search

urol-e5 / timeseries

Data generated from e5 time series sampling in Moorea
3 stars 0 forks source link

Problem in TP3 pi_curve_rates.rmd - error in mutate() intervals lines 66-70 #19

Closed AHuffmyer closed 3 years ago

AHuffmyer commented 3 years ago

In the TP3 pi_curve_rates.rmd script there is a problem in lines 66-70 in chunk that uses time breaks in samples to link O2 data with light levels. The script is the same as other timepoints that are working, so I suspect this issue lies in the data frames. This script is required to run bayesian and parameters scripts for the same timepoint.

AHuffmyer commented 3 years ago

This is also occurring in TP4 rmd.

AHuffmyer commented 3 years ago

See if this resolves with using quadratic nls fit.

AHuffmyer commented 3 years ago

Issue is still present - open issue

AHuffmyer commented 3 years ago

@daniellembecker I see your name on this script - any chance you have insight on this issue?

AHuffmyer commented 3 years ago

Since the script is the same, is there a change in file format or similar that started at timepoint 3?

daniellembecker commented 3 years ago

Hmm I will have a look at it and we can brainstorm together! All I did previously was copy the script and adjust it from TP1, but could be a time format issue which happens every so often. There is nothing I can think of with the format of data that was entered that would be different.

AHuffmyer commented 3 years ago

Great! Since its also happening in TP 4 it makes me think the file formats are different, but I couldn't see anything obvious..

AHuffmyer commented 3 years ago

Since the raw data files look the same I wonder if there is a mis match in the metadata files.

hputnam commented 3 years ago

I did a test of all of timepoint 2 files in the timepoint 3 code and the code ran successfully, so it is not a code issue per se, but something with the input files. I suggest running them one at a time to see if it is all files or a particular one.

daniellembecker commented 3 years ago

I was able to run through the TP3 and TP4 code and data on my computer so we think it may be an Rstudio background issue possibly? Still TBD

hputnam commented 3 years ago

It is a typo issue. the file is named POR-367, while the metadata file lists Poc-367 in run1. Then ACR -173 in the metadata and ARC-173 in the filename. I corrected the acropora name issue. I am not sure which is correct POC or POR, so I will leave that one to you. what I did to trouble shoot is to first put all the data files in a folder called test inside the pi_curves folder.
then I moved the files back into the pi_curves folder starting with first I move 1 sample from run1 and all the blanks and made sure the code ran. then I added back the data files one run at a time and knitted between each one.

hputnam commented 3 years ago

I corrected both issues. The id should be POR-367. I pushed this and TP3 should run. Now we need to deal with TP4

AHuffmyer commented 3 years ago

I have been able to fix these problems and both TP4 and TP3 are running! When you pull, you will see edits on scripts and renaming files. However, we now have a new problem in TP4. There is an error (Error: Problem with mutate() input regs. x invalid 'length.out' argument Input regs is `furrr::future_map(...)') on line 123 of pi_curve_rates.rmd in TP4. I am working to diagnose this now, but am not sure where the error is coming from.