So, I'm attempting to knit a R document to a HTML file however, when it knits it produces this error "#Error in table(StudentSurvey$Gender, StudentSurvey$Smoke): object 'StudentSurvey' not found"
For reference this is my R code.
read.csv("StudentSurvey.csv")
barplot(table(StudentSurvey$Gender, StudentSurvey$Smoke), legend=TRUE)
boxplot(StudentSurvey$Pulse ~ StudentSurvey$Smoke , xlab = "Smoke" , ylab = "Pulse")
I'm unsure whats wrong, I've tried to troubleshoot by changing my Rworking directory and ensure that "StudentSurvey.csv" is in there, but alas this issue appears to be happening. If it isn't immediately apparent I'm extremely new to R as I'm using it for the first time in UNI so apologies if this is a simple fix.
you just need to assign the output of read.csv() to an object.
StudentSurvey <- read.csv("StudentSurvey.csv")
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'm trying to Knit an Rmd file to Word, and keep encountering the following error message:
Error Message from RStudio
My line 28 is as follows:
NN <- make_Weka_filter("weka/filters/unsupervised/attribute/NumericToNominal")
I use NN later to apply the filter function to my testing and training data (I'm attempting a classification model for the Federalist papers)
trainfed <- NN(data=trainfed, control= Weka_control(R="1-3"), na.action = NULL)
testfed <- NN(data=testfed, control= Weka_control(R="1,3"), na.action = NULL)
When I run all of this either in blocks in my instance of RStudio, or just line by line - I have no issues. I can view the output in window, in line, and even in the viewer pane.
However, as soon as I start to try to Knit to Word I get the error mentioned above.
Is it possible to Knit to Word with RWeka package in use? I've seen many of these filed, but never really one with an answer to the error in finding the function on whatever instance Rmarkdown Knits from...
Can anybody advise? Thank you!
I am getting an error when I am trying to run the code below in R-Studio 3.3.2 on a Mac (OS Sierra)
devtools::install_github('ramnathv/rCharts')
install.packages("knitr")
require(rCharts)
require(knitr)
haireye <- as.data.frame(HairEyeColor)
n1 <- nPlot(Freq ~ Hair, group = 'Eye', type = 'multiBarChart',
data = subset(haireye, Sex == 'Male')
)
n1$save('fig/n1.html', cdn = TRUE)
cat('<iframe src="fig/n1.html" width= 100%, height=600</iframe>')
Pls see output below:
Error in file(con, "w") : cannot open the connection
In addition: Warning message: In file(con, "w") : cannot open file 'fig/n1.html': No such file or directory
But I am able to generate the reqd bar graph in the viewer when I use:
n1$show(cdn = TRUE)
in lieu of n1$save('fig/n1.html', cdn = TRUE)
To take care of write permission issues (if any), I also tried including the line below, altering the WD path wherever necessary.
knitr::knit2html('Users/documents/n1.html')
But it did not help. I see the n1.html file created but it only opens an empty browser.
Any help to resolve this is appreciated.
Best,
S
A lot of times we face this error due to caching in RStudio and in that case, actual code errors don't show up. Restart RStudio and this error will be gone and actual code errors would show.
You have two separate problems.
The connection error appears because the fig/ folder does not exist. Create the folder and the save command will work. R has functions to check the existance of directories and create new ones if you would like to do it in your code.
The second problem comes from the way you save, you should use n1$save('fig/n1.html', standalone = TRUE). Here you have a similar situation.
As a side-note, I would say rCharts is not currently developed or mantained at all, so I would recommend you to use another library for your charts. In my opinion Plotly is quite nice. rCharts brought the NVD3 project to R and the chart style is in my opinion really nice. However, as far as I know both projects are stopped so I would look for a library that is still alive.
I have fixed this problem with good old rm(list=ls()) . I know I have
fallen into sequences where the error stops execution of my script. I fix the error, and then it won't run. This is likely due to lazy evaluation but it is a near impossible problem to diagnose, so the solution at the top works almost all the time.
I am trying to create a script that I run about once a week. The goal is that it will go out and check an MS Excel file that a co-worker manages. It then tests to see if the date the file was modified is newer then the last time it was imported. If it is newer, it will import the file (I am using readxl package - WONDERFUL!) into a new object that is a named with the date the original Excel file was last modified included in the object name. I have everything working except for the assignment of the imported data.frame to a new object that includes the date.
An example of the code I am using is:
First I create an object with a path pointing to the file of interest.
pfdFilePath <- file.path("H:", "3700", "3780", "002-00", "3.
Project Information", "Program", "RAH program.xls")
after testing to verify the file has been modified, I have tried simple assignment ("test" is just an example for simplification):
paste("df-", as.Date(file.info(pfdFilePath)$mtime), sep = "") <- "test"
But that code produces an error:
Error in paste("df-", as.Date(file.info(pfdFilePath)$mtime), sep = "") <- "test" :
target of assignment expands to non-language object
I then try the assign function:
assign(paste("df-", as.Date(file.info(pfdFilePath)$mtime), sep = ""), "test")
Running this code creates an object that looks to be okay, but when I evaluate it, or try using str() or class() I get the following error:
Error in df - df-2016-08-09 :
non-numeric argument to binary operator
I am pretty sure this is an error that has to do with the environment I am using assign, but being relatively new to R, I cannot figure it out. I understand that the assign function seems to be frowned upon, but those warnings seem to centered on for-loops vs. lapply functions. I am not really iterating within a function though. Just a dynamically named object whenever I run a script. I can't come up with a better way to do it. If there is another way to do this that doesn't require the assign function, or a better way to use assign function , I would love to know it.
Thank you in advance, and sorry if this is a duplicate. I have spent the entire evening digging and can't derive what I need.
Abdou provided the key.
assign(paste0("df.", "pfd.", strftime(file.info(pfdFilePath)$mtime, "%Y%m%d")), "test01")
I also converted to the cleaner paste0 function and got rid of the dashes to avoid confusion. Lesson learned.
Works perfectly.
The below error keeps coming up inconsistently when I try to read excel files into R using the 'XLConnect' package.
Error in ls(envir = envir, all.names = private) :
invalid 'envir' argument
I have actually run into this error while even using other packages that read excel files like package 'xlsx' and 'xlsReadWrite'. Many times restarting the R session solves this problem, which leads me to think that something else I am doing in my R session is changing the environment and not allowing me to load excel files anymore. Below is the latest example of code that is causing this error. In this case I know that the following coding sequence is causing the error to appear - but why is that happening? And how can I get past this error if I need the chron package.
library("XLConnect")
wb2 <- loadWorkbook("excel_file", create = FALSE)
library(chron)
wb2 <- loadWorkbook("excel_file", create = FALSE)
Anyone else run into this issue before? Any help on this issue is greatly appreciated!
Before reopening the workbook try removing the reference to previously opened one, so:
rm(wb2)
wb2 <- loadWorkbook("excel_file", create = FALSE)
Also, make sure that "excel_file" is not open by excel or any other program while you run the R test.
I've seen the same error come up when using XLConnect and the above seemed to help.
Had this problem a couple of times and the call stack looks like this message is generated when a "OutOfMemory" Exception is thrown.
To solve this problem I used:
options( java.parameters = "-Xmx4g" )
to increase the heap size rJava is able to use.
Debugging with options(error=utils::recover) helped a lot, because the R error messages are not very specific.