Central function to calculate a phenology

Calculate a phenology (or its subparts) with a specific model.

Usage

phenology(
  .model,
  .data = NULL,
  .dates = NULL,
  .win = NULL,
  .ext = "tif",
  .onset = NULL,
  .diapause = NULL,
  .mortality = NULL,
  .submodels = c("onset", "diapause", "mortality", "development"),
  .setup_only = FALSE,
  .stations = NULL,
  .storage = NULL,
  .quiet = FALSE,
  ...
)

bso_phenology(
  .model = "bso",
  .data = NULL,
  .dates = NULL,
  .win = NULL,
  .ext = "tif",
  .onset = NULL,
  .diapause = NULL,
  .mortality = NULL,
  .submodels = c("onset", "diapause", "mortality", "development"),
  .setup_only = FALSE,
  .stations = NULL,
  .storage = NULL,
  .quiet = FALSE,
  ...
)

Arguments

.model

A phenology model or a model name (see model(), model_combine()).

.data

Data that will be passed to the model. It can be one of the following:

Character string: The raster data will be loaded from the path specified. The files have to be named like the respective model inputs.
Named list: Each element contains the input data according to its name.
Data frame (station data): Should have the columns date and station (name of the station). Additional columns have to be named like the respective model inputs.
Additionally, data can be passed through the ... argument.

Look at the model application manuals to find out which inputs are required by a specific model: model.bso.apply, model.phenips.apply, model.rity.apply, model.chapy.apply, model.joensson.apply, model.lange.apply, model.phenips_clim.apply.

.dates

Vector of dates that the data should be restricted to.

.win

SpatExtent to set a window (area of interest) if .data is a path to load the raster data from.

.ext

Extension of the files that should be used if .data is a path to load the raster data from.

.onset, .diapause, .mortality

Pass custom or precalculated phenological events to the model. See create_events to find out how to create events manually. Alternatively, the return value of get_onset_rst(), get_diapause_rst() or get_mortality_rst() could be used (with as_doy = FALSE) to extract the respective phenological event from another phenology. In that case, that phenology must match the temporal and spatial extent of the other inputs.

.submodels

Character vector. Specifies which submodels should be calculated. Can be a subset of c('onset', 'diapause', 'mortality', 'development').

.setup_only

If TRUE only the inputs will be preprocessed without calculating any submodels. The preprocessed data can be used as input for other phenology() calls and can be accessed via get_input_data().

.stations

Assign stations to the phenology. See stations_create() for details.

.storage

If set, the path specified here will be used to save the (intermediate) results. If phenology() is called successively with a growing amount of data, the calculations will continue where they stopped. This can save calculation time especially for large raster inputs. Note that this will only work of raster inputs and if terra::sources() is not empty. Otherwise the results of the calculations will be saved but successive calculations are not possible. If no input data is passed, the phenology will be loaded from the storage.

.quiet

If TRUE, messages are suppressed.

...

Parameters that will be passed to the model. Must be named according to the model inputs. See .data for alternative ways to pass data to the model.

Value

A phenology as a list. Look here to find out how a phenology can be analysed. It is not recommended to access the list elements directly.

Functions

bso_phenology(): As BSO works a bit different than the other models, a seperate phenology function is implemented for this model. Note that while the onset and the development submodels are needed to be taken from BSO, the diapause and the mortality submodels are compatible with other models.

The function returns a BSO phenology as a list. Look here to find out how a BSO phenology can be analysed. It is not recommended to access the list elements directly. To be able to use the functions that are available for phenology objects returned by phenology(), call bso_translate_phenology().

Examples

# \donttest{
# calculate phenology
p <- phenology('phenips-clim', barrks_data())
#> 
#> === calculate phenology with model `phenips-clim` ===
#> 
#> -- setup --
#> parameter dd_onset
#> parameter btmean
#> parameter btmax
#> parameter teff
#> > calculate amplitude
#> > get effective temperature from temperature/amplitude
#> parameter fly
#> 
#> -- onset --
#> > calculate the base onset
#> > add 0 degree days to get the onset of the first 10 % beetles
#> 
#> -- diapause --
#> 
#> -- mortality --
#> 
#> -- development --
#> > generation 1
#> > generation 2

# plot calculated generations
gens <- get_generations_rst(p)
terra::plot(gens)

# }