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  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)

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 
ObsModel 
an optional integer that specifies the distribution for positive catch rates (Default=2, i.e., Gamma)

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 spatiotemporal 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) 
Tagged list containing inputs to function Build_TMB_Fn()
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