normalizePath error after creating github repository in Rstudio, using subdirectories in my analysis?

Hi,

I'm struggling my way through coding a function in R to run a simulation. I recently found out about how github repositories work and the ability to view old version as I continue to develop my simulation function. I just installed a github repository in Rstudio and have run into an issue that I can't seem to find a solution to. I'd prefer to keep my files organized and have stored analyses i'm running in Mplus in a subdirectory. When I went to run the runModels command(part of MplusAutomation package) I got an error.

runModels(target = "C:/Users/gitz1/Desktop/smallsamplebayesian/mplusinp/",
#issue with filefilter as of 1.2.2021
filefilter = "threeitemML.inp",
replaceOutfile="always",
showOutput = F,
logFile="MH_RunLog.txt")

The error I get when running this is:

Running model: threeitemML.inp
System command: C:\WINDOWS\system32\cmd.exe /c cd "C:\Users\gitz1\Desktop\smallsamplebayesian" && "Mplus" "threeitemML.inp"
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
path[1]="threeitemML.inp": The system cannot find the file specified

I figured out that if I moved the "threeitemML.inp", to the respository folder ""C:/Users/gitz1/Desktop/smallsamplebayesian/" I had no issue.

Is it easier to just work out of one respository and not use subfolders? Is there an easy way to work out of subfolders when I have a function wrapped about this that will specifically call files out of the subfolder?