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urol-e5 / timeseries

Data generated from e5 time series sampling in Moorea
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Blanks are being lost/removed in PI_curves_rates.Rmd script in Timepoint 1 #13

Closed AHuffmyer closed 3 years ago

AHuffmyer commented 3 years ago

Lines 149-184: Blank values (colony.id = "BK") are not included in "pr" data frame. It appears that these blanks are unintentionally lost upstream in the script (likely when assigning identifiers from metadata in lines 52-61).

jrcunning commented 3 years ago

The issue actually appears to be that many of the PI curve data files (in data/1_pi_curves), including all the blanks, have been deleted. Looks like all the data files were deleted with bd548443e0cc5ca4040742123abc4fa52bf284ad, then added back in with 1a13a5f5fbf76a93ac51d1141bfc6271529f7eaf, then many were deleted again with 82ccd71efcdba90835031965f33a5ac05d6fdd4e. Seems like some git issues led to inadvertent deletion of these files, but they can be brought back from earlier commits! LMK if you need help with this...

AHuffmyer commented 3 years ago

Interesting. In the .Rmd file, the blanks are present in the metadata file that is loaded ("BK" colony ID) in line 49. But, they are lost/removed in the next code in line 53 - I see now that is because a data file does not exist for them in 1_pi_curves as you said. I haven't restored files from previous commits before. Do you have any tips on how I can do this without causing other problems?

jrcunning commented 3 years ago

There is probably a way to recover from old commits, but I had copies archived locally so I went ahead and replaced all the PI curve .csv files in 1_pi_curves with these archived copies I had (see ea0317990cb2a5fe05664b5a54a35c3c31b07082). These copies were last modified Feb. 12th, 2020, shortly after the first timepoint trip, so they should be good unless anyone needed to modify them for any reason after that date. Quickly scanning the git history it only appears files were deleted/readded but not modified, but would be good to confirm. If everything runs now and you feel good about it, close this issue!

AHuffmyer commented 3 years ago

Thank you for your help!