Description Usage Arguments Value
MakeInput_Fn
builds a tagged list of inputs for TMB
1 2 3 4 5 6 7 8  MakeInput_Fn(Version, Nfactors, DF, loc_xy, method = "mesh",
Nobsfactors = 0, Kappa_Type = "Constant", ObsModel = NULL,
Aniso = FALSE, Include_Omega = TRUE, Include_Epsilon = TRUE,
EncounterFunction = 2, Correlated_Overdispersion = FALSE,
Include_Phi = TRUE, Include_Rho = TRUE, Use_REML = FALSE, X_ik = NULL,
X_nl = NULL, X_ntl = NULL, a_n = NULL, YearSet = NULL,
IndependentTF = c(FALSE, FALSE), CheckForBugs = TRUE,
CorrGroup_pp = NULL, ...)

Version 
a version number (see example for current default). 
Nfactors 
The number of dynamic factors used to approximate spatiotemporal variation 
DF 
a data frame of data where each row is a unique sample and with the following columns

loc_xy 
Locations for each station 
method 
The method for approximating spatial variation (options: "grid" or "mesh") 
Nobsfactors 
The number of factors used to approximate overdispersion among levels of 
Kappa_Type 
Whether the decorrelation distance is constant for all factors or not (Default="Constant") 
ObsModel 
The observation model used 
Include_Omega 
Whether to estimate purely spatial variation (Default=TRUE) 
Include_Epsilon, 
Whether to incldue spatiotemporal variation (Default=TRUE) 
EncounterFunction, 
The link between density and encounter probability; 0=twoparameter logistic relationship; 1=twoparameter logistic relationship with lessthanone saturation; 2=oneparameter saturating relationship (Default=1) 
Correlated_Overdispersion, 
Whether to estimate overdispersion (only possible if TowID is present in 
Include_Phi 
Whether to estimate each factor in equilibrium (FALSE) or with a fixed offset from equilibrium (TRUE), Default=TRUE 
Include_Rho 
Whether to estimate the magnitude of temporal autocorrelation (Default=TRUE) 
Use_REML 
Whether to use REML estimation 
X_ik 
A matrix specifying measured variables that affect catchability for each sample (Default is turned off) 
X_nl 
A matrix specifying measured variables that affect density for each sample (Default is an intercept) 
X_ntl 
An array specifying measured variables that affect density and vary over time (Default is off) 
a_n 
A vector giving the area associated with mesh vertex used when calculating indices of abundance (Default is even weighting of sample locations) 
YearSet 
A vector of levels of the 
IndependentTF 
Whether the spatiotemporal variation (IndependentTF[1]) or overdispersion (IndependentTF[2]) is independent among species (Default is both are correlated) 
CheckForBugs 
Whether to check inputs for obvious problems (Default=TRUE) 
CorrGroup_pp 
