I am doing some analysis in Rstudio and at the moment - as I am refreshing my knowledge of R after a few decades away from S - this involves writing lots of one-liner statements which operate on test datasets, and then inspecting/testing the output, then finally scaling it up when I've checked all the little bits work.
So my history is full of syntax errors and similar. But I am making progress every time I work, and each time I work there are statements that worked, that I want to save, in order to document the bits of the session that are worth saving. Is there any established way of extracting these from my history for re-use, in RStudio? Should I just scroll through after each session and copy and paste them into a textfile with a word processor? Or is there something more clever than that that I can do, staying within RStudio?
The easiest way to see your history, is to hit Ctrl-4 and that will bring up the history window. You can copy this to source and then edit it, or where ever. However, for what you are doing it is probably better to edit directly into a source window.
The setup I use is to have a script window open, and use ctrl-enter to run the current line.
To make this easier go into Tools>Options>Code Editing and ensure that "focus console after executing from source" is unchecked and your cursor will stay in the script after the line is executed.
You can now type your lines and edit them until they do what you want, then move on to the next when it works. Once you get to the end you have built up your script already. Also since your "history" is just their in front of you, it is much easier to skip back to older lines and rerun or modify them. If you want to run a block of code, simply highlight the block and hit ctrl-enter.
In the history panel in RStudio (top right panel), you can click "send to source" and it will copy the line you have selected over to whatever .R file you have open in the top left panel.
Related
I'm sharing a small but annoying issue that sometimes pops up when I'm using shortcuts to insert operators while working on a markdown file in R : the operator either does not get written, or even worse gets written on another file.
So let's say I am working on the file "report.rmd", and I want to insert the pipe operator using Ctrl+Maj+M, or the assignment operator using "Alt+-", and I have the file "test.R" opened. Well, I therefore type the aforementioned shortcuts and...nothing happens on my markdown file. But some nice operators that had nothing to do there get written on my test.R file.
The only way I found to solve this problem is to close and reopen RStudio (restarting unfortunately doesn't solve the issue).
While this is quite a minor problem, it's incredibly annoying. Did it ever happen to anyone of you, and if so do you know where it comes from and how to solve it?
Edit:
Although I am still running into this issue (without being able to reproduce it consistently) I came into a somewhat lighter solution. Instead of restarting R, simply closing all tabs (closing just the problematic one doesn't work) solves the problem. I hope this helps narrowing down the possible origins of the problem.
Short Answer
re-define the key combo to Ctrl+Shift+ \ , assuming this does not create a conflict
Background
I've had a similar problem for a while, too. In my case, the shortcut never works. I can not find the source. I even found a conflict with Ctrl+Shift+M assigned to 2 Editor functions.
Image:Screen Capture 2 conflicting hotkey assignments
However, a simple key reassignment of the one that is not the pipe operator ("Expand to Matching")
Image:screen capture showing the hotkey conflict solveddidn't solve the issue in my case.
Solution
Here's what did the job for me
I managed to assign a different combo (that hasn't been assigned yet) and that is comfortable enough in the sense of its location on the keyboard
go to Tools → Modify Keyboard Shortcuts...
In the filter box, write "Pipe"
Direct the cursor to the text box showing the current shortcut, and press the new combo (e.g. Ctrl+Shift+ \ ), then Enter.
Remember to hit Apply
Make sure the new Combo isn't a duplicate of another command, by going back to step 1 and sorting the list by Shortcut, then scrolling down to find your new one. if there is an ovelap, consider changing one of them.
When closing R Studio at the end of a R session, I am asked via a dialog box: "Save workspace image to [working directory] ?"
What does that mean? If I choose to save the workspace image, where is it saved? I always choose not to save the workspace image, are there any disadvantages to save it?
I looked at stackoverflow but did not find posts explaining what does the question mean? I only find a question about how to disable the prompt (with no simple answers...): How to disable "Save workspace image?" prompt in R?
What does that mean?
It means that R saves a list of objects in your global environment (i.e. where your normal work happens) into a file. When R next loads, this list is by default restored (at least partially — there are cases where it won’t work).
A consequence is that restarting R does not give you a clean slate. Instead, your workspace is cluttered with existing stuff, which is generally not what you want. People then resort to all kinds of hacks to try to clean their workspace. But none of these hacks are reliable, and none are necessary if you simply don’t save/restore your workspace.
If I choose to save the workspace image, where is it saved?
R creates a (hidden) file called .RData in your current working directory.
I always choose not to save the workspace image, are there any disadvantages to save it?
The advantage is that, under some circumstances, you avoid recomputing results when you continue your work later. However, there are other, better ways of achieving this. On the flip side, starting R without a clean slate has many disadvantages: Any new analysis you now start won’t be in a clean room, and it won’t be reproducible when executed again.
So you are doing the right thing by not saving the workspace! It’s one of the rules of creating reproducible R code. For more information, I recommend Jenny Bryan’s article on using R with a Project-oriented workflow
But having to manually reject saving the workspace every time is annoying and error-prone. You can disable the dialog box in the RStudio options.
The workspace will include any of your saved objects e.g. dataframes, matrices, functions etc.
