Merge pull request #3 from Mtrsh/patch-4

Update issues_examples.R

analysis/issues_examples.R

@@ -1,13 +1,99 @@
 # issue described by Myriam Terristi (unnumbered, not on github):
 # error when making land mask tidy
 
+settings <- list(
+  fileprefix = "test",  # simulation name defined by the user
+  model = "pmodel",     # in future could also be "biomee", but not yet implemented
+  year_start = 2018,    # xxx not yet handled
+  year_end = 2018,      # xxx not yet handled
+  grid = list(          # a list specifying the grid which must be common to all forcing data
+    lon_start = -179.75,
+    dlon = 0.5,
+    len_ilon = 720,
+    lat_start = -89.75,
+    dlat = 0.5,
+    len_ilat = 360
+  ),
+  file_landmask = "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation.nc",
+  dir_landmask_tidy = "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation_tidy/",
+  file_elv = "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation.nc",
+  dir_elv_tidy = "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation_tidy/",
+  save_drivers = TRUE,   # whether rsofun driver object is to be saved. Uses additional disk space but substantially speeds up grsofun_run().
+  dir_drivers = here::here("input/tidy/"),  # path where rsofun drivers are to be written
+  overwrite = FALSE,    # whether files with tidy forcing data and drivers are to be overwritten. If false, reads files if available instead of re-creating them.
+  spinupyears = 10,     # model spin-up length
+  recycle = 1,          # climate forcing recycling during the spinup
+  dir_out = here::here("output/tidy/"),     # path for tidy model output
+  dir_out_nc = "xxx",  # xxx not yet handled
+  save = list(         # a named list where names correspond to variable names in rsofun output and the value is a string specifying the temporal resolution to which global output is to be aggregated. 
+    gpp = "mon"
+  ),
+  nthreads = 1,   # distribute to multiple nodes for high performance computing - xxx not yet implemented
+  ncores_max = 1  # set to 1 for un-parallel run
+)
+
 error <- map2tidy::map2tidy(
-  nclist = ???,
+  nclist = settings$file_landmask,
   varnam = "elevation",
   lonnam = "lon",
   latnam = "lat",
+  timenam= NA,
+  timedimnam= NA,
   do_chunks = TRUE,
-  outdir = ???,
+  outdir = settings$dir_landmask_tidy,
   fileprefix = "WFDEI-elevation",
-  overwrite = TRUE
+  overwrite = settings$overwrite
 )
+
+> rlang::last_trace()
+<error/purrr_error_indexed>
+Error in `purrr::map()`:
+ℹ In index: 1.
+Caused by error in `purrr::map()`:
+ℹ In index: 1.
+Caused by error in `nc_atts.NetCDF()`:
+! specified variable not found
+---
+Backtrace:
+     ▆
+  1. ├─map2tidy::map2tidy(...)
+  2. │ └─purrr::map(...)
+  3. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
+  4. │     ├─purrr:::with_indexed_errors(...)
+  5. │     │ └─base::withCallingHandlers(...)
+  6. │     ├─purrr:::call_with_cleanup(...)
+  7. │     └─map2tidy (local) .f(.x[[i]], ...)
+  8. │       └─map2tidy::nclist_to_df_byilon(...)
+  9. │         └─purrr::map(...)
+ 10. │           └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
+ 11. │             ├─purrr:::with_indexed_errors(...)
+ 12. │             │ └─base::withCallingHandlers(...)
+ 13. │             ├─purrr:::call_with_cleanup(...)
+ 14. │             └─map2tidy (local) .f(.x[[i]], ...)
+ 15. │               └─map2tidy::nclist_to_df_byfil(...)
+ 16. │                 ├─... %>% lubridate::ymd()
+ 17. │                 ├─ncmeta::nc_atts(filnam, timenam)
+ 18. │                 └─ncmeta:::nc_atts.character(filnam, timenam)
+ 19. │                   ├─ncmeta::nc_atts(nc, variable = variable)
+ 20. │                   └─ncmeta:::nc_atts.NetCDF(nc, variable = variable)
+ 21. │                     └─base::stop("specified variable not found")
+ 22. ├─lubridate::ymd(.)
+ 23. │ └─lubridate:::.parse_xxx(...)
+ 24. │   ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)
+ 25. │   └─base::lapply(list(...), .num_to_date)
+ 26. ├─stringr::str_remove(., " 0:0:0")
+ 27. │ └─stringr::str_replace(string, pattern, "")
+ 28. │   └─stringr:::check_lengths(string, pattern, replacement)
+ 29. │     └─vctrs::vec_size_common(...)
+ 30. ├─stringr::str_remove(., " 00:00:00")
+ 31. │ └─stringr::str_replace(string, pattern, "")
+ 32. │   └─stringr:::check_lengths(string, pattern, replacement)
+ 33. │     └─vctrs::vec_size_common(...)
+ 34. ├─stringr::str_remove(., "days since ")
+ 35. │ └─stringr::str_replace(string, pattern, "")
+ 36. │   └─stringr:::check_lengths(string, pattern, replacement)
+ 37. │     └─vctrs::vec_size_common(...)
+ 38. ├─dplyr::pull(., value)
+ 39. ├─dplyr::filter(., name == "units")
+ 40. └─tidyr::unnest(., cols = c(value))
+>