Errors while running climate matching

[SanderDevisscher]

This line of code is the probable cause of the error below:

trias/R/climate_match.R

Line 167 in 6c1dc31

if(length(taxon_key) == 1 & is.na(taxon_key)){

Error in if (length(taxon_key) == 1 & is.na(taxon_key)) { :
the condition has length > 1

this is an other error I get:

Error:
! Can't subset .data outside of a data mask context.

the error only occurs when maps == TRUE
this is the rlang::last_error() printout:

Backtrace:

1. trias::climate_match(...)
2. leaflet::addCircleMarkers(...)
3. leaflet::invokeMethod(...)
4. leaflet::evalFormula(list(...), data)
5. leaflet evalAll(list)
6. base::lapply(x, evalAll)
7. leaflet FUN(X[[i]], ...)
8. leaflet:::resolveFormula(x, data)
9. [ base::eval(...) ] with 1 more call
   Run rlang::last_trace() to see the full context.

and the last_trace:

1. ├─trias::climate_match(...)
2. │ └─... %>% ... at trias/R/climate_match.R:491:4
3. ├─leaflet::addPolygons(., data = sea, fillColor = "#e0e0e0", weight = 0.5)
4. │ ├─... %>% expandLimitsBbox(pgons)
5. │ └─leaflet::invokeMethod(...)
6. │ └─leaflet::dispatch(...)
7. ├─leaflet::expandLimitsBbox(., pgons)
8. │ └─leaflet::expandLimits(map, bbox[2, ], bbox[1, ])
9. ├─leaflet::addLayersControl(., baseGroups = ~.data$acceptedScientificName)
10. │ ├─leaflet::invokeMethod(...)
11. │ │ └─crosstalk::is.SharedData(data)
12. │ └─leaflet::getMapData(map)
13. ├─leaflet::addLegend(...)
14. │ ├─leaflet::invokeMethod(map, data, "addLegend", legend)
15. │ │ └─crosstalk::is.SharedData(data)
16. │ └─leaflet::getMapData(map)
17. ├─leaflet::addLegend(...)
18. │ ├─leaflet::invokeMethod(map, data, "addLegend", legend)
19. │ │ └─crosstalk::is.SharedData(data)
20. │ └─leaflet::getMapData(map)
21. ├─leaflet::addCircleMarkers(...)
22. │ ├─... %>% expandLimits(pts$lat, pts$lng)
23. │ └─leaflet::invokeMethod(...)
24. │ └─leaflet::evalFormula(list(...), data)
25. │ └─leaflet evalAll(list)
26. │ └─base::lapply(x, evalAll)
27. │ └─leaflet FUN(X[[i]], ...)
28. │ └─leaflet:::resolveFormula(x, data)
29. │ └─base::eval(f[[2]], metaData(data), environment(f))
30. │ └─base::eval(f[[2]], metaData(data), environment(f))
31. │ ├─acceptedScientificName
32. │ └─rlang:::$.rlang_fake_data_pronoun(.data, acceptedScientificName) #=> suspected cause of error
33. │ └─rlang:::stop_fake_data_subset(call)
34. │ └─rlang::abort(...)
35. └─leaflet::expandLimits(., pts$lat, pts$lng)

[SanderDevisscher]

sf does not work while intersecting with the observed$"1980-2016" shape due to validity issues.

Originally I used this more up to date 1980 - 2016 shape from Beck et al. 2018 to intersect with observations after 2000.
But since it does not work as wished I'm forced to switch to using 2001 - 2025 shape from Rubel & Kottek 2010

below the code I used in an effort to fix the 1980-2016 shape

else{
        obs_shape <- sf::st_as_sf(observed$"1980-2016", crs = 4326)
        obs_shape <- sf::st_cast(obs_shape, to = "POLYGON")
        obs_shape <- sf::st_make_valid(obs_shape)
        obs_shape <- obs_shape %>% 
          rename(GRIDCODE = gridcode)
      }

and a print out of the error

! Assigned data value must be compatible with existing data.
✖ Existing data has 10000 rows.
✖ Assigned data has 2 rows.
ℹ Only vectors of size 1 are recycled.

[SanderDevisscher]

I just need to fix the errors with the maps

[SanderDevisscher]

and switch those to sf use