Failed to run example in original MountainPlot release

[ArtPoon]

art@orolo:~/git/clustuneR$ git checkout v1.0
Previous HEAD position was 899a799 Once Over
HEAD is now at ef294dc Delete example.fasta
art@orolo:~/git/clustuneR$ cd scripts
art@orolo:~/git/clustuneR/scripts$ ls
comp_Lib.R  MountainPlot.R
art@orolo:~/git/clustuneR/scripts$ Rscript MountainPlot.R -f ../ExampleData/Example_tn93.txt -o Example

Error in file(file, "rt") : cannot open the connection
Calls: impTN93 -> read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '../ExampleData/Example_tn93.txt': No such file or directory
Execution halted

[ArtPoon]

Directory and filenames are wrong, this command is running:

art@orolo:~/git/clustuneR/scripts$ Rscript MountainPlot.R -f ../example/example_tn93.txt -o Example

Warning messages:
1: glm.fit: fitted probabilities numerically 0 or 1 occurred 
2: glm.fit: fitted probabilities numerically 0 or 1 occurred 
3: glm.fit: algorithm did not converge 
4: glm.fit: fitted rates numerically 0 occurred 
5: glm.fit: algorithm did not converge 
6: glm.fit: fitted rates numerically 0 occurred 
null device 
          1 

This produced the following image in Rplots.pdf:

Based on the accession numbers in example_tn93.txt, these data were derived from the Seattle HIV data set in the "Public health in genetic spaces" paper. The GAIC profile looks the same as what was published: https://academic.oup.com/view-large/figure/200752183/veaa011f4.tif

[stevenweaver]

Hi @ArtPoon,

This is great. While #12 is remediated, would it be possible to provide the *.rds data for Canada and Tennessee?

Best, Steven

[ArtPoon]

Hi @stevenweaver - sorry again for the delayed response. You should be able to find equivalent data here: https://github.com/PoonLab/tn/tree/master/data where na is Canada and tn is Tennessee. The sequences are random permutations but should give the same results.