View source: R/VAST_condition.R
VAST_condition | R Documentation |
Fits data loaded in your R session or data that is downloaded from the Northwest Fisheries Science Center data warehouse to a VAST::make_model using TMBhelper::fit_tmb. See the sections below for more details on how the model is configured.
VAST_condition(
conditiondir,
settings,
spp,
overdispersion,
data = NULL,
sensitivity = TRUE,
compiledir = conditiondir
)
conditiondir |
A directory, either a full or relative path, that will be used to save the results. The directory will be created recursively if it does not already exist. |
settings |
A list of settings used to run the spatiotemporal model. The full
list of necessary settings can be seen by running |
spp |
A character value that includes the survey acronym and the species name
in latin with all words separated by an underscore.
For example, |
overdispersion |
A vector of two integer values named "eta1" and "eta2"
that specify how overdispersion is modeled.
|
data |
A data frame that can be passed to the conditioning function such that no data will be downloaded. todo: document the columns that are needed. |
sensitivity |
logical; run sensitivity analyses specific to a given survey. For example, the Triennial survey can be split into two separate surveys and limited to 366 m depth. |
compiledir |
A file path, either relative or full, to a directory where
the VAST cpp file will be compiled leading to three files saved to the disk.
Thus, users should have both read and write capabilities within this
directory. A single file path can be used for multiple models allowing for
the model to be only compiled once rather than multiple times.
This file path is tranfered to the |
Nothing is returned by the function, but the function saves .RData
files to the disk in conditiondir
.
The US West Coast has operated using two passes of the survey area, where
each pass is done during a different time of year. If you think that migration
happens temporally and this migration will affect spatial density, then you
should include pass as a covariate. The default is to ignore pass, but I
presume that many US West Coast users will want to change this using the
settings
argument.
Kelli F. Johnson
See get_settings()
for a list of default settings. Anything not
included in your own list supplied to the settings argument will be taken from this
default list.
## Not run:
# Use the default settings to run the model for WCGBTS - sablefish
VAST_condition(conditiondir = getwd(), settings = get_settings(),
spp = settings$Species, sensitivity = FALSE)
## End(Not run)
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