In my R Shiny program, I have a snippet of code as follows:
read.xlsx(wb,sheet=5,rows=5,cols=9)
When I run my program, the error it generates is as follows:
Error in read.xlsx.Workbook(wb, sheet = 5, rows = 5, cols = 9)
rows must be an integer vector else NULL or NA
What I Understand:
The workbook object "wb" has been defined. It is in no way causing the issue. I believe that declaring "rows" and "cols" is causing in issue. By using the help() function, I found that these are parameters in the function for read.xlsx. However, when I checked the online documentation, I found that the parameters called are supposed to be rowIndex and colIndex. I do not want to use parameters such as startRow because I only want a specific value.
What I Don't Understand
I don't understand what the problem is. The numbers should be vectors. In any case, when I use the as.vector command like so,
read.xlsx(wb,sheet=5,rows=as.vector(5),cols=as.vector(9))`
I get the same error. I honestly do not know where my problem is, and I hope one of you folks can help me with this syntactical issue.
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 am using mFD package to run a code. I am using two datasets to run this code. One is :
and the another data is:
My code look like:
alpha_fd_indices <- mFD::alpha.fd.multidim(
sp_faxes_coord = sp_faxes_coord [ , c("PC1", "PC2", "PC3", "PC4", "PC5")],
asb_sp_w = as.matrix(species),
ind_vect = c("fdis", "fmpd", "fnnd", "feve", "fric", "fdiv", "fori", "fspe", "fide"),
scaling = TRUE)
And the error message is:
Error in sp_coord_all_asb[[k]] <- sp_faxes_coord_k :
attempt to select less than one element in OneIndex
Can anyone help me to solve this problem?
After struggling with this issue myself I found that the mFD package requires row names for your 'asb_sp_w' matrix here.
From the code for the 'alpha.fd.multidim' function I found that this function runs a loop for each of the community rows of the asb_sp_w matrix but it does this by getting the rownames() from this matrix in the line:
k <- rownames(asb_sp_w)[n].
My workaround was to give each of the rows some fake row names (or your community sample names) and this should allow the function to run without error.
I'm not sure if there is a practical usage for mFD to keep this in the function or not so maybe someone else can comment on this.
I am new to programming and trying to learn R using swirl.
In one of the exercises I was told to use the summary function on a dataset. However I encountered a discrepancy in the way the summary was printed:
Instead of summarizing the categorical variable values, it instead says something about length, class and mode.
I went around searching for why this might be happening to no avail, but I did manage to find what the output is supposed to look like:
Any help would be greatly appreciated!
This behaviour is due to the option stringsAsFactors, which is FALSE by default on R 4. Previously it was TRUE by default:
From R 4 news: "now uses a `stringsAsFactors = FALSE' default, and hence by default no longer converts strings to factors in calls to data.frame() and read.table()."
A way to return to the previous behaviour with the same code is to run options(stringsAsFactors=T) before building dataframes. However, there is a warning saying this option will eventually be removed, as explained here.
For your new code, you can use the stringsAsFactors parameter, for instance data.frame(..., stringsAsFactors=T).
If you already have dataframes and you want to convert them, you could use this function to convert all character variables (you will have to adapt if only some variables need conversion):
to.factors <- function(df) {
i <- sapply(df, is.character)
df[i] <- lapply(df[i], as.factor)
df
}
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.
I am fairly new to R, so my apologies if this question is a bit silly.
I am calling a function in an external package ('mmlcr', although I don't think that is directly relevant to my problem), and one of the required inputs (data) is a data.frame. I compose the data.frame from various data using the following approach (simplified for illustration):
#id, Time, and value are vectors created elsewhere in the code.
myData = data.frame(a=id, b=Time, c=value)
out <- mmlcr( input1, input2, data=myData, input4)
Which throws the error:
Error in is.data.frame(data) : object 'myData' not found
The debugger indicates that this error is thrown during the mmlcr() call.
I then added a print(ls()) immediately prior to the mmlcr() call, and the output confirmed that "myData" was in my function workspace; further is.data.frame(myData) returned TRUE. So it seems that "myData" is successfully being created, but for some reason it is not passing into the mmlcr() function properly. (Commenting this line causes no error to be thrown, so I'm pretty sure this is the problematic line).
However, when I put the exact same code in a script (i.e., not within a function block), no such error is thrown and the output is as expected. Thus, I assume there is some scoping issue that arises.
I have tried both assignment approaches:
myData = data.frame(a=id, b=Time, c=value)
myData <- data.frame(a=id, b=Time, c=value)
and both give me the same error. I admit that I don't fully understand the scope model in R (I've read about the differences between = and <- and I think I get it, but I'm not sure).
Any advice you can offer would be appreciated.
MMLCR is now deprecated and you should search for some alternatives. Without looking too much into it, I sleuthed through an old repo and found the culprit:
m <- eval(m, data)
in the function mmlcr.default. There are a lot of reasons why this is bad, but scoping is the big one. R has this issue with the subset.data.frame function, see my old SO question. Rather than modify the source code, I would find a way to do your function with a subroutine using a for, repeat, or while loop.