I need to create word cloud which include composed words. In this link Making a wordcloud, but with combined words?
I find the response where I should use quanteda library. I installed it but when I start to adapt the code posed in the above link here:
# detect the collocations
colls <- collocations(docs, n = 200, size = 2)
The program returns this error:
Error in collocations(docs, n = 1500, size = 2) : could not find
function "collocations"
It's really weird because according to https://www.rdocumentation.org/packages/quanteda/versions/0.9.6-9/topics/collocations
the docs should be a Corpus object which is the case :
> class(docs)
[1] "SimpleCorpus" "Corpus"
what do you think?
thank you for your suggestions !
Have u library() your package?
If u do not, try
library("quanteda")
textstat_collocations is the only function of that package similar to that you are looking for:
colls <- textstat_collocations(docs, n = 200, size = 2)
I think they just changed it's name. As you can see in the documentation:
https://cran.r-project.org/web/packages/quanteda/quanteda.pdf
There is only a textstat_collocations function.
When I added the fully qualified name from the documentation
myVar <- quanteda.textstats::textstat_collocations(.....)
RStudio installed the quanteda.textstats library and now is working.
Related
I want to create a CytoTree CYT object in R to analyse my .FCS files. When I am using the Quick start code in the package description, I will always get an error when running the createCYT() function that says:
Error in createCYT(raw.data = fcs.data, normalization.method = "log") :
2022-09-26 15:46:26 meta.data must be a data.frame
As the function should not rely on any meta data and that object is optional, I do not know how to solve the error.
Here is the description:
https://ytdai.github.io/CytoTree/quick-start.html#quick-start-code
I thank you very much in advance for your help!
BR
I have encountered same problem previously.
In the end it worked only when the data.frame was added (yes, even though it should not depend on it).
Here is how:
meta.data <- data.frame(cell = rownames(fcs.data), stage = gsub(".fcs.+", "", rownames(fcs.data)))
meta.data$stage <- factor(as.character(meta.data$stage))
You may as well have a look at the Cytotree PDF in case of more issues.
I may not be using the terminology correctly here so please forgive me...
I have a case of one package 'overwriting' a function with the same name loaded by another package and thus changing the behavior (breaking) of a function.
The specific case:
X <- data.frame ( y = rnorm(100), x1 = rnorm(100), x2 = rnorm(100) )
library(CausalImpact)
a <- CausalImpact::CausalImpact( X, c(1,75), c(76, 100) ) # works
library(bfast) # imports quantmod which loads crappy version of as.zoo.data.frame
b <- CausalImpact::CausalImpact( X, c(1,75), c(76, 100) ) # Error
I know the error comes from two versions of the function as.zoo.data.frame.
The problematic version is imported by bfast from the package 'quantmod' (see https://github.com/joshuaulrich/quantmod/issues/168). Unfortunately their hotfix did not prevent this error. Super annoying.
I can hack around this specific problem, but I was wondering if there is a general way to like 'de-register' this function variant from the search path. Neither detach nor unloadNamespace remove the offending function (same behavior after). An explanation and similar problem is discussed here and here, but I wasn't able to find a general solution. For instance I'd rather just remove this function than clone and re-write CausalImpact to deal with this behavior.
From R 3.6.0 onwards, there is a new option called "conflicts.policy" to handle this within an established framework. For small issues like this, you can use the new arguments to library(). If you aren't yet to 3.6, the easiest solution might be to explicitly namespace CausalImpact when you need it, i.e. CausalImpact::CausalImpact. That's a mouthful, so you could do causal_impact <- CausalImpact::CausalImpact and use that alias.
# only attach select
library(dplyr, include.only = "select")
# exclude slice/arrange from being attached.
library(dplyr, exclude = c("slice", "arrange"))
library(bfast, exclude = "CausalImpact") should solve your problem.
Attach means that they are available for use without explicit prefixing with their package. In either of these cases, something like dplyr::slice would work just fine.
