Predict from SDM — predict

The resulting pred.tif is masked to the boundary provided to the pred_limit argument of prep_sdm; or generated in prep_sdm from the pred_limit, limit_buffer and pred_clip arguments.

Usage

predict_sdm(
  prep,
  full_run,
  out_dir,
  file_name = "pred.tif",
  use_env_naming = FALSE,
  predictors = NULL,
  is_env_pred = FALSE,
  terra_options = NULL,
  doClamp = TRUE,
  force_new = FALSE,
  do_gc = FALSE,
  check_tifs = FALSE,
  handle_errors = TRUE,
  ...
)

Arguments

prep: Character or named list. If character, the path to an existing prep.rds. Otherwise, the result of a call to prep_sdm() with return_val = "object".
full_run: Character or named list. If character, the path to an existing full_run.rds. Otherwise, the result of a call to run_full_sdm() with return_val = "object".
out_dir: Character. Name of directory into which .tifs will be saved. Will be created if it does not exist.
file_name: Character. Name to give the output prediction .tif.
use_env_naming: Logical. If TRUE, and is_env_pred is TRUE, naming will ignore file_name and instead generate a name matching name_env_tif() with layer being this_taxa from prep and start_date being the minimum available start_date from the predictors. pred appears between this_taxa and start_date.
predictors: Character. Vector of paths to predictor .tif files.
is_env_pred: Logical. Does the naming of the directory and files in predictors follow the pattern required by envRaster::parse_env_tif()?
terra_options: Passed to terra::terraOptions(). e.g. list(memfrac = 0.6)
doClamp: Passed to terra::predict() (which then passes as ... to fun). Possibly orphaned from older envSDM?
force_new: Logical. If output files already exist, should they be remade?
do_gc: Logical. Run base::rm(list = ls) and base::gc() at end of function? Useful to keep RAM use down when running SDMs for many, many taxa, especially if done in parallel.
check_tifs: Logical. Check if any output .tif files error on terra::rast() and delete them if they do. Useful after a crash during predict.
handle_errors: Logical. Use purrr::safely when predicting, enabling the capture of (m)any errors (which are then written to the log). Suggest turning off (i.e. handle_errors = FALSE) when running in a targets pipeline.
...: Passed to ... in terra::mask() - the last step in the envSDM::predict_sdm process. Used to provide additional arguments to terra::writeRaster.

Value

Character path to predicted file, usually 'pred.tif'. Output .tif and .log, written to out_dir.

Examples


out_dir <- file.path(system.file(package = "envSDM"), "examples")

# setup -------
data <- readRDS(fs::path(out_dir, "data.rds"))

# predictors -------
preds <- fs::dir_ls(fs::path(out_dir, "tif"))

# Best combo--------
## run full SDM --------
future::plan(future::multisession())

furrr::future_pwalk(list(data$prep
                  , data$tune
                  , data$out_dir
                  )
             , \(a, b, c) run_full_sdm(prep = a
                                       , tune = b
                                       , out_dir = c
                                       , use_metric = "combo"

                                       # passed to tune_sdm via dots
                                       , metrics_df = envSDM::sdm_metrics
                                       #, force_new = FALSE
                                       )
             )


## predict -------
furrr::future_pwalk(list(data$prep
                  , data$out_dir
                  )
             , \(a, b) predict_sdm(prep = a
                                   , full_run = fs::path(b, "full_run.rds")
                                   , out_dir = b
                                   , predictors = preds
                                   , check_tifs = TRUE
                                   #, force_new = FALSE
                                   )
             )
#> Warning: UNRELIABLE VALUE: Future (<unnamed-73>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-73> (9220e353f90d2e3fdca4103a4d4c0f1f-73); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-74>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-74> (9220e353f90d2e3fdca4103a4d4c0f1f-74); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-75>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-75> (9220e353f90d2e3fdca4103a4d4c0f1f-75); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-76>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-76> (9220e353f90d2e3fdca4103a4d4c0f1f-76); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-77>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-77> (9220e353f90d2e3fdca4103a4d4c0f1f-77); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-78>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-78> (9220e353f90d2e3fdca4103a4d4c0f1f-78); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-79>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-79> (9220e353f90d2e3fdca4103a4d4c0f1f-79); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-80>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-80> (9220e353f90d2e3fdca4103a4d4c0f1f-80); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-81>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-81> (9220e353f90d2e3fdca4103a4d4c0f1f-81); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-82>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-82> (9220e353f90d2e3fdca4103a4d4c0f1f-82); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-83>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-83> (9220e353f90d2e3fdca4103a4d4c0f1f-83); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-84>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-84> (9220e353f90d2e3fdca4103a4d4c0f1f-84); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-85>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-85> (9220e353f90d2e3fdca4103a4d4c0f1f-85); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-86>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-86> (9220e353f90d2e3fdca4103a4d4c0f1f-86); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-87>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-87> (9220e353f90d2e3fdca4103a4d4c0f1f-87); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-88>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-88> (9220e353f90d2e3fdca4103a4d4c0f1f-88); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-89>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-89> (9220e353f90d2e3fdca4103a4d4c0f1f-89); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-90>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-90> (9220e353f90d2e3fdca4103a4d4c0f1f-90); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-91>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-91> (9220e353f90d2e3fdca4103a4d4c0f1f-91); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-92>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-92> (9220e353f90d2e3fdca4103a4d4c0f1f-92); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-93>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-93> (9220e353f90d2e3fdca4103a4d4c0f1f-93); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-94>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-94> (9220e353f90d2e3fdca4103a4d4c0f1f-94); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-95>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-95> (9220e353f90d2e3fdca4103a4d4c0f1f-95); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]
#> Warning: UNRELIABLE VALUE: Future (<unnamed-96>) unexpectedly generated random numbers without specifying argument 'seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced. To disable this check, use 'seed=NULL', or set option 'future.rng.onMisuse' to "ignore". [future <unnamed-96> (9220e353f90d2e3fdca4103a4d4c0f1f-96); on 9220e353f90d2e3fdca4103a4d4c0f1f@bi-mod-01<800160>]

future::plan(future::sequential())

## visualise-------
# just use one taxa
vis_data <- data |>
  dplyr::filter(taxa == "chg")

tifs <- fs::path(vis_data$out_dir[file.exists(fs::path(vis_data$out_dir, "pred.tif"))], "pred.tif")

names <- paste0("hold_prop "
                , vis_data$hold_prop
                , "; stretch "
                , vis_data$stretch
                , "; spatial_folds "
                , vis_data$spatial_folds
                )

r <- terra::rast(tifs)
names(r) <- names
terra::panel(r, cex.main = 0.6, nc = 2)