I'm all new to R, and the rgl packageand having searched all over all day for a solution...
I'm trying to use rgl's text3d function with unicode text. I have no problem plotting the same chars in 2D (using text()), but in 3D, instead of rendering the symbols it just writes out the UTF-8 char codes (unless they're ascii chars).
I'm reading in data from file where the column "vowel" contains the symbols to be plotted (e.g. "e i ə ɪ ɒ" etc.), and cols "F1", "F2" and "F3" contain the values to be plotted. The file is read in with read.delim with encoding="UTF-8"; and inspecting the data in the RGui shows the UTF-8 char codes for any non-ascii symbols.
Sample data (comma-delimited)
vowel,F1,F2,F3
i,424.1352452,1985.143387,2549.272611
e,515.0401373,1693.077496,2534.527142
ə,408.8233704,1589.12993,2567.448424
ɒ,490.6565129,1070.564989,2590.467597
ɪ,405.5223379,1665.733731,2261.069994
u,360.0803517,1798.355786,2354.845875
ɜ,541.6360766,1323.593646,2435.121753
ɑ,718.8871543,1139.013741,2820.694337
ɑ,629.1691413,1064.047107,2910.997552
ɪ,375.0097039,2091.996102,2648.991664
This is the code I've been testing with:
d <- read.delim("my.filename", header=TRUE, sep=",", encoding="UTF-8")
Plotting in 3D (plots things like "<\U+0252>" etc. (escaped here!) for all non-ASCII chars):
library(rgl)
cols <- c("F1", "F2", "F3");
plot3d(d[,cols], xlab="F1", ylab="F2", zlab="F3", type="n");
text3d(d[,cols], col=1, text=d$vowel);
Plotting in 2D (works):
cols <- c("F1", "F2");
plot(d[,cols], xlab="F1", ylab="F2", type="n");
text(d[,cols], col=1, labels=d$vowel);
Does it have something to do with OpenGL? I've installed freetype, hoping that might solve the issue, but I haven't managed to point R to it - so it issues warnings "par3d(useFreeType = TRUE) : FreeType not supported in this build" and "In par3d(useFreeType = TRUE) : font family "sans" not found, using "bitmap""...
Having spent several hours battling R for freetype, I was hoping someone here can tell me whether freetype will even solve the issue??! If yes, a hint as to what "Set the environment variable LIB_FREETYPE to give the full path to the install directory" (from rgl README) is trying to tell me to do would be hugely appreciated!
Thank you.
My sessionInfo:
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
LC_COLLATE=English_United Kingdom.1252
LC_CTYPE=English_United Kingdom.1252
LC_MONETARY=English_United Kingdom.1252
LC_NUMERIC=C
LC_TIME=English_United Kingdom.1252
attached base packages:
stats graphics grDevices utils datasets methods base
other attached packages:
rgl_0.93.975
You need to have FreeType installed.
Make sure you have FreeType and FreeType Open GL libraries installed, then reinstall rgl in R and then everything works.
See here also : http://www.smnd.sk/kotanyi/index.php?page=rgl
Related
I am having an issue with the emf() function from the devEMF package.
The code I am using -
library(devEMF)
emf(file = "trial.emf")
plot(1:10, seq(10, 100, 10), type = "l", xlab = "Time", ylab = "Distance")
#sample plot
dev.off()
This does not have the plot line but does have everything else (labels, axis ticks, title).
Am I missing some graphics package?
sessionInfo()
#R version 3.3.2 (2016-10-31)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows 7 x64 (build 7601) Service Pack 1
#locale:
#[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United #
#States.1252
#[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
#[5] LC_TIME=English_United States.1252
#attached base packages:
#[1] stats graphics grDevices utils datasets methods base
#other attached packages:
#[1] devEMF_3.6
#loaded via a namespace (and not attached):
#[1] tools_3.3.2
Some of the defaults in that function are not ideal if you are trying to view outside of LibreOffice.
try this:
library(devEMF)
emf(file = "trial.emf", emfPlus = FALSE)
plot(1:10, seq(10, 100, 10), type = "l", xlab = "Time", ylab = "Distance")
dev.off()
Make sure that emfPlus = FALSE. If you view the plot generated by emfPlus = TRUE in LibreOffice you will see it looks fine. Use emfPlus = FALSE when working with other viewers.
Most likely the program being used to view the resulting emf graphic does not support EMF+ records.
