Using this works in R console:
plot(G)
but when typed into a cell in jupyter I get:
starting httpd help server ... done
and no graph.
So here is what I did.
Into Anaconda 2.7.11, I installed R essentials
conda install -c r r-essentials
started up jupyter
notebook jupyter
installed needed reqs, XML and googleVIS, by typing this into a cell
options(repos=structure(c(CRAN="https://cloud.r-project.org/")))
install.packages('googleVis')
install.packages('XML')
typed this code into a cell
suppressPackageStartupMessages(library(googleVis))
library(googleVis)
library(XML)
url <- "http://en.wikipedia.org/wiki/List_of_countries_by_credit_rating"
x <- readHTMLTable(readLines(url), which=3)
levels(x$Rating) <- substring(levels(x$Rating), 4,
nchar(levels(x$Rating)))
x$Ranking <- x$Rating
levels(x$Ranking) <- nlevels(x$Rating):1
x$Ranking <- as.character(x$Ranking)
x$Rating <- paste(x$Country, x$Rating, sep=": ")
G <- gvisGeoChart(x, "Country", "Ranking", hovervar="Rating",
options=list(gvis.editor="S&P",
projection="kavrayskiy-vii",
colorAxis="{colors:['#91BFDB', '#FC8D59']}"))
then
plot(G)
This code works fine when typed directly into an R console and makes a nice map. But something is causing jupyter to choke on starting a server. I guess since jupyter itself is web page running in a server there is some sort of problem with a web page starting a server?
I have the same issue. According to this demonstration, all you need in an R console is to additionally add this line after loading the library:
library(googleVis)
op <- options(gvis.plot.tag='chart')
The introduction of tag can also be found here in googleVis's documentation. After trying it in Jupyter all I got is a block of .json data and it cannot compile into an interactive graph.
Hope this help in anyway. I will probably try something like plotly, which does work on jupyter.
Related
I'm doing an R project on RStudio (RStudio 2021.09.1+372 "Ghost Orchid" Release for Windows), (R version 4.1.2).
I'm working on Windows 10 x64.
I want to create an Undirected Graph from a dataset:
library(gRbase)
library(gRim)
library(gRain)
data(BodyFat)
BodyFat <- BodyFat[-c(31,42,48,76,86,96,159,169,175,182,206),]
BodyFat$Age <- sqrt(BodyFat$Age)
BodyFat$Weight <- sqrt(BodyFat$Weight)
names(BodyFat)[names(BodyFat) == 'BodyFat'] <- 'BodyFatPerc'
gRbodyfat <- BodyFat[,2:15]
graph.MyGraph <- cmod(~.^., data = gRbodyfat)
AIC.MyGraph <- gRbase::stepwise(graph.MyGraph)
I'm still exploring RStudio and graphical models, so I run these lines from the console, one by one.
When I run the last line of code, R session aborts and I get the following pop-up message:
I've also tried the following lines of code (I changed the last line):
library(gRbase)
library(gRim)
library(gRain)
data(BodyFat)
BodyFat <- BodyFat[-c(31,42,48,76,86,96,159,169,175,182,206),]
BodyFat$Age <- sqrt(BodyFat$Age)
BodyFat$Weight <- sqrt(BodyFat$Weight)
names(BodyFat)[names(BodyFat) == 'BodyFat'] <- 'BodyFatPerc'
gRbodyfat <- BodyFat[,2:15]
graph.MyGraph <- cmod(~.^., data = gRbodyfat)
AIC.MyGraph <- stepwise(graph.MyGraph)
but I get the same problem. I tried three or four times running those lines of code, R aborted everytime.
My gRbase, gRim, gRain, Rgraphviz and RBGL libraries are in the home folder:
C:/Users/MyUser/Documents/R/win-library/4.1
Any advice?
EDIT:
I've tried uninstalling/reinstalling R, Rtools, RStudio, reinstalling libraries, updating them, I've tried launching RStudio as Administrator, I've tried changing computer.
The last thing I tried is this:
uninstalling R, Rtools and RStudio
deleting .RData and .Renviron files in the Documents folder
deleting all libraries
downloading R (latest version) from CRAN webpage and installing it as Administrator
downloading Rtools (latest version from webpage) and installing it as Administrator
creating the .Renviron file as described here
downloading RStudio (latest version from webpage) and installing it as Administrator
installing BiocManager as described here (when asked to update Matrix library I said NO, I thought it could be the problem)
installing gRbase, gRim, gRain libraries as described here (when asked to update fansi library I said NO because it said "There are binary versions available but the source versions are later", I thought it could be the problem)
Tried again the lines of code
Still got the problem, R session aborted again.
