim(x)[2] > 1, list(c(0, 1)), list(0.2)))[[1]])
if (is.null(col)) col = rainbow(dim(x)[1])
if (is.null(legend.text) & dim(x)[2] > 1) legend.text = rownames(x)
if(!is.null(legend.text))
if (sum(is.na(legend.text)) > 0) legend.text = NULL
else if (length(legend.text) == 1)
if (legend.text[[1]] == F) legend.text = NULL
if(length(args.legend)==1)
if(sum(is.na(args.legend))>0 | sum(args.legend==F)>0) legend.text = NULL
if (is.null(xlim))
if (!horiz) {
b = barplot(x2, beside = beside, horiz = horiz, plot = F, add = add, ...)
xlim = c(min(b) - (width[1]/2), max(b) + (width[1]/2))
if (!is.null(legend.text)) xlim[2] = xlim[2] * xlim.factor
}
else {
if (beside) { xlim = c(min(c(min(x), 0)), max(c(max(x), 0)))
} else { xlim = c(min(c(min(colSums(x)), 0)), max(c(max(colSums(x)), 0)))
}
if (!is.null(legend.text)) xlim[2] = xlim[2] * xlim.factor
}
if (is.null(ylim))
if (!horiz) {
if (beside) { ylim = c(min(c(min(x), 0)), max(c(max(x), 0)))
} else { ylim = c(min(c(min(colSums(x)), 0)), max(c(max(colSums(x)), 0)))
}
}
else {
b = barplot(x2, beside = beside, horiz = horiz, plot = F, add = add, ...)
ylim = c(min(b) - (width[1]/2), max(b) + (width[1]/2))
}
if (!is.null(names.arg)) {
if (length(names.arg) == 1)
if (is.na(names.arg))
names.arg = rep(NA, dim(x)[2])
if (dim(x)[2] == 1)
rownames(x) = names.arg
else colnames(x) = names.arg
}
else names.arg = ifelse(dim(x)[2] == 1, list(rownames(x)), list(colnames(x)))[[1]]
if (automar) mar=ifelse(horiz,list(qqBaseX::mar(labels2=names.arg)),list(qqBaseX::mar(labels1=names.arg)))[[1]]
if (is.numeric(mar)) {
mar0 = par("mar")
par(mar = mar)
}
b = NULL
if (grid.mode == 0) {
b = as.matrix(barplot(x2, beside = beside, horiz = horiz,
density = density, angle = angle, xlim = xlim, ylim = ylim, plot = plot,
las = las, add = add, adj = adj, main = main, sub = sub,
col = NA, xlab = xlab, ylab = ylab, border = NA, axes = F,
names.arg=ifelse(default.labels == T, list(names.arg), list(rep(NA, dim(x)[2])))[[1]], ...))
}
else {
b = as.matrix(barplot(x2, border = border, xlab = xlab,
ylab = ylab, names.arg = ifelse(default.labels == T, list(names.arg), list(rep(NA, dim(x)[2])))[[1]],
beside = beside, horiz = horiz, density = density,
angle = angle, col = col, xlim = xlim, ylim = ylim, main = main,
sub = sub, plot = plot, las = las, axes = F, add = add,
adj = adj, ...))
}
abline2 = function(xl, xlf, ...) {
xaxp <- ifelse((length(dev.list())>0|plot==T), list(par("xaxp")), list(c(0,1,5)))[[1]]
yaxp <- ifelse((length(dev.list())>0|plot==T), list(par("yaxp")), list(c(0,1,5)))[[1]]
segments(x0 = min(xl), y0 = seq(yaxp[1], yaxp[2], (yaxp[2] -
yaxp[1])/yaxp[3]), x1 = max(xl)/xlf, y1 = seq(yaxp[1],
yaxp[2], (yaxp[2] - yaxp[1])/yaxp[3]), ...)
}
abline3 = function(xl, xlf, ...) {
xaxp <- ifelse((length(dev.list())>0|plot==T), list(par("xaxp")), list(c(0,1,5)))[[1]]
yaxp <- ifelse((length(dev.list())>0|plot==T), list(par("yaxp")), list(c(0,1,5)))[[1]]
segments(y0 = min(xl), x0 = seq(xaxp[1], xaxp[2], (xaxp[2] -
xaxp[1])/xaxp[3]), y1 = max(xl)/xlf, x1 = seq(xaxp[1],
xaxp[2], (xaxp[2] - xaxp[1])/xaxp[3]), ...)
}
if (plot!=F)
if (!horiz) {
if (grid != F)
abline2(xlim, ifelse(!is.null(legend.text), xlim.factor, 1), col = grid.col)
}
else {
if (grid != F)
abline3(ifelse((length(dev.list())>0|plot==T), list(par("usr")), list(c(0,1,0,1)))[[1]][3:4], 1, col = grid.col)
}
if (grid.mode == 0 & plot != F)
b = as.matrix(barplot(x2, border = border, xlab = NA, ylab = NA, names.arg = rep(NA, dim(x)[2]),