I teach a lab and I have my students write their answers in .Rmd files. For grading, I download and render them as pdfs in a batch. I use the following script to render everything and save in a file.
library(rmarkdown)
# Handy functions for concatenating strings because I want to do it like a Python
# programmer damnit!
`%s%` <- function(x,y) {paste(x,y)}
`%s0%` <- function(x,y) {paste0(x,y)}
# You should set the working directory to the one where the assignments are
# located. Also, make sure ONLY .rmd files are there; anything else may cause
# a problem.
subs <- list.files(getwd()) # Get list of files in working directory
errorfiles <- c() # A vector for names of files that produced errors
for (f in subs) {
print(f)
tryCatch({
# Try to turn the document into a PDF file and save in a pdfs subdirectory
# (you don't need to make the subdirectory; it will be created automatically
# if it does not exist).
render(f, pdf_document(), output_dir = getwd() %s0% "/pdfs")
},
# If an error happens, complain, then save the name in errorfiles
error = function(c) {
warning("File" %s% "did not render!")
warning(c)
errorfiles <- c(errorfiles, f)
})
}
This last assignment I forgot to set error=TRUE in the chunks, so documents will fail to compile if errors are found and I will have to go hunt those errors down and fix them. I tried to modify this code so that I set the parameter error=TRUE as default outside the document. Unfortunately, I've been working at this for hours and have found no way to do so.
How can I change this code so I can change this parameter outside the documents? (Bear in mind that I don't own the computer so I cannot install anything, but the packages knitr and rmarkdown are installed.)
Related
I am trying to create objects from all files in working directory with name of the original file. I tried to go the following way, but couldn't solve appearing problems.
# - SETTING WD
getwd()
setwd("PATH TO THE FILE")
library(readxl)
# - CREATING OBJECTS
file_objects <- list.files()
xlsx_objects <- unlist(grep(".xlsx",file_objects,value = T))
for (i in xlsx_objects) {
xlsx_objects[i] <- read_xlsx(xlsx_objects[i], header = T)
}
I tried to paste [i]item from "xlsx_objects" with path to WD but it only created a list of files names from docs in WD.
I also find information, that read.csv can read only one file at the time, but I guess that it should be the case with for loop, right? It is reading only one file at the time.
Using lapply (as described in this forum) I was able to get the data in the environment, but argument header didn't work, I lost names of my docs in that object which does not have desired structure. I am though looking for having these files in separated objects without calling every document exclusively.
IIUC, you could do something like:
files = list.files("PATH TO THE FILE", full.names = T, pattern = 'xlsx')
list_files = map(files, readxl::read_excel)
(You can't use read.csv to read excel files)
Also I recommend reading about R Projects so you don't have to use setwd() ever again, which makes your code harder to reproduce down the pipeline
I have alot of different scripts in R that sources one another with source(). Im looking for a way to create an overview diagram, that links each script visually, so i can easily see the "source hierarchy" of my code.
The result could look something like:
I hope there is a solution, that doesnt require a software license.
Hope it makes sence! :)
I can suggest you use Knime. it has the kind of diagram you are looking for. It has some scripts already wrote to clean, visualize data and write output and has integration with R and Python.
https://docs.knime.com/?category=integrations&release=2019-12
https://www.knime.com/
Good luck.
For purposes of example change directory to an empty directory and run the code in the Note at the end to create some sample .R files.
In the first two lines of the code below we set the files variable to be a character vector containing the paths to the R files of interest. We also set st to the path to the main source file. Here it is a.R but it can be changed appropriately.
The code first inserts the line contained in variable insert at the beginning of each such file.
Then it instruments source using the trace command shown so that each time source is run a log record is produced. We then source the top level R file.
Finally we read in the log and use the igraph package to produce a tree of source files. (Any other package that can produce suitable graphics could be used instead.)
# change the next two lines of code appropriately.
# Settings shown are for the files generated in the Note at the end
# assuming they are in the current directory and no other R files are.
files <- Sys.glob("*.R")
st <- "a.R"
# inserts indicated line at top of each file unless already inserted
insert <- "this.file <- normalizePath(sys.frames()[[1]]$ofile)"
for(f in files)
inp <- readLines(f)
ok <- !any(grepl(insert, inp, fixed = TRUE)) # TRUE if insert not in f
if (ok) writeLines(c(insert, input), f)
}
# instrument source and run to produce log file
if (file.exists("log")) file.remove("log")
this.file <- "root"
trace(source, quote(cat("parent:", basename(this.file),
"file:", file, "\n", file = "log", append = TRUE)))
source(st) # assuming a.R is the top level program
untrace(source)
# read log and display graph
DF <- read.table("log")[c(2, 4)]
library(igraph)
g <- graph.data.frame(DF)
plot(g, layout = layout_as_tree(g))
For example, if we have the files generated in the Note at the end then the code above generates this diagram:
Note
cat('
source("b.R")
source("c.R")
', file = "a.R")
cat("\n", file = "b.R")
cat("\n", file = "C.R")
I have a shiny app that allows the user to download an HTML file (knitted from a .Rmd file) that includes the code used to run the analysis based on all the user inputs. I am trying to write the base .Rmd file that gets altered when user inputs vary. I am having trouble including user input variables (e.g. input$button1) into R code chunks. Say the user input for input$button1 = "text1".