As alluded in JMT2080AD's answer, the devEMF library can produce either "EMF" or "EMF+" files. The newer EMF+ format (https://msdn.microsoft.com/en-us/library/cc230724.aspx) has been around since 2007 and is supported by more recent closed-source programs (i.e., Office 2010) but support is missing from old programs (e.g., older versions of Adobe Illustrator) and spotty in many open-source programs (e.g., LibreOffice, Inkscape).
For better or for worse, EMF+ records are embedded within EMF comment records, which means older programs will silently ignore them.
I find that the devEMF defaults produce acceptable files for Microsoft Office 2010 and LibreOffice >5.1.6. While LibreOffice support for EMF+ is incomplete, the unsupported features are turned off by default in the call to emf(). That said, JMT2080AD's suggestion of setting emfPlus = FALSE in the call to emf() is likely to make the files viewable by more programs (at the cost of losing features such as transparency and anti-aliasing).
(Disclosure: I am the author of the devEMF package)
While running:
reg_model = glmer(modeling1 ~ pTOT_VIOPT_CT + (1|STUDY_CODE_ALIAS),
data=data_CACZ, family=binomial)
I am getting the error:
Error in .fixupDimnames(.Object#Dimnames) :
could not find function "lengths"
Not sure what could be the possible reason.
FYI: I am putting below the sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rcpp_0.11.5 lme4_1.1-10 Matrix_1.2-3 car_2.0-21 MASS_7.3-29
loaded via a namespace (and not attached):
[1] grid_3.0.2 lattice_0.20-29 minqa_1.2.4 nlme_3.1-118 nloptr_1.0.4 nnet_7.3-7 splines_3.0.2 tools_3.0.2
(From the maintainer of 'Matrix'): This is indeed really strange,
but differently than #nicola suggests.
It is okay to update Recommended packages such as Matrix without updating R. That's indeed one feature of these.
Matrix 1.2-3 is indeed the current version of Matrix on CRAN, which is good.
However, since Matrix 1.2-2, there is the following code in Matrix/R/zzz.R :
if(getRversion() >= "3.2.0") {
......
} else {
......
lengths <- function (x, use.names = TRUE) vapply(x, length, 1L, USE.NAMES = use.names)
}
But that code only works correctly for you, when the Matrix package is built from the source with a correct version of R, i.e. in your case with a version of R before 3.2.0.
This (correctly built) happens for all platforms but Windows (the broken by choice one).
If you really don't want (or can't easily) upgrade your version of R,
you have two other options:
downgrade your version of Matrix to the one that comes with your version of R. As you probably have installed the new Matrix replacing the old one, you need to get that and replace the newer version of Matrix. HOWEVER, I guess you would also have to downgrade lme4, and in the end you suffer too much.
Safer and in principle correct: Install the 'Rtools' collection for Windows (you need the one that matches your version of R !)
including C compiler etc, until the following works correctly
install.packages("Matrix", type = "source")
The work to do this may well be worth it. You will be able to install other R packages from their source, which is very useful anyway
(I would not want to live without this possibility if I had to work with Windows).
When trying to run the sample code that is in the Minet paper / vignette I am experiencing a nunber of issues, e.g.
mim <- build.mim(discretize(syn.data), estimator)
Error in build.mim(dataset, estimator, disc, nbins):
could not find function "mutinformation"
I have also received other errors such as "unknown estimator" when trying methods prefixed with "mi." e.g. "mi.empirical."
I am running windows 8.1. Any help would be much appreciated!
EDIT 1: Additional Information
After playing around some more, the main problem I am having is when trying to use the discretize function like so:
> data(syn.data)
> disc <- "equalwidth"
> nbins <- sqrt(nrow(syn.data))
> ew.data <- discretize(syn.data, disc, nbins)
Error: could not find function "discretize"
This causes the same Error in all functions e.g. build.mim or minet which utilise discretize. I can run build.mim successfully without including discretize.
In addition, I am getting errors if I use minet (whilst excluding the discretize argument) with any of the mi.* estimation methods, e.g.
> res<-minet(syn.data,"mrnet","mi.empirical","equal width",10)
Error in build.mim(dataset, estimator, disc, nbins) :
could not find function "mutinformation"
However, running the same function with the "spearman" estimator works fine.
