In the following page, I find a function check_rhat(). However in the R console, there does not exist even if using rstan:::.
So, I made a similar function for diagnosis of rhats in my package, but, if there exist some function to evaluate the rhat I want to use it (if it exists).
https://betanalpha.github.io/assets/case_studies/divergences_and_bias.html
That function comes into the R session via source("stan-utility.R") and is defined here. It is not in the rstan package.
Related
I'm attempting to scale a dataset by its unit variance using the scaling_UV() function in R from the santaR package. I have installed and loaded the santaR library but I am still being told that the scaling_UV() function could not be found.
How can I use this function or is there another function that performs the same operation? I will even perform the scaling manually if necessary.
I assume you have already used library(santaR) without errors.
If the function is exported by the package, santaR::scaling_UV() should work.
You can also try santar:::scaling_UV() (notice the three colons).
According to the documentation, the function should be present in version 1.2.3
I have been trying to perform the horse approach for finding the best model to run on the time series data but when I run ts_backtesting function, there is a message in console that
Error in ts_backtesting(x) : could not find function "ts_backtesting"
Can anyone please help me know why I am getting such error and how to avoid that.
I checked the latest version of the package, didn't find this function anymore
https://cran.r-project.org/web/packages/TSstudio/index.html,
instead, a function called 'train_model' can be used to do a similar thing.
In R, I'm getting an error "could not find function...". The function is present inside the package. Still when I run the package, getting the error.
I am getting this error in the ChainLadder package while running MackChainLadderFunctions.R. For example, the function checktriangle is present inside the package in Chainladder.R. Still, R is not able to recognize the function or call the function.
Two problems here.
function names are case-sensitive (checkTriangle, not checktriangle)
checkTriangle is not exported from the package (i.e., it's a private function intended for use within the package only), so you need ::: to access it ... try ChainLadder:::checkTriangle.
Using private functions is "at your own risk/programmer beware"; private functions are undocumented, may change in future versions, etc.. If you can find a way to do what you need to do with public functions, that is generally preferred.
AFAICT you're running into this problem because you're trying to source() (or cut-and-paste) package code in your R session. This shouldn't happen if you load the package with library("ChainLadder") and use the public functions (if it does, please edit your question to give a little more context about how you're using the package ...)
I'm building an R package for the first time and am having some trouble. I am doing an R CMD Check and am getting the following error:
get.AlignedPositions: no visible global function definition for 'subject'
I am not sure what is causing this. I don't even have a "subject" variable in my code. The code is rather lengthy so I rather not paste all of it unless someone asks in a comment. Is there something specific I should look for? The only thing I can think of is that I have a line like this:
alignment <-pairwiseAlignment(pattern = canonical.protein, subject=protein.extracted, patternQuality=patternQuality,
subjectQuality=subjectQuality,type = type, substitutionMatrix= substitutionMatrix,
fuzzyMatrix=fuzzyMatrix,gapOpening=gapOpening,gapExtension=gapExtension,
scoreOnly=scoreOnly)
but subject is defined by the pairwiseAlignment function in the Biostrings package. Thank you for your help!
R spotted a function, subject, being used without a function called subject being available. One possible reason for this is explained in this discussion on R-devel. In that case code is used conditionally, e.g. if a certain package is installed we use its functionality. When checking the package on a system which does not have this package installed, we run in to these kinds of warnings. So please check if this might be the case. Alternatively, you might have made a mistake by calling subject while no function existed, e.g. subject was not a function but just an object.
I am looking for a way to embed the fix() function within a script. Basically, here's what I'm currently doing:
I load a certain package. For example, library(PerformanceAnalytics)
I call the fix() function to edit a couple functions within the loaded package. Example, fix(VaR).
Then, using R's built-in editor, I copy-paste my function over the one originally loaded from the package.
Finally, I source in my .R script which calls the above functions I fixed and performs the computations I need.
Essentially, I'd like to streamline Step 3 above. Rather than having to manually type fix(function) and copy-paste over the original functions within the loaded package, I'd rather just have it done within a script I source.
Is there anyway to accomplish this?
FYI, I have reached out to the package's creator and loading a re-compiled version of the package with my modified code is out of the question.
Maybe source your functions and then use assignInNamespace?
EDIT #1:
The above won't work because assignInNamespace doesn't alter objects that have been exported. Instead,
put your functions in a file (foo.R)
load the package
then source(foo.R) or
sys.source(foo.R, envir=attach(NULL, name="myenv"))
Your functions will be higher up on the search list if you load them after the package, so R will find them before getting to the package's functions with the same name.
EDIT #2:
I didn't realize VaR called unexported functions in the namespace. That's why EDIT #1 doesn't work. To get it to work, you would need to explicitly reference all unexported PerformanceAnalytics functions used in VaR (e.g. change VaR.Gaussian to PerformanceAnalytics:::VaR.Gaussian).
See this post on R-devel for a couple other approaches. I couldn't quickly get Prof. Ripley's solution to work (I get the same error as in EDIT #1) and I didn't try Gabor's solution.
You can edit the body directly, discussed here:
What ways are there to edit a function in R?
You can download the packages source from CRAN. Edit the function (it will be found in PackageName/R), then install this package into R and just use it that way.
You can even change the package name in the DESCRIPTION file ... call it "PerformanceAnalytics2", then in R you just library(PerformanceAnalytics2) and use it as you would the original package.