lr_get_spec values all NAs

[itamshab]

I'm trying to convert multiple .csv files to a matrix for downstream analysis, using lr_get_spec, however all values are returned NAs.

Script used
spec <- lr_get_spec( where = getwd(), ext = "csv", lim = c(450,4500), sep = ",", subdir = FALSE, subdir.names = FALSE, ignore.case = TRUE, interpolate = TRUE )

Attaching zip of .csv files.
a4_bulk(12).zip

Thanks!

[Bisaloo]

Thank you very much for the report! It should be now fixed.

You can install the development version with the fix by running:

install.packages("lightr", repos = "https://dev.ropensci.org")

The problem was that the data in your file is stored with decreasing wavelengths where all the examples I had until now have increasing wavelengths. So I didn't take this case into account. Out of curiosity where does this data come from? Do you have raw files from your spectrometer or does it only return csv?

[itamshab]

Hi Hugo, Thanks for the fix, I will try it later today. The data comes from a Bruker Vertex70 as OPUS files. Exporting to a shareable version is painful: I convert to csv using the Spectragtyph software, and use R to remove rows with text and save back as individual files. Then I call lr_get_spec to create a matrix that I analyze with e.g. the *pls* package. If you know a better solution, please let me know! Best, Itamar

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On Sun, Nov 1, 2020 at 3:24 AM Hugo Gruson ***@***.***> wrote: Thank you very much for the report! It should be now fixed. You can install the development version with the fix by running: install.packages("lightr", repos = "https://dev.ropensci.org") The problem was that the data in your file is stored with decreasing wavelengths where all the example I had until now have increasing wavelengths. So I didn't take this case into account. Out of curiosity where does this data come from? Do you have raw files from your spectrometer or does it only return csv? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOPOZF3BANMFFLLAADYMHI3SNULKRANCNFSM4TF7YR6Q> .

[Bisaloo]

It does sound painful indeed. I don't know a better way right now since I'm not familiar with this format but if you can send me an example OPUS file, I can try to add a parser in lightr. Then you would be able to run lr_get_spec() directly on these files. This is precisely the use case I have in mind for lightr.

[itamshab]

That would be excellent! Here are a couple of OPUS files. Let me know if you need extra info.

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On Sun, Nov 1, 2020 at 11:25 AM Hugo Gruson ***@***.***> wrote: It does sound painful indeed. I don't know a better way right now since I'm not familiar with this format but if you can send me an example OPUS file, I can try to add a parser in lightr. Then you would be able to run lr_get_spec() directly on these files. This is precisely the use case I have in mind for lightr. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOPOZF6AGRKU3C5GDFHENK3SNWDZBANCNFSM4TF7YR6Q> .

[Bisaloo]

@itamshab I didn't receive the attached files. I think you need to connect on GitHub (and not answer by email) to share them.

Alternatively, you can send them at the email address listed here: https://www.normalesup.org/~hgruson/contact.html

[Bisaloo]

FYI, the request to parse OPUS files is now tracked in #31. I'll try to get on it soon.