Edit 2: Output of sessionInfo()
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] minet_3.20.0
loaded via a namespace (and not attached):
[1] tools_3.1.0
discretize() is a function from the package infotheo that you can find in CRAN. There are some references to that package in the minet documentation. Maybe the authors of minet have moved some functionality to the infotheo package but since it is not a dependency it does not get installed automatically. It may be worth contacting the authors about this.
library(infotheo)
data(syn.data)
disc <- "equalwidth"
nbins <- sqrt(nrow(syn.data))
ew.data <- discretize(syn.data, disc, nbins)
The same applies for the multiinformation() function(). It is part of the infotheo package.
I am trying to put Vietnamese labeling in R graphs. I use RStudio and save my code using UTF-8 encoding. It handles the Vietnamese characters I put in the code well, I mean everything shows up in the code properly. However, in the graphs I make, while many characters display OK, several important ones do not show up properly, including
đ - which displays incorrectly as d
ư - which displays incorrectly as u
ơ - which displays incorrectly as o
ă - which displays incorrectly as a
Unfortunately this makes my graphs look unprofessional and untrustworthy.
I would really appreciate it if someone can help me figure this out.
Thanks much!
Trang
#DWin: I am on Windows 7, and here is my sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] MASS_7.3-17 MatchIt_2.4-20 tools_2.15.0
#krlmlr: Here's my code for a simple graph:
knorelative.count <- matrix(nrow=5,ncol=1)
knorelative.count[,1] <- c(1579,638,215,100,120)
par(mar=c(2,4,4,2))
barplot(prop.table(knorelative.count),beside=TRUE,
yaxt="n",ylim=c(0,.6),
legend=c("không ai biết",
"không biết nhiều hơn biết",
"nửa biết, nửa không biết",
"biết nhiều hơn không biết",
"tất cả đều biết"),
main="Người khác trong gia đình, họ hàng biết hay không")
axis(2,at=seq(0,.6,.1),labels=paste(100*seq(0,.6,.1),"%",sep=""),las=1)
When I run this, the đ in the main title and the two ơ's and the đ in the legend turn into d and o.
You are often safer specifying unicode characters by their hex codes:
plot(1:4,rep(1,4),pch=c("\u0111","\u01B0","\u01A1","\u0103"),cex=4)
For any Vietnamese folks out there who run into the same problem, here's an example for the fix using hex codes suggested by James:
print("trường")
[1] "truờng"
print("tr\u01B0ờng")
[1] "trường"
While I can type Vietnamese, in this example the word trường, into my R console ok, any kind of output (e.g. print, graph) fails to display the character ư. Replacing ư with the hex code fixes the output.
(Note: I used the function paste earlier, but then edited this based on James's suggestion to stick the hex code in the character string.)
I am so thankful to learn this way. I will do this for the report I am currently writing.
Trang
You save code in another file. Example: folder R/graph_display.R
After that run this code
eval(parse("R/graph_display.R", encoding = "UTF-8"))
I've tried to write reproducable example below. It is a mix of .Rmd and .r . Hopefully you can see why.
The problem I have is that non-english characters are treated differently depending on whether code is run directly in the console or when Knitted to HTML.
In the example below I create a small data.frame with characters ü and ö, write it to csv, then read it back in again.
If the writing and reading both take place inside or outside a chunk, then all is well.
But if the writing and reading take place in different places then a different encoding is used (I think). and characters get mixed up.
This means that when reading in data I need a different encoding when compiling an .Rmd file than when working directly in R.
As far as I can see the locale is always the same, so I don't understand what's going on.
Any ideas?
Write and read csv directly to create new datafile
df2 <- data.frame(Cäl1 = c(1,2), Col2 = c("ü","a"))
write.csv(df2, file="df2.csv")
read.csv("df2.csv")
Sys.getlocale(category = "LC_ALL")
Now try Knitting the whole document (just running the chunk behaves differently)
```{r read_inside}
read.csv("df2.csv")
Sys.getlocale(category = "LC_ALL")
```
this second chunk will work because the data.frame is created inside the chunk
```{r write_read_inside}
df2 <- data.frame(Cäl1 = c(1,2), Col2 = c("ü","a"))
write.csv(df2, file="df2.csv")
read.csv("df2.csv")
Sys.getlocale(category = "LC_ALL")
```
Session Info:
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.15.0
So the answer is to guarantee UTF8 encoding, e.g. write.csv(..., fileEncoding = 'UTF-8'). The root problem was actually that RStudio uses UTF8 by default, but R uses the native encoding of the OS by default. We can either ask R to use UTF8 in write.csv, or ask RStudio to use native encoding (options(encoding = 'native.enc')).