I am wondering if there is a function to clear the console in R and, in particular, RStudio I am looking for a function that I can type into the console, and not a keyboard shortcut.
Someone has already provided such a function in this StackExchange post from 2010. Unfortunately, this depends on the RCom package and will not run on Mac OS X.
cat("\014")
is the code to send CTRL+L to the console, and therefore will clear the screen.
Far better than just sending a whole lot of returns.
If you are using the default R console, the key combination Option + Command + L will clear the console.
You may define the following function
clc <- function() cat(rep("\n", 50))
which you can then call as clc().
shell("cls") if on Windows,
shell("clear") if on Linux or Mac.
(shell() passes a command (or any string) to the host terminal.)
cat("\f") may be easier to remember than cat("\014").
It works fine for me on Windows 10.
In Ubuntu-Gnome, simply pressing CTRL+L should clear the screen.
This also seems to also work well in Windows 10 and 7 and Mac OS X Sierra.
Here's a function:
clear <- function() cat(c("\033[2J","\033[0;0H"))
then you can simply call it, as you call any other R function, clear().
If you prefer to simply type clear (instead of having to type clear(), i.e. with the parentheses), then you can do
clear_fun <- function() cat(c("\033[2J","\033[0;0H"));
makeActiveBinding("clear", clear_fun, baseenv())
I developed an R package that will do this, borrowing from the suggestions above. The package is called called mise, as in "mise en place." You can install and run it using
install.packages("mise")
library(mise)
mise()
Note that mise() also deletes all variables and functions and closes all figures by default. To just clear the console, use mise(vars = FALSE, figs = FALSE).
In linux use system("clear") to clear the screen.
If you are using the default R console CTRL + L
RStudio - CTRL + L
cat("\014") . This will work. no worries
You can combine the following two commands
cat("\014");
cat(rep("\n", 50))
Another option for RStudio is rstudioapi::sendToConsole("\014"). This will work even if output is diverted.
sink("out.txt")
cat("\014") # Console not cleared
rstudioapi::sendToConsole("\014") # Console cleared
sink()
I know this question is very old, but I found myself visiting it many times looking for a totally different answer:
n = 20
for (i in 0:n) {
cat(100*i/n, "% \r")
flush.console()
Sys.sleep(0.01) #do something slow
}
flush.console() will kind of "clear the console in r and studio", maybe not in OP's terms but still.
This code will act like a progress bar in the console. For each iteration, the percentage is incremented and then erased on the next iteration.
Note that this won't work without \r or with an \n, for some reason.
Related
I'm having an issue where if I execute several lines of code at once and one of them has an error, the lines below don't get executed.
For example if I have:
table(data$AGE)
table(dataREGION)
table(date$SEXE)
I get the table for the first line, and then
Error in table(dataREGION) : object 'dataREGION' not found
>
And the last line does not execute.
Does anyone know why it does that and how to fix it?
(I work with R 4.2.2 and RStudio 2022.12.0+353 "Elsbeth Geranium" Release)
Thanks!
Have a nice day,
Cassandra
Fixed: In Global Options > Console, under "Execution" uncheck the "Discard pending console input on error"
It seems like you want to use try().
try(table(data$AGE), silent = F, outFile = T)
try(table(dataREGION)) # also works without any params
try(table(date$SEXE))
You can also use tryCatch() if you want more control but it doesn't seem necessary for your purpose.
__
As for why your dataREGION doesn't exectue:
Hazarding a guess it might be because you forgot the $ between data and REGION
I am currently learning Julia and have been practicing in the Jupyter notebook environment. However, the ProgressBar package (similar to TQDM in python) is updated every new line instead of updating on the same line (picture attached). Is there any way to fix this? Thanks.
UPDATE : Here is the full function that I wrote.
function spike_rate(raw_dat, width)
N = size(raw_dat)[1]
domain = collect(1:N);
spike_rat = zeros(N);
for i in ProgressBar(1:N)
dx = i .- domain;
window = gaussian.(dx, width);
spike_rat[i] = sum(window .* raw_dat) ./ width;
end
return spike_rat;
end
This seems to be a known issue with ProgressBars.jl, unfortunately. It's not clear what changed to make these progress bars not work properly anymore, but the maintainer's comment says that tqdm uses "a custom ipywidget" to make this work for the Python library, and that hasn't been implemented for the Julia package yet.
To expand on #Zitzero's mention of ] up, that calls Pkg.update() which also prints a progress bar - so the suggestion is to use the mechanism Pkg uses for it. Pkg has an internal module called MiniProgressBars which handles this output.
Edit: Tim Holy's ProgressMeter package seems well-maintained, and is a much better option than relying on an internal non-exported Pkg submodule with no docs. So I'd recommend ProgressMeter over the below.
The Readme mentions a caveat regarding printing additional information with the progress bar when in Jupyter, which likely applies to MiniProgressBar as well. So, using ProgressMeter, and separating the progress output vs other relevant output to different cells, seems like the best option.
(not recommended)
using Pkg.MiniProgressBars
bar = MiniProgressBar(; indent=2, header = "Progress", color = Base.info_color(),
percentage=false, always_reprint=true)
bar.max = 100
# start_progress(stdout, bar)
for i in 1:100
sleep(0.05) # replace this with your code
# print_progress_bottom(stdout)
bar.current = i
show_progress(stdout, bar)
end
# end_progress(stdout, bar)
This is based on how Pkg uses it, from this file. The commented out lines (with start_progress, print_progress_bottom, and end_progress) are in the original usage in Pkg, but it's not clear what they do and here they just seem to mess up the output - maybe I'm using them wrongly, or maybe Jupyter notebooks only support a subset of the ANSI codes that MiniProgressBars uses.