```{r}
results <- someFun(input$button1)
```
And I'd like to have it knitted like this:
```{r}
results <- someFun('text1')
```
Every time I download the knitted HTML though, I get input$button1 getting written to file. I would also like to be able to produce an .Rmd file that is formatted with this substitution. It seems like knit_expand() might be the key, but I can't seem to relate available examples to my specific problem. Is the proper way to knit_expand() the whole .Rmd file and specify explicitly all the parameters you want subbed in, or is there a more elegant way within the .Rmd file itself? I would prefer a method similar to this, except that instead of using the asis engine, I could use the r one. Any help would be greatly appreciated. Thanks!
Got it. Solution below. Thanks to Yihui for the guidance. The trick was to knit_expand() the whole .Rmd file, then writeLines() to a new one, then render. With hindsight, the whole process makes sense. With hindsight.
For the example, p1 is a character param 'ice cream' and p2 is an integer param 10. There is a user-defined param in ui.R called input$mdType that is used to decide on the format provided for download.
Rmd file:
Some other text.
```{r}
results <- someFun("{{p1}}", {{p2}})
```
in the downloadHandler() within server.R:
content = function(file) {
src <- normalizePath('userReport.Rmd')
# temporarily switch to the temp dir, in case you do not have write
# permission to the current working directory
owd <- setwd(tempdir())
on.exit(setwd(owd))
file.copy(src, 'userReport.Rmd')
exp <- knit_expand('userReport.Rmd', p1=input$p1, p2=input$p2)
writeLines(exp, 'userReport2.Rmd')
out <- rmarkdown::render('userReport2.Rmd', switch(input$mdType,
PDF = pdf_document(), HTML = html_document(), Word = word_document()))
}
file.rename(out, file)
}
Resulting userReport2.Rmd before rendering:
```{r}
results <- someFun("ice cream", 10)
```
I have a file that I open using wdGet(filename="exOut.doc",visible=FALSE). This file already has images in it that I've inserted using html and cat(img, file=outputDoc, sep="\n", append=TRUE).
I need to insert a table at the end of the document, but wdTable(format(head(testTable))) places the table at the very top of the word document. How can I fix this?
Also, second problem: I have a lot of tables I need to insert into my document and hence make use of a loop. Below is sample code that demonstrates my problem. Here's the really weird part for me: when I step through the code and run each line after another, it produces no error and I have an output document. If I run everything at once I get a 'cannot open the connection error'. I don't understand how this can be. How is it possible that running each line one at a time produces a different result than running all of that exact same code all at once?
rm(list=ls())
library(R2wd)
library(png)
outputForNow<-"C:\\Users\\dirkh_000\\Downloads\\"
outputDoc<-paste(outputForNow,"exOut.doc",sep="")
setwd(outputForNow)
# Some example plots
for(i in 1:3)
{
dir.create(file.path(paste("folder",i,sep="")))
setwd(paste("folder",i,sep="")) # Note that images are all in different folders
png(paste0("ex", i, ".png"))
plot(1:5)
title(paste("plot", i))
dev.off()
setwd(outputForNow)
}
setwd(outputForNow)
# Start empty word doc
cat("<body>", file="exOut.doc", sep="\n")
# Retrieve a list of all folders
folders<-dir()[file.info(dir())$isdir]
folders<-folders[!is.na(folders)]
# Cycle through all folders in working directory
for(folder in folders){
setwd(paste(outputForNow,folder,sep=""))
# select all png files in working directory
for(i in list.files(pattern="*.png"))
{
temp<-paste0('<img src=','\"',gsub("[\\]","/",folder),"/", i, '\">')
cat(temp, file=outputDoc, sep="\n", append=TRUE)
setwd(paste(outputForNow,folder,sep=""))
}
setwd(outputForNow)
cat("</body>", file="exOut.doc", sep="\n", append=TRUE)
testTable<-as.data.frame(cbind(1,2,3))
wdGet(filename="exOut.doc",visible=FALSE)
wdTable(format(head(testTable))) ## This produces a table at the top and not the bottom of the document
wdSave(outputDoc)
wdQuit() # NOTE that this means that the document is closed and opened over and over again in the loop otherwise cat() will throw an error
}
The above code produces:
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
Can anyone tell me why this occurs and how to fix it? Please and thank you. Please do recommend a completely different approach if you know I'm going about this the wrong way, but please also explain what it is that I'm doing wrong.