A friend of mine doing a similar project used gRbase::stepwise function, so I inserted his code in the console and the function worked. So I think the problem might be the object of the function, graph.MyGraph. The cmod function works fine, so maybe there's a problem with gRbodyfat, which is used to build graph.MyGraph.
If I run these lines (I tried changing the dataset, I used BodyFat instead of gRbodyfat):
graph.MyGraph <- cmod(~.^., data = BodyFat)
AIC.MyGraph <- gRbase::stepwise(graph.MyGraph)
I get the following error:
Error in dim(res) <- c(NSEL, NSET) :
dims [product 210] do not match the length of object [14]
Don't know what to do.
EDIT:
I've tried debugging gRbase::stepwise function and I get this:
The problem appears to be the iModel function.
EDIT:
I've discovered that if I use graph.MyGraph <- cmod(~.^1, data = gRbodyfat) the gRbase::stepwise function works fine.
I am trying to run below code where I want to read csv file and then write "sas7bdat". I have tried below code.
we already have prerequisite library installed on the system for R.
from rpy2 import robjects
robjects.r('''
library(haven)
data <- read_csv("filename.csv")
write_sas(data, "filename.sas7bdat")
''')
After running above code, there are no output get generated by this code and even I am not getting any error.
Expected output: trying to read .csv file and then that data i want to export in .sas7bdat format. (In Standard python 3.9.2 Editor)
python do not have such functionality/library hence I am trying this way to export data in .sas7bdat format.
Plz Suggest some change in above code or any other way in python through which I can create/export .sas7bdat format in python.
Thanks.
I had experience using R in Python Jupyter Notebooks, it is a bit complicated at beginning, but it did work. Here I just pasted my personal notes, hope these help:
# Major steps in installing "rpy2":
# Step 1: install R on Jupyter Notebook: conda install -c r r-essentials
# Step 2: install the "rpy2" Python package: pip install rpy2 (you may have to check the version)
# Step 3: create the environment variables: R_HOME, R_USER and R_LIBS_USER
# you can modify these environment variables in the system settings on your windows PC or use codes to set them every time)
# load the rpy2 module after installation
# Then you will be able to enable R cells within the Python Jupyter Notebook
# run this line in your Jupyter Notebook
%load_ext rpy2.ipython
My work was to do ggplot2 in Python, so I did:
# now use R to access this dataframe and plot it using ggplot2
# tell Jupyter Notebook that you are going to use R in this cell, and for the "test_data" generated using the Python
%%R -i test_data
library(ggplot2)
plot <- ggplot(test_data) +
geom_point(aes(x,y),size = 20)
plot
ggsave('test.png')
Please before you run the code make sure that haven and reader are installed in your R kernel.
from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage
string = """
write_sas <- function(file, col_names = TRUE, write_to){
data <- readr::read_csv(file, col_names = col_names)
haven::write_sas(data, path = write_to)
print(paste("Data is written to ", write_to))
}
"""
rwrap = SignatureTranslatedAnonymousPackage(string, "rwrap")
rwrap.write_sas( file = "https://robjhyndman.com/data/ausretail.csv",
col_names = False,
write_to = "~/Downloads/filename.sas7bdat")
You can use any of the R function arguments. same as I used col_names
I installed rmr2 in R with Cloudera Quickstart 5.7.0 as per Jeremy and Chandra. I tried a simple mapreduce program as per [Chandra]:
small.ints <- to.dfs(1:1000)
out <- mapreduce(input = small.ints, map = function(k, v) keyval(v, v^2))
df <- as.data.frame(from.dfs(out))
and the output of df is:
data frame with 0 columns and 0 rows
and from.dfs(out) shows:
$key
NULL
$val
NULL
Other examples from [Jeremy] and [Chandra] are also producing the same output although mapreduce shows _SUCCESS in the generated /tmp directory. Any suggestions?
to.dfs and from.dfs seem to be working fine. I tried:
small.ints <- to.dfs(1:1000)
out <- from.dfs(small.ints)
out
and this produces the numbers from 1 to 1000.