There is a way, the package module does that as far as I know when you do:
] up
Could you share a little of your code?
For example, where you define what is written to the console.
One guess is that
print("text and progressbar")
instead of
println("text and progressbar")
could help, because println() always creates a new line, while print() should just overwrite you current line.
I'm having trouble getting 'choice' to create output. When the graphical interface launches, I am selecting a partition with the space bar. This creates a black circle around the partition, indicating it has been selected. When I click 'return', nothing happens.
I checked my working directory to look for the output files, but they are not there. I used getwd() to ensure that I have the correct setwd(). No dice.
There was a similar question posted: Exporting result from kml package in R; however, the answer does not work for me.
Any suggestions? I am using R 3.1.0 GUI Mavericks build(6734) and XQuartz 2.7.6. Thanks for any help getting this working.
Here is my code:
setwd("/Users/eightfrench")
mydata <- read.csv("hcris_long3.csv")
cldHCRIS <- clusterLongData(traj=mydata)
kml(cldHCRIS,nbClusters=2:4,nbRedrawing=2,toPlot="both")
X11(type="Xlib")
choice(cldHCRIS, typeGraph= "bmp")
I had the same problem when using RStudio and i solved it just opening the x11 device with no specification. Like this:
setwd("/Users/eightfrench")
mydata <- read.csv("hcris_long3.csv")
cldHCRIS <- clusterLongData(traj=mydata)
kml(cldHCRIS,nbClusters=2:4,nbRedrawing=2,toPlot="both")
X11()
choice(cldHCRIS, typeGraph= "bmp")
Hope this also works for you.
The new version of kml (2.3) fix that, it provide a key to export data with linux as well (not "return" since getGraphicsEvent does not accept "return" using linux, so I have to map another key : 'm')
Christophe
UPDATE: Thanks to Joshua's comment I realized the problem wasn't being inside a function, but inside a script. So I've edited the question and also provided my own answer.
When I use plot.xts() interactively it pops up a graphics window. I just tried it from inside a function (I'm troubleshooting a unit test and wanted some visual help) but nothing appeared. Aha, says I, I know the trick, just use print.
But print(plot.xts(x)) still shows no chart and instead prints my xts object! I.e. it does exactly the same as print(x).
The script I use to run unit tests is:
#!/usr/bin/Rscript --slave
library('RUnit')
options(warn=2) #Turn warnings into errors
#By naming the files runit.*.R, and naming the functions test*(), we can use
# all the defaults to defineTestSuite().
#NOTE: they have a weird default random number generator, so changed here
# to match the R defaults instead.
test.suite=defineTestSuite('tests',dirs=file.path('tests'),
rngKind = "Mersenne-Twister", rngNormalKind = "Inversion")
test.result <- runTestSuite(test.suite)
printTextProtocol(test.result)
The script below does two things:
plot to a device file, as you would in headless setting such as a webserver,
plot a screen device, I use x11() but you could use win().
There is no limitation imposed by Rscript. And this has nothing to do with xts as you could just as easily plot an xts object.
#!/usr/bin/Rscript
set.seed(42)
x <- cumsum(rnorm(100))
png("/tmp/darren.png")
plot(x)
dev.off()
x11()
plot(x)
Sys.sleep(3) # could wait for key pressed or ...
You cannot use graphics (or input functions like readline) when using RScript. However an RScript is still just R, so when you want to add something interactive (e.g. for troubleshooting) start R, then type:
source('run_tests.R')
When run this way, a line like this shows the chart:
plot(x$High);cat("Press a key");readline()
When run directly from the commandline with ./run_tests.R that line gets quietly ignored.
I have written a function, which takes some time to run (due to a 1000+ loop on a huge dataset in combination with forecasting model testing).
To have any idea on the status, while the function is called, I use the message command inside the for-loop in the function. The problem is that all the messages are shown in the console after the function is finished, instead of showing immediately. So it doesn't help me :)
I tried to find a solution on Stackoverflow, but didn't found one. I looked for instance on the question "showing a status message in R". All answers and example codes in that topic still give me only text in the console after a function is processed instead of immediately.
How to solve this? Is there maybe a setting in R which prevents immediate printing of message text in the console?
note: examples I tried below, which give the same results as my function; showing text after processing the function.
example1 (Joshua Ulrich):
for(i in 1:10) {
Sys.sleep(0.2)
# Dirk says using cat() like this is naughty ;-)
#cat(i,"\r")
# So you can use message() like this, thanks to Sharpie's
# comment to use appendLF=FALSE.
message(i,"\r",appendLF=FALSE)
flush.console()
}
example2 (Tyler):
test.message <- function() {
for (i in 1:9){
cat(i)
Sys.sleep(1)
cat("\b")
}
}
edit: the first example does work ('flush console' was the problem)...but when I tested it, I commented out flush console for some reason :S
test.message <- function() {
for (i in 1:9){
cat(paste(as.character(i),'\n'))
flush.console()
Sys.sleep(1)
}
}
which is similar to the recommendation by fotNelton.
Edit: ttmaccer is most likely right. I've just tested on a Ubuntu server and the code works without flushing the console.
I seem to think this maybe a windows specific problem. On linux or running R in a cygwin shell the flush.console() may not be needed.
You may be interested in using one of the progress bar functions (winProgressBar, tkProgressBar, or txtProgressBar). The win version only works on windows, but the win and tk versions have the advantage that they do not clutter your output, but rather open another small window and display the progress there.
The progress through a loop can be shown with the progress bar, but other detailed information can be updated and shown with the label argument.