To start the DescTools package and a Word document, use something like this (obviously, modified for your path structure):
library(DescTools)
library(RDCOMClient)
report <- GetNewWrd(template = "C:/Users/Rees/Documents/R/win-library/3.0/R2DOCX/templates/TEMPLATE_03.docx")
ADDED BASED ON COMMENT
Create a template for your report in Word. Perhaps you call it TEMPLATE.docx. Save it in your Document director (or whatever directory you keep Word documents in. Then
report <- GetNewWrd(template = " "C:/Users/dirkh_000/Documents/TEMPLATE.docx")
Thereafter, each time you create a plot, add this line:
WrdPlot(wrd = report)
The plot is inserted in the TEMPLATE.docx Word document in the specified directory.
The same for WrdTable(wrd = report)
I have a program in R. Sometimes when I save history, they do not write into my history file. I lost some histories a few times and this really drive me crazy.
Any recommendation on how to avoid this?
First check your working directory (getwd()). savehistory() saves the history in the current working directory. And to be honest, you better specify the filename, as the default is .History. Say :
savehistory('C:/MyWorkingDir/MySession.RHistory')
which allows you to :
loadhistory('C:/MyWorkingDir/MySession.RHistory')
So the history is not lost, it's just in a place and under a name you weren't aware of. See also ?history.
To clarify : the history is no more than a text file containing all commands of that current session. So it's a nice log of what you've done, but I almost never use it. I construct my "analysis log" myself by using scripts, as hinted in another answer.
#Stedy has provided a workable solution to your immediate question. I would encourage you to learn how to use .R files and a proper text editor, or use an integrated development environment (see this SO page for suggestions). You can then source() in your .R file so that you can consistently replicate your analysis.
For even better replicability, invest the time into learning Sweave. You'll be glad you did.
Check the Rstudio_Desktop/history_database file - it stores every command for any working directory.
See here for more details How to save the whole sequence of commands from a specific day to a file?
Logging your console on a regular basis to **dated* files is handy. The package TeachingDemos has a great function for logging your console session, but it's written as a singleton, which is problematic for automatic logging, since you wouldn't be able to use that function to create teaching demo's if you use it for logging. I re-used that function using a bit of meta-programming to make a copy of that functionality that I include in the .First function in my local .Rprofile, as follows:
.Logger <- (function(){
# copy local versions of the txtStart,
locStart <- TeachingDemos::txtStart
locStop <- TeachingDemos::txtStop
locR2txt <- TeachingDemos:::R2txt
# creat a local environment and link it to each function
.e. <- new.env()
.e.$R2txt.vars <- new.env()
environment(locStart) <- .e.
environment(locStop) <- .e.
environment(locR2txt) <- .e.
# reference the local functions in the calls to `addTaskCallback`
# and `removeTaskCallback`
body(locStart)[[length(body(locStart))-1]] <-
substitute(addTaskCallback(locR2txt, name='locR2txt'))
body(locStop)[[2]] <-
substitute(removeTaskCallback('locR2txt'))
list(start=function(logDir){
op <- options()
locStart(file.path(logDir,format(Sys.time(), "%Y_%m_%d_%H_%M_%S.txt")),
results=FALSE)
options(op)
}, stop = function(){
op <- options()
locStop()
options(op)
})
})()
.First <- function(){
if( interactive() ){
# JUST FOR FUN
cat("\nWelcome",Sys.info()['login'],"at", date(), "\n")
if('fortunes' %in% utils::installed.packages()[,1] )
print(fortunes::fortune())
# CONSTANTS
TIME <- Sys.time()
logDir <- "~/temp/Rconsole.logfiles"
# CREATE THE TEMP DIRECORY IF IT DOES NOT ALREADY EXIST
dir.create(logDir, showWarnings = FALSE)
# DELETE FILES OLDER THAN A WEEK
for(fname in list.files(logDir))
if(difftime(TIME,
file.info(file.path(logDir,fname))$mtime,
units="days") > 7 )
file.remove(file.path(logDir,fname))
# sink() A COPY OF THE TERMINAL OUTPUT TO A DATED LOG FILE
if('TeachingDemos' %in% utils::installed.packages()[,1] )
.Logger$start(logDir)
else
cat('install package `TeachingDemos` to enable console logging')
}
}
.Last <- function(){
.Logger$stop()
}
This causes a copy of the terminal contents to be copied to a dated log file. The nice thing about having dated files is that if you use multiple R sessions the log files won't conflict, unless you start multiple interactive sessions in the same second).