sdmTMB::sdmTMB()run_sdmtmb.RdRun sdmTMB::sdmTMB()
run_sdmtmb(
dir_main = getwd(),
data,
family,
formula,
n_knots = 500,
share_range = FALSE,
sdmtmb_control = sdmTMB::sdmTMBcontrol(newton_loops = 3),
...
)A string specifying a path where results will be saved. The default is your current working directory.
A data frame containing tow-level information on catch weight and effort. Additional columns can be present such as depth.
The family and link. Supports gaussian(), Gamma(),
binomial(), poisson(), Beta(),
nbinom2(),
truncated_nbinom2(),
nbinom1(),
truncated_nbinom1(),
censored_poisson(),
gamma_mix(),
lognormal_mix(),
student(),
tweedie(), and
gengamma().
Supports the delta/hurdle models:
delta_beta(),
delta_gamma(),
delta_gamma_mix(),
delta_lognormal_mix(),
delta_lognormal(), and
delta_truncated_nbinom2(),
For binomial family options, see 'Binomial families' in the Details
section below.
Model formula. IID random intercepts are possible using
lme4 syntax, e.g., + (1 | g) where g is a column of class
character or factor representing groups. Penalized splines are possible via
mgcv with s(). Optionally a list for delta (hurdle) models. See
examples and details below.
An integer specifying the number of knots you want in your mesh that is created by fmesher. More knots is not always better. The default is to use 500 knots. Future work will look at specifying a threshold distance between points rather than number of knots.
Logical, whether or not to share the range between the spatial and spatiotemporal fields. This defaults to FALSE, but adds extra parameters. The default in sdmTMB is TRUE, and sharing the range may improve estimation for data limited applications
Optional list, in the format of sdmTMB::sdmTMBcontrol().
By default, this is includes 3 newton loops
Optional arguments passed to sdmTMB::sdmTMB(). Note that users
cannot pass anisotropy because this are set
internal to this function, where anisotropy = TRUE because the coastline
of the western coastline of the U.S.A. is not perpendicular to the country
and three newton loops are specified in the control parameters.
An list object of class sdmTMB. This object is returned by sdmTMB::sdmTMB()
when fitting data to the model.