🧱 Helper to extract final spectra as matrix

[philipp-baumann]

as discussed #27 , now in a separate issue.

[pierreroudier]

Thanks for the dedicated issue.

In terms of user interface, I think this option should essentially be a switch between a list (with full metadata, which is currently returned to the user) and a matrix.

The rationale is:

• a chemometrician wanting to pull spectra to either calibrate a model or generate predictions would call read_opus with data_only = TRUE so a matrix is returned and can be pre-processed directly.
• a more advanced user might turn data_only to FALSE for more advanced checks on the data, and a more thorough look at the metadata -- and could of course use a lapply call on that list to combine whatever piece of the data is interesting.

Finally, I'd suggest to change the argument name, and use a simpler and more common matrix = TRUE|FALSE.

Example call:

# Select all OPUS files from a range of folders
opus_fns <- list.files("some/project/folder/", pattern = glob2rx("my_project-*.0"), full.names = TRUE)

# Directly read and assemble MIR matrix from the selected files
mir_mat <- read_opus(
  opus_fns,
  matrix = TRUE,
  progress = TRUE
)

# Quick plot
matplot(t(mir_mat))

[philipp-baumann]

Thanks for the dedicated issue.

In terms of user interface, I think this option should essentially be a switch between a list (with full metadata, which is currently returned to the user) and a matrix.

The rationale is:

* a chemometrician wanting to pull spectra to either calibrate a model or generate predictions would call `read_opus` with `data_only = TRUE` so a matrix is returned and can be pre-processed directly.

* a **more advanced user** might turn `data_only` to `FALSE` for more advanced checks on the data, and a more thorough look at the metadata -- and could of course use a `lapply` call on that list to combine whatever piece of the data is interesting.

Finally, I'd suggest to change the argument name, and use a simpler and more common matrix = TRUE|FALSE.

Example call:

# Select all OPUS files from a range of folders
opus_fns <- list.files("some/project/folder/", pattern = glob2rx("my_project-*.0"), full.names = TRUE)

# Directly read and assemble MIR matrix from the selected files
mir_mat <- read_opus(
  opus_fns,
  matrix = TRUE,
  progress = TRUE
)

# Quick plot
matplot(t(mir_mat))

Thanks for the nice summaries of use cases. I would not rename to matrix, because it hides the intent what the function does. Yes, it does return a matrix, but it is not clear that this switch is for all parameters and data vs. final spectra only. @pierreroudier @ThomasKnecht I would suggest to either make matrix_spectra or matrix_spec in case we moved away from data_only

[philipp-baumann]

Because it is quite an important argument for controlling read_opus() behavior and user experience, these two steps seem important:

1. make it very clear in the argument name what the output is ( @pierreroudier above), and that only (final) spectra are returned vs. all data and parameters.
2. document this argument really concisely.

[ThomasKnecht]

currently it is possible to only parse the data. the combination to a matrix should in my opinion be made in an extra function.