RStudio not showing output in Console when using a variable? - r

Currently learning RStudio but for some reason my Console isn't outputting my code? Not sure if there was a setting I may have toggled but it seems to only affect me when I have a variable in my code?
For example:
when working the ToothGrowth dataset
data("ToothGrowth")
View(ToothGrowth)
This executes and I can view the table of the data in a separate tab.
However, when I try to filter it
data("ToothGrowth")
View(ToothGrowth)
filtered_tg = filter(ToothGrowth, dose=0.5)
View(filtered_tg)
Nothing Returns, a formatted table doesn't open and an empty line is returned in the console window.
This is just one example, even when i try something as simple as
number = 10
number
I would expect, in return;
[1] 10
But console is empty.
Looking for solutions online, I've seen maybe i didn't close a bracket or parenthesis and to include CloseAllConnections() if there was a '+' showing in the console (which there isn't).
Working on rstudio cloud so is there a reset somewhere that I could possibly try?
Thanks for any and all help!

I changed the function as follows:
filtered_tg = filter(ToothGrowth, dose=="0.5")
View(filtered_tg)
After running these commands it was viewed as the table of the data in a separate tab 👇
Output

Related

Using GoogleVis in R inside Power BI

I am trying to replicate these:
https://radacad.com/interactive-map-using-r-and-power-bi-create-custom-visual-part-1
Is it possible to use R Plotly library in R Script Visual of Power BI?
The issue with Plotly is that for my dataset it is so slow even when I am compiling that in R. takes several minutes. So, I have decided to replace it with googleVis which is really fast (I am open any other interactive Gantt Chart in R).
Here is my code in R:
df <- data.frame(Values)
library("googleVis")
#df$Project.Name <- toString(df$Project.Name)
df$Processed_start_date_cut <- as.Date(df$Processed_start_date_cut)
df$Processed_End_date <- as.Date(df$Processed_End_date)
#df$Milestone <- toString(df$Milestone)
g <- gvisTimeline(data=df,
rowlabel="Project.Name",
barlabel="Milestones",
start="Processed_start_date_cut",
end="Processed_End_date",
options=list(timeline="{rowLabelStyle:{fontName:'Helvetica',
fontSize:10, color:'#603913'},
barLabelStyle:{fontName:'Garamond',
fontSize:12}}",
backgroundColor='#ffd',
height=350 ))
cat(g$html$chart, file="out.html")
I have tried it in R and it works great. In BI this works for the first time, but when I change any filters, nothing shows up in this newly developed pbivis item unless I go to another tab of my report and then come back to this tab which has this newly developed pbivis (this was the reason I thought it is not working at first, sorry).
See the screenshot
I have also noticed that if I maximize this item (pbivis), then the chart disappears (i.e. shows nothing).
I guess I need a kind of code for refreshing the visuals which possibly can come before df <- data.frame(Values), maybe something like F5 in IE.
Also tried this and did not work:
if (file.exists("out.html"))
#Delete file if it exists
file.remove("out.html")
As user3867743 suggested, the issue is related to
cat(g$html$chart, file="out.html")
After replacing it by
print(g, file="out.html")
It has started working fine.

R Need to restart RStudio to view and save in a file using dev.copy() and dev.off()

