As user, I'd like to have all asked parameters as entry of the `fm_load_data()` correctly documented

[statnmap]

As user, I'd like to have all parameters possible as entry of the functions correctly documented, so that I can adapt the model to my datasets

Client - Validation

• [x] fm_load_data() allows to change parameters species, fleet, fitted_data, survey_data_file, vmslogbook_data_file, study_domain_file, year_start, year_end, month_start, month_end, time_step, k, grid_xmin, grid_xmax, grid_ymin, grid_ymax and seed

=> https://balglave.github.io/FishMap/reference/fm_load_data.html

• [x] All params of fm_load_data() are documented

=> https://balglave.github.io/FishMap/reference/fm_load_data.html => https://github.com/balglave/FishMap/blob/main/man/fm_load_data.Rd

• [x] The parameters time_step and fitted_data have a proper default value

=> https://balglave.github.io/FishMap/reference/fm_load_data.html

• [x] An error is raised if incorrect parameters are provided

We specify possible values with match.atg() :

=> https://github.com/balglave/FishMap/blob/main/R/fm_load_data.R

match.arg() returns an error for incorrect values :

The error behavior is integrated in the test of the function :

=> https://github.com/balglave/FishMap/blob/main/tests/testthat/test-fm_load_data.R

• [x] non-default values are now specified for running examples and tests

In test :

=> https://github.com/balglave/FishMap/blob/main/tests/testthat/test-fm_load_data.R

In examples :

=> https://github.com/balglave/FishMap/blob/main/vignettes/user-running-fishmap.Rmd

Dev - Tech

• [x] retrieve info from excel file from client https://github.com/balglave/FishMap/files/10982407/functions_parameters.xlsx
• [x] adjust fm_load_data() inputs according to excel file
• [x] add a parameter seed = 29510
• [x] add withr::local_seed(seed = seed) at the beginning of function
• [x] use match.arg() at the beginning of fm_load_data() to restrict parameters to expected values
• [x] specify non-default parameters in test and examples
• [x] use full path inputs (no system.file call in function load_data())
• [x] add test to verify match.arg behavior
• [x] create same ticket for fm_fit_model() once this one is in pre-val

Client inputs

To be able to write the correct documentation, could you please list all parameters that you would like to see in the parameters of the functions, separated by family and by function

To do so, we will ask you to list the parameters as a 'roxygen' documentation for each function.
_If you think it would be better to move some parameters in the fm_fit_model(), it is still time to ask._

You can look at the current documentation of each function to see what already exists: https://balglave.github.io/FishMap/reference/index.html

We would need this information:

• Function among fm_load_data(), fm_fit_model(), fm_generate_graphs()
• Name of the parameter
• Type
• Description
• Default value (can be empty)

You can give this information as a csv/Excel file if you want to, or any other mean that suits you

[JCasemajor]

Hi, here are the parameters we would like to see in the functions.

functions_parameters.xlsx

Note that we removed anisotropy and const_spphab from fm_fit_model() and added fitted_data to fm_load_data().

[JCasemajor]

Je valide.

[balglave]

Je valide