Saving it into your working directory will allow you to load this back in next time you open up RStudio so you can continue exactly where you left off. No real disadvantage if you can recreate everything from your script next time and if your script doesn't take a long time to run.
The only thing I have to add here is that you should consider seriously that some people may be working on ongoing projects, i.e. things that aren't accomplished in one day and thus must save their workspace image so as to not start from the beginning again.
I think, best practice is: its ok to save your workspace, but your code only really works if you can clear your entire workspace and then rerun it completely with no errors!
I would like to access the history of what have been typed in the source panel in RStudio.
I'm interested in the way we learn and type code. Three things I would like to analyse are: i) the way a single person type code, ii) how different persons type code, iii) the way a beginner improve typing.
Grabbing the history of commands is quite satisfying as first attempt in this way but I would like to reach a finer granularity and thus access the successive changes, within a single line in a way.
So, to be clear, I'm neither looking for the history of commands or for a diff between different versions of and .R file.
What I would like to access is really the successive alterations to the source panel that are visible when you recursively press Ctrl+Z. I do not know if there is a more accurate word for what I describe, but again what I'm interested in is how bits of code are added/moved/deleted/corrected/improved in the source panel but not necessary passed to the Console and thus absent from the history of command.
This must be somewhere/somehow saved by RStudio as it is accessible by the later. This may be saved in a quite hidden/private/memory/process/... way and I have a very vague idea of how a GUI works. I do not know it if would be easily accessible, then programmaticaly analyzed, typically if we could save a file from it. Timestamps would be the cherry on top but I would be happy without.
Do you have idea how to access this history?
RStudio's source panel is essentially a view to an Ace Editor. As such you'd need to access the editor session's editSession and use getDocument or getWordRange along with the undo of the editSession's undoManager instance.
I don't think you'll be doing that from within RStudio without hacking on the RStudio code unless the RStudio Addin api is made to pass-thru editor events in the future.
It might be easier to write a session recorder as changes are made rather than try to mess with the undo history. I imagine you could write an Addin that calls a javascript to communicate over the existing RStudio port using the Ace Editor's events (ie. onChange).
As #GegznaV said, RStudio saves code history to a ".RHistory" file. It's in the "Documents" folder on my computer. It's probably the same folder if you're using Windows. If you do not know the location, you can find the file by searching.
It also allows saving RStudio history to a file manually. There is a "Save" button in the History panel. So you can also get a timestamp. You can ask different users to save their code history after they have finished writing code. It may be indirectly useful to your research.
Say I enter the following commands into the console in Rstudio
x=seq(0,1e11, by=.01)
plot(x,sin(x))
Clearly this is a very silly thing to do. But my question is how do you terminate this process? I couldn't find this answered anywhere.
Attempted solutions: pressing ctrl+q, pressing esc, going to session->interupt R, going to session->terminate R. Nothing seems to work. This seems to be specific to plotting, for example if you run a stupidly large loop, most of the above options seem to work as expected.
Ideally I'd like a solution that doesn't lose the R script I have been working on in the console (as I haven't saved it in awhile).
Re-posting my comment as an answer since it seems to have solved your problem.
Save early, save often, cry less.
Try clicking the little red
stop icon above the console panel (unlikely to work if you've done
all that you've done already).
Try copy/pasting the script out to
a text editor.
Try killing just the rsession process through your
OS (might leave RStudio open). The good news is that RStudio is
often pretty smart about backing up working copies of scripts, so
you might find it's still there even if you have to kill the whole
program.
Entering dev.null() in the console will kill any plots and I find it's less likely to crash RStudio than some of the options given by Ari B. Friedman.
That said, save early save often is always sound advice.
If I type a line of R code at the cursor and press 'Enter' I can immediately retrieve that code by pressing the up-arrow key once. However, if I am typing a line of code and accidentally press the down-arrow key once then that line of code disappears and I cannot retrieve it. This is a minor, but ever-present annoyance, most frustrating when typing data into a vector.
Is there a way to retrieve a line of code after accidentally pressing the down-arrow key?
I am using a Windows machine and the R GUI found on my desktop immediately after installation... ...I think one of the questions during installation is whether I want a short-cut on my desktop, and I select 'yes'.
this is completely dependent on the GUI. I believe (but am not certain) that RStudio, for example, preserves what you have typed.
While not a direct solution, what might be helpful is to use edit in an external window. I dont use windows, but I suspect if you hit ctrl+n you will get an editor in which you can then use F5 or ctrl+R to execute that specific line.
Personally, I use Sublime Text 2, and cmd+enter gets my code executed at the console
I found that if I open R and click File then New Script in the R menu an editor will open. I can type a line of R code in that editor. Then I can highlight that line of code and press Ctrl+R, as mentioned in Ricardo Saporta's answer and djhurio's comment. By pressing Ctrl+R that line of R code will execute. The line of R code remains visible in the editor and seems safe from being lost even if I accidentally hit the down-arrow key.
Hopefully this builds on Ricardo Saporta's answer enough to warrant being posted as another answer, although I would not have figured this out without Ricardo's and djhurio's help.
P.S.
In retrospect, I see now this is what Ricardo meant in his second comment beneath his answer.