I am trying to create a plot and eventually save it as a file. But because I am making a lot of changes and want to test it out, I want to be able to view and save the plot at the same time. I have looked at this page to do what I want to do but in my system, it does not seem to be working as it is supposed to.
Here are my codes:
png('Save.png')
sample.df <- data.frame(group = c('A','B','A','C','B','A','A','C','B','C','C','C','B'),
X = c(2,11,3,4,1,6,3,7,5,9,10,2,8),
Y = c(3,8,5,2,7,9,3,6,6,1,3,4,10))
plot(Y ~ X, data = sample.df)
dev.copy(png, 'Save.png')
dev.off()
There are several issues (I am new to R so I might be missing something entirely):
(1) When I use png(), I cannot view the plot in RStudio so I used dev.copy() but it does not allow me to view my plot in R studio
(2) Even after I use dev.off(), I cannot view the saved file until I close the RStudio (says "Windows Photo Viewer can't open this picture because the picture is being edited in another program"). I need to restart every time so it is very inconvenient.
What am I doing wrong and how could I view and view saved file without restarting RStudio every time? Thank you in advance!
Addition
Based on Love Tätting's comments, when I run dev.list(), this is what I get.
> png('Save.png')
>
> sample.df <- data.frame(group = c('A','B','A','C','B','A','A','C','B','C','C','C','B'),
+ X = c(2,11,3,4,1,6,3,7,5,9,10,2,8),
+ Y = c(3,8,5,2,7,9,3,6,6,1,3,4,10))
>
> plot(Y ~ X, data = sample.df)
>
> dev.copy(png, 'Save.png')
png
3
> dev.off()
png
2
> dev.list()
png
2
> dev.off()
null device
1
> dev.list()
NULL
Why do I not get RStudioGD?
RStudio has its own device, "RStudioGD". You can see it with dev.list(), where it by default is the first and only one.
R's design for decoupling rendering and backend is by the abstraction of devices. Which ones you can use is platform and environment dependent. dev.list() shows the stack of current devices.
If I understand your problem correctly you want to display the graph first in RStudio, and then decide whether you want to save it or not. Depending on how often you save th image you could use the 'export' button in the plot pane in RStudio and save it manually.
Otherwise, your choice of trying to copy it would be the obvious one for me as well.
To my knowledge the device abstraction in R does not allow one to encapsulate the device as an object, so one for example could make it an argument to a function that does the actual plot. Since dev.set() takes an index as argument, passing the index as argument will be dependent on state of the stack of devices.
I have not come up with a clean solution to this myself and have sometimes retorted to bracketing the plot rendering code with a call to a certain device and saving it right after, and switching device depending on a global.
So, if you can, use RStudios export functionality, otherwise an abstraction would need to maintain the state of the global stack of devices and do extensive testing of its state as it is global and you cannot direct a plot call to a certain device, it simply plots to the current device (to my knowledge).
Edit after OP comment
It seems that it is somewhat different behaviour you are experiencing if you cannot watch the file after dev.off, but also need to quit RStudio. For some type of plot frameworks there is a need to call print on the graphical object to have it actually print to the file. Perhaps this is done by RStudio at shutdown as part of normal teardown procedures of open devices? In that ase the file should be empty if you forcibly look in its contents before quiting RStudio.
The other thing that sometimes work is to call dev.off twice. I don't know exactly why, but sometimes more devices get created than I have anticipated. After you have done dev.off, what does dev.list show?
Edit after OP's edit
I can see that you do, png(); dev.copy(); dev.off(). This will leave you with one more device opened than closed. You will still have the first graphics device that you started open as can be seen when you do the listing. You can simply remove dev.copy(). The image will be saved on dev.off() and should be able to open from the filesystem.
As to why you cannot see the RStudio graphics device, I am not entirely sure. It might be that other code is messing with your device stack. I would check in a clean session if it is there to make sure other code isn't tampering with the device stack. From RStudio forums and other SO questions there seem to have been plot pane related problems in RStudio that have resolved after updating RStudio to the latest. If that is a viable solution for you I would try that.
I've just added support for RStudio's RStudioGD device to the developer's version of R.devices package (I'm the author). This will allow you to do the following in RStudio:
library("R.devices")
sample.df <- data.frame(
group = c('A','B','A','C','B','A','A','C','B','C','C','C','B'),
X = c(2,11,3,4,1,6,3,7,5,9,10,2,8),
Y = c(3,8,5,2,7,9,3,6,6,1,3,4,10)
)
figs <- devEval(c("RStudioGD", "png"), name = "foo", {
plot(Y ~ X, data = sample.df)
})
You can specify any set of output target types, e.g. c("RStudioGD", "png", "pdf", "x11"). The devices that output to file will by default write the files in folder figures/ with filenames as <name>.<ext>, e.g. figures/foo.png in the above example.
The value of the call, figs, holds references to all figures produced, e.g. figs$png. You can open them directly from R using the operator !. For example:
> figs$png
[1] "figures/foo.png"
> !figs$png
[1] "figures/foo.png"
The latter call should show the PNG file using your system's PNG viewer.
Until I submit these updates to CRAN, you can install the developer's version (2.15.1.9000) as:
remotes::install_github("HenrikBengtsson/R.devices#develop")

