Description Usage Arguments Value
Data_Fn
builds a tagged list of data inputs used by TMB for running the model
1 2 3 4 5 6 7 8 9 10 11  Data_Fn(Version, FieldConfig, OverdispersionConfig = c(eta1 = 0, eta2 = 0),
ObsModel_ez = c(PosDist = 1, Link = 0), VamConfig = c(Method = 0, Rank =
0, Timing = 0, Estimate_B0 = 0), b_i, a_i, c_iz, s_i, t_iz, a_xl, MeshList,
GridList, Method, v_i = rep(0, length(b_i)), e_i = c_iz[, 1],
PredTF_i = rep(0, length(b_i)), X_xj = NULL, X_xtp = NULL,
Q_ik = NULL, Aniso = 1, Network_sz = NULL, F_ct = NULL, F_init = 1,
RhoConfig = c(Beta1 = 0, Beta2 = 0, Epsilon1 = 0, Epsilon2 = 0),
t_yz = NULL, CheckForErrors = TRUE, yearbounds_zz = NULL,
Options = c(SD_site_logdensity = 0, Calculate_Range = 0,
Calculate_effective_area = 0, Calculate_Cov_SE = 0, Calculate_Synchrony = 0,
Calculate_proportion = 0))

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 spatiotemporal 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 factoranalysis covariance 
OverdispersionConfig 
OPTIONAL, a vector of format c("eta1"=0, "eta2"="AR1") governing any correlated overdispersion among categories for each level of v_i, where eta1 is for encounter probability, and eta2 is for positive catch rates, where 0 is off, "AR1" is an AR1 process, and >0 is the number of elements in a factoranalysis covariance 
ObsModel_ez 
an optional matrix with two columns where first column specifies the distribution for positive catch rates, and second element specifies the functional form for encounter probabilities

VamConfig 
Options to estimate interactions, where first slot selects method for forming interaction matrix, the second indicates rank, the third indicates whether to incorporate effect of 
b_i 
Sampled biomass for each observation i 
a_i 
Sampled area for each observation i 
c_iz 
Category (e.g., species, lengthbin) for each observation i 
s_i 
Spatial knot (e.g., grid cell) for each observation i 
t_iz 
Matrix where each row species the time for each observation i (if t_iz is a vector, it is coerced to a matrix with one column; if it is a matrix with two or more columns, it specifies multiple times for each observation, e.g., both year and season) 
a_xl 
Area associated with each knot 
MeshList, 
tagged list representing location information for the SPDE mesh hyperdistribution, i.e., from 
GridList, 
tagged list representing location information for the 2D AR1 grid hyperdistribution, i.e., from 
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 
e_i 
Error distribution for each observation i (by default 
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) 
F_ct 
OPTIONAL, matrix of fishing mortality for each category c and year t (only feasible when using a Poissonlink delta model and specifying temporal structure on intercepts, and mainly interpretable when species interactions via VamConfig) 
RhoConfig 
OPTIONAL, vector of form c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilon2"=0) specifying whether either intercepts (Beta1 and Beta2) or spatiotemporal variation (Epsilon1 and Epsilon2) is structured among time intervals (0: each year as fixed effect; 1: each year as random following IID distribution; 2: each year as random following a random walk; 3: constant among years as fixed effect; 4: each year as random following AR1 process) 
t_yz 
OPTIONAL, matrix specifying combination of levels of 
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) 
yearbounds_zz 
OPTIONAL, matrix with two columns, giving first and last years for defining one or more periods (rows) used to calculate changes in synchrony over time (only used if 
Options 
OPTIONAL, a vector of form c('SD_site_logdensity'=0,'Calculate_Range'=0,'Calculate_effective_area'=0,'Calculate_Cov_SE'=0,'Calculate_Synchrony'=0,'Calculate_proportion'=0), where Calculate_Range=1 turns on calculation of center of gravity, and Calculate_effective_area=1 turns on calculation of effective area occupied 
Tagged list containing inputs to function VAST::Build_TMB_Fn()
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