IIASA 2023 work

[Nowosad]

Improvements (see https://github.com/Nowosad/lsm2023improvements):

• [x] create an "extras" mechanism for calculate_lsm() (and other related functions) to speed-up calculations of many metrics at the same time (see https://github.com/r-spatialecology/landscapemetrics/issues/154 and https://github.com/r-spatialecology/landscapemetrics/issues/199) [jn: added to the commoncalc branch]
• [x] test if as.int() gives any speed improvements [no visible improvements or deterioration in terms of speed; however the internal matrix object should be smaller, and thus I would suggest doing it]
• [x] clean Rcpp code [jn: added some const and &]
• [x] check if using terra::focalCpp would be beneficial (see https://github.com/r-spatialecology/landscapemetrics/issues/224) [jn: in short, no. It only makes practical sense if the metrics are calculated using a C++ code]
• [x] try the new_tibble(list( approach [jn: the performance gain is ~20ms; rewritting is probably not worth it] [jn: later, we discovered that actually this was very important to improve window_lsm speed]
• [x] rcpp_get_coocurrence_matrix_single is used directly and indirectly by ~10 metrics -- there should be a way to improving this part
• [x] confirm that everything works as expected
• [x] clean and document the new changes (version 2.1) [jn: see https://github.com/r-spatialecology/landscapemetrics/blob/commoncalcs/NEWS.md#landscapemetrics-210]

Bug fixes:

• [x] https://github.com/r-spatialecology/landscapemetrics/issues/300
• [x] https://github.com/r-spatialecology/landscapemetrics/issues/215
• [x] https://github.com/r-spatialecology/landscapemetrics/issues/301

Questions to answer:

• [x] https://github.com/r-spatialecology/landscapemetrics/issues/298

Misc:

• [x] https://github.com/r-spatialecology/landscapemetrics/issues/260
• [x] update the FRAGSTATS tests -- https://github.com/r-spatialecology/landscapemetrics/issues/294
• [x] rerender the book chapter to check 3.1 version
• [ ] create a data base of metrics properties

[kadyb]

test if as.int() gives any speed improvements

The object is R matrix/array or SpatRaster? If SpatRaster, then the object is held in memory as float.

[Nowosad]

@kadyb yep -- we have a SpatRaster, but then we convert it into a matrix (as.matrix(x, wide = TRUE)). The resulting matrix is either double (when as.int is not used previously) or integer (when as.int is applied beforehand).

[mhesselbarth]

I think once your merged the PR with the common calculates, we can also close this issue again?

[Nowosad]

Yep -- I plan to work on the remaining points during the next week and then I will undraft the PR.

[Nowosad]

See https://jakubnowosad.com/lsm2023improvements/

[Nowosad]

@mhesselbarth My 2.1 changes are ready for your review and merge -- see https://github.com/r-spatialecology/landscapemetrics/pull/308

[mhesselbarth]

PR is merged to main and commoncalcs deleted. Will update the CRAN version soon.