For more information, you can see ?library. Also, the R-Core member Luke Tierney wrote a blog explaining how the conflicts.policy works. You can find that here
Here's an answer that works, but is less preferable than de-registering a S3 method because it involves replacing the registered version in the S3 Methods table with the desired method:
library(CausalImpact)
library(bfast)
assignInNamespace("as.zoo.data.frame", zoo:::as.zoo.data.frame, ns = asNamespace("zoo"))
based partially on #smingerson's suggestion in the comments
I am having trouble using R, 'tm' package, to read in .pdf files.
Specifically, I try to run the following code:
library(tm)
filename = "myfile.pdf"
tmp1 <- readPDF(PdftotextOptions="-layout")
doc <- tmp1(elem=list(uri=filename),language="en",id="id1")
doc[1:15]
...which gives me the error:
Error in readPDF(PdftotextOptions = "-layout") :
unused argument (PdftotextOptions = "-layout")
I assume this is due to the fact that the pdftotext program (part of xpdf, http://www.foolabs.com/xpdf/download.html) has not been installed correctly on my machine, so that R cannot access it.
What are the steps to install xpdf/pdftotext correctly such that the above R code can be executed? (I am aware of similar questions already posted, however they don't address the same issue)
PdftotextOptions is no parameter of readPDF. readPDF has a control parameter, which expects a list. So correct use would be:
if(all(file.exists(Sys.which(c("pdfinfo", "pdftotext"))))) {
tmp1 <- readPDF(control = list(text = "-layout"))
doc <- tmp1(elem=list(uri=filename),language="en",id="id1")
}
Set
setwd('C:/xpdf/bin64')
It works for me.
I was reading this article: Visualizing Tables with plot.table. In it there is a mention of a function plota.format(). I tried running that function with my data to see the visualization. But I am getting the following error:
Error: could not find function "plota.format"*
My question is: Which package does plota.format() belong to?
Thanks!
It doesn't seem like it's an actual package, but you can get it with the following (which I borrowed from the author's github
> library(RCurl)
> sit <- getURLContent(
'https://github.com/systematicinvestor/SIT/raw/master/sit.gz',
binary = TRUE, followlocation = TRUE, ssl.verifypeer = FALSE)
> con <- gzcon(rawConnection(sit, 'rb'))
> source(con)
> close(con)
> plota.format
The source code looks like it's not formatted as source code normally is, so I'm guessing this might be the only way. If you take a look at ls() now, you'll see you've got all the functions in the package so you might want to save them.
It appears to be in the package Systematic Investor Toolbox, described in the link you posted. You can view it on GitHub here.
Is there a R library that supports neo4j? I would like to construct a R graph (e.g. igraph) from neo4j or - vice versa - store a R graph in neo4j.
More precisely, I am looking for something similar to bulbflow for Python.
Update
There is a new neo4j driver for R that looks promising: http://nicolewhite.github.io/RNeo4j/. I changed the correct answer.
This link might be helpful. I'm going to connect ne04j with R in the following days and will try first with the provided link. Hope it helps.
I tried it out and it works well. Here is the function that works:
First, install and load packages and then execute function:
install.packages('RCurl')
install.packages('RJSONIO')
library('bitops')
library('RCurl')
library('RJSONIO')
query <- function(querystring) {
h = basicTextGatherer()
curlPerform(url="localhost:7474/db/data/ext/CypherPlugin/graphdb/execute_query",
postfields=paste('query',curlEscape(querystring), sep='='),
writefunction = h$update,
verbose = FALSE
)
result <- fromJSON(h$value())
#print(result)
data <- data.frame(t(sapply(result$data, unlist)))
print(data)
names(data) <- result$columns
}
and this is an example of calling function:
q <-"start a = node(50) match a-->b RETURN b"
data <- query(q)
Consider the RNeo4j driver. The function shown above is incomplete: it cannot return single column data and there is no NULL handling.
https://github.com/nicolewhite/RNeo4j
I tried to use the R script (thanks a lot for providing it) and it seems to me that you can directly use :
/db/data/cypher
instead of
db/data/ext/CypherPlugin/graphdb/execute_query
(with neo4j 2.0).
Not sure if it fits your requirements but have a look at Gephi.
http://gephi.org/.