Data_Fn: Build data input for geostatistical delta-GLMM

In nwfsc-assess/geostatistical_delta-GLMM: Package for conducting spatial estimation of CPUE index standardization (fisheries, ecology, etc)

Build data input for geostatistical delta-GLMM

Description

Data_Fn builds a tagged list of data inputs used by TMB for running the model

Usage

Data_Fn(Version, FieldConfig, ObsModel = 2, b_i, a_i, s_i, t_i, a_xl,
  MeshList, GridList = NULL, Method = "Mesh", v_i = rep(0, length(b_i)),
  PredTF_i = rep(0, length(b_i)), X_xj = NULL, X_xtp = NULL,
  Q_ik = NULL, Aniso = 1, RhoConfig = c(Beta1 = 0, Beta2 = 0, Epsilon1 =
  0, Epsilon2 = 0), Options = c(SD_site_density = 0, SD_site_logdensity = 0,
  Calculate_Range = 0, Calculate_evenness = 0, Calculate_effective_area = 0),
  CheckForErrors = TRUE, Alpha = 2)

Arguments

Version	a version number (see example for current default).
FieldConfig	a vector of format c("Omega1"=0, "Epsilon1"=10, "Omega2"="AR1", "Epsilon2"=10), where Omega refers to spatial variation, Epsilon refers to spatio-temporal variation, Omega1 refers to variation in encounter probability, and Omega2 refers to variation in positive catch rates, where 0 is off, "AR1" is an AR1 process, and >0 is the number of elements in a factor-analysis covariance
ObsModel	an optional integer that specifies the distribution for positive catch rates (Default=2, i.e., Gamma) ObsModel=0 Normal ObsModel=1 Lognormal ObsModel=2 Gamma ObsModel=11 Mixture lognormal ObsModel=12 Mixture gamma ObsModel=4 Zero-adjusted negative binomial ObsModel=5 Zero-inflated negativee binomial ObsModel=6 Conway-Maxwell-Poisson distribution
b_i	Sampled biomass for each observation i
a_i	Sampled area for each observation i
s_i	Spatial knot (e.g., grid cell) for each observation i
t_i	Time interval (e.g., year) for each observation i
a_xl	Area associated with each knot
MeshList,	tagged list representing location information for the SPDE mesh hyperdistribution
GridList,	tagged list representing location information for the 2D AR1 grid hyperdistribution
Method,	character (either "Mesh" or "Grid") specifying hyperdistribution (Default="Mesh")
v_i	OPTIONAL, sampling category (e.g., vessel or tow) associated with overdispersed variation for each observation i
PredTF_i	OPTIONAL, whether each observation i is included in the likelihood (PredTF_i[i]=0) or in the predictive probability (PredTF_i[i]=1)
X_xj	OPTIONAL, matrix of static density covariates (e.g., measured variables affecting density, as used when interpolating density for calculating an index of abundance)
X_xtp	OPTIONAL, array of dynamic (varying among time intervals) density covariates
Q_ik	OPTIONAL, matrix of catchability covariates (e.g., measured variables affecting catch rates but not caused by variation in species density) for each observation i
Aniso	OPTIONAL whether to assume isotropy (Aniso=0) or geometric anisotropy (Aniso=1)
RhoConfig	OPTIONAL, vector of form c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilon2"=0) specifying whether either intercepts (Beta1 and Beta2) or spatio-temporal variation (Epsilon1 and Epsilon2) is structured among time intervals
Options	OPTIONAL, a vector of form c('SD_site_density'=0,'SD_site_logdensity'=0,'Calculate_Range'=0,'Calculate_evenness'=0,'Calculate_effective_area'=0), where Calculate_Range=1 turns on calculation of center of gravity, and Calculate_effective_area=1 turns on calculation of effective area occupied
CheckForErrors	OPTIONAL, whether to check for errors in input (NOTE: when CheckForErrors=TRUE, the function will throw an error if it detects a problem with inputs. However, failing to throw an error is no guaruntee that the inputs are all correct)
Alpha	order of SPDE mesh (default = 2, alternative = 1)

Value

Tagged list containing inputs to function Build_TMB_Fn()

nwfsc-assess/geostatistical_delta-GLMM documentation built on July 8, 2023, 4:49 a.m.