I figured this out now. I installed rmr2 from within RStudio and somehow the library was not available to the script even though the mapreduce function seems to run successfully. I was surprised that in one of the logs, I read that rmr2 was not found, but the script still gave me a _SUCCESS!
I eventually installed rmr2 fresh in R (using sudo R), with the required packages, reshape2 and caTools, and everything seems to work fine now.
I am trying to run an R script from the Windows command prompt (the reason is that later on I would like to run the script by using VBA).
After having set up the R environment variable (see the end of the post), the following lines of code saved in R_code.R work perfectly:
library('xlsx')
x <- cbind(rnorm(10),rnorm(10))
write.xlsx(x, 'C:/Temp/output.xlsx')
(in order to run the script and get the resulting xlsx output, I simply type the following command in the Windows command prompt: Rscript C:\Temp\R_code.R).
Now, given that this "toy example" is working as expected, I tried to move to my main goal, which is indeed very similar (to run a simple R script from the command line), but for some reason I cannot succeed.
Again I have to use a specific R package (-copula-, used to sample some correlated random variables) and export the R output into a csv file.
The following script (R_code2.R) works perfectly in R:
library('copula')
par_1 <- list(mean=0, sd=1)
par_2 <- list(mean=0, sd=1)
myCop.norm <- ellipCopula(family='normal', dim=2, dispstr='un', param=c(0.2))
myMvd <- mvdc(myCop.norm,margins=c('norm','norm'),paramMargins=list(par_1,par_2))
x <- rMvdc(10, myMvd)
write.table(x, 'C:/Temp/R_output.csv', row.names=FALSE, col.names=FALSE, sep=',')
Unfortunately, when I try to run the same script from the command prompt as before (Rscript C:\Temp\R_code2.R) I get the following error:
Error in FUN(c("norm", "norm"))[[1L]], ...) :
cannot find the function "existsFunction"
Calls: mvdc -> mvdcCheckM -> mvd.has.marF -> vapply -> FUN
Do you have any idea idea on how to proceed to fix the problem?
Any help is highly appreciated, S.
Setting up the R environment variable (Windows)
For those of you that want to replicate the code, in order to set up the environment variable you have to:
Right click on Computer -> Properties -> Advanced System Settings -> Environment variables
Double click on 'PATH' and add ; followed by the path to your Rscript.exe folder. In my case it is ;C:\Program Files\R\R-3.1.1\bin\x64.
This is a tricky one that has bitten me before. According to the documentation (?Rscript),
Rscript omits the methods package as it takes about 60% of the startup time.
So your better solution IMHO is to add library(methods) near the top of your script.
For those interested, I solved the problem by simply typing the following in the command prompt:
R CMD BATCH C:\Temp\R_code2.R
It is still not clear to me why the previous command does not work. Anyway, once again searching into the R documentation (see here) proves to be an excellent choice!
When I compute an ROC plot with the package pROC, I get the following error in RStudio v. 99.9.9:
## Loading required package: tcltk
## Warning: couldn't connect to display ":0"
## Error: [tcl] invalid command name "toplevel".
I thought this was an issue in my OS (Debian with r-base 3.1 installed from APT depending on tcl/tk lib version 8.5), but when evaluating the same code through the terminal, I get the plot rendered without the same error.
Here is a simple example following some pROC example code that will generate the error when knitted in RStudio, but works in vanilla R:
```{r markdown.test}
library(pROC)
features <- runif(25)
labels <- as.factor(runif(25) < 0.75)
lda.model <- lda(as.matrix(features),labels)
lda.pred <- predict(lda.model,as.matrix(features))
lda.roc <- plot.roc(lda.pred$posterior[,1],
c(labels),
ci=TRUE, of="se", #specificities = seq(0,100,5),
ci.type="shape",
ci.col="#1c61b6AA")
```
The error occurs when the confidence interval parameters are added to the call.
Is there something missing from my RStudio install/config, or is this a bug?
Blast from the past! I see that same error today on an instance of RStudio installed in the IBM computing environment called CP4D. Did you ever find an answer?
I think the way to fix on your Macintosh is to install Quartz and let it serve as the X11 server to display output from programs like tcltk or maybe even hist() or quartz() devices. (my team wrote install instructions https://pj.freefaculty.org/guides/crmda_guides/47.mac_R_setup).
I'm not sure what I'll do on the CP4D thing, since it is running inside a Web browser.