Object created via read.csv disappears after script finishes

I am not a programmer and have less than a month of experience with R but have been writing simple scripts that read from external CSV files for the past week. The function below, which reads data from a CSV file, was originally more complex but I repeatedly shortened it during troubleshooting until I was left with this:
newfunction <- function(input1, input2) {
processingobject <- read.csv("processing-file.csv")
print(head(processingobject))
}
I can print both the head and the entire processingobject within the script without a problem, but after the script ends processingobject no longer exists. It never appears in the RStudio global environment pane. Shouldn't processingobject still exist after the script terminates?
The script runs without displaying any error or warning messages. I tried assigning processingobject to a second variable: processingobject2 <- processingobject but the second variable doesn't exist after the script ends either. I also tried clearing the global environment and restarting RStudio, but that did not work either. If at the prompt after the script I type processingobject I get the message "Error: object 'processingobject' not found". The CSV file itself is perfectly normal as far as I can tell.
Obviously, I must be doing something very stupid. Please help me. Thanks.
You need to use return in your function and reproducible examples are always a good idea. It makes it easier for people to help you out.
ncol<- 10
nrow<- 100
x <- matrix(runif(nrow*ncol),nrow,ncol)
write.csv(x,file="example_data.csv")
newfunction <- function(input1) {
processingobject <- read.csv("example_data.csv")
result <- apply(processingobject,2,function(x)x*input1) #doing something to csv with input
print(head(result))
return(result)
}
newcsv <-newfunction(3)

Cannot get verbose=FALSE working for "joinCountryData2Map"

I am using 'R Presentation' from R Studio to create a slide show for my project. I am using the below code and whatever I do I am not able to get rid of the output message from the code. I do not want the progress message to be included in my presentation slide.
I have the below portion of code in a different chunk , but that did not help me either. I cleared cache and tried all stuffs, but could not get rid of the progress message.
Any idea how to get rid of the output message ?
sPDF <- joinCountryData2Map(subset(world_all, year==year.list[i]),joinCode = "ISO3 ,nameJoinColumn = "country_code" , mapResolution = "coarse",verbose=FALSE)
it generates below output message , which I do not want to show in my presentation slide
154 codes from your data successfully matched countries in the map 0
codes from your data failed to match with a country code in the map 90
codes from the map weren't represented in your data
That did not work either.
Then I went to the source code of that function and found that a "cat" command is being used to print the messages. So, I muted the cat command output using the below method , and it worked !!
capture.output( 'the whole function' , file='NUL' )
Yes; verbose=BOOL controls whether or not the progress messages are printed, not the final message. I'd suggest experimenting with wrapping the call in a call to suppressMessages, and seeing what happens.

R scripting in SPSS Modeler 16: change default "rowCount=1000" for modelerData

When applying R transform Field operation node in SPSS Modeler, for every script, the system will automatically add the following code on the top of my own script to interface with the R Add-on:
while(ibmspsscfdata.HasMoreData()){
modelerDataModel <- ibmspsscfdatamodel.GetDataModel()
modelerData <- ibmspsscfdata.GetData(rowCount=1000,missing=NA,rDate="None",logicalFields=FALSE)
Please note "rowCount=1000". When I process a table with >1000 rows (which is very normal), errors occur.
Looking for a way to change the default setting or any way to help to process table >1000 rows!
I've tried to add this at the beggining of my code and it works just fine:
while(ibmspsscfdata.HasMoreData())
{
modelerData <-rbind(modelerData,ibmspsscfdata.GetData(rowCount=1000,missing=NA,rDate="None",logicalFields=FALSE))
}
Note that you will consume a lot of memory with "big data" and parameters of .GetData() function should be set accordingly to "Read Data Options" in node setting.

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