Errors/warnings with example data

[rspfau]

Attempting to execute:

getTopLoc(GPD = "SimPurePops.txt", panel.size = 50, where.PLINK = your_plink_path, where.PGDspider = your_pgdspider_path)

Resulting messages in console:

Reading Data Creating training and working datasets Calculating Fst 'java' is not recognized as an internal or external command, operable program or batch file. 'cd C:/software/PGDSpider_2.1.1.5/ && java -Xmx1024m -Xms512m -jar PGDSpider2-cli.jar -inputfile GPD_for_GET_TOP_LOC.txt -inputformat GENEPOP -outputfile for_FST.txt -outputformat FSTAT -spid GP_FSTAT.spid' execution failed with error code 1problem copying C:\software\PGDSpider_2.1.1.5\for_FST.txt to C:\Users\pfau\Dropbox\hybriddetective\for_FST.txt: No such file or directorycannot open file 'for_FST.txt': No such file or directoryError in file(file, "r") : cannot open the connection

[yamilapcardoso]

Hello, do you have a file to use as example in hybriddetective? or where is the file "ExampleSNPdata.txt" from Jeffery et al. 2017. Thanks

[rystanley]

There was a rendering issue with the readme that happened with a github update, this unfortunately masked the documentation and example use of each file. The .pdf that was included was only to show general structure and that data is not available. However, there is example data built into the package that should be accessible using the code provided in the main page readme.

[yamilapcardoso]

Hello Ryan, thanks for your message!! I have some problems to run hybriddetective and paralleNewhybrid with my data:

-When a run parallenewhybrid all simulations and replicates has as results all individuals F2 with 1 of probability -The command to check the converge nh_preCheckR(PreDir = "/DetectiveHybrid/NH.Results/") PrecheckR Progress: Error in txtProgressBar(min = 0, max = length(tbCheck), style = 3) : must have 'max' > 'min'

Thank you for helping me! Yamila

El mar, 9 de nov. de 2021 a la(s) 20:16, Ryan Stanley ( @.***) escribió:

There was a rendering issue with the readme that happened with a github update, this unfortunately masked the documentation and example use of each file. The .pdf that was included was only to show general structure and that data is not available. However, there is example data built into the package that should be accessible using the code provided in the main page readme.

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[castef]

@yamilapcardoso Hi Yamila, I am having the same issue with nh_preCheckR,

nh_preCheckR(PreDir = (paste0(path.hold, "/NH.Results/"))) PrecheckR Progress: Error in txtProgressBar(min = 0, max = length(tbCheck), style = 3) : es muss 'max' > 'min' sein

How did you solved it in the end, do you remember? Thanks C

[rystanley]

We are trying to work through errors in this package as best we can. Unfortunately I am not the primary owner of the base code so wasn't getting notifications of the issues. We will go through this doing the best we can. Very much apologize for the late reply and slowness in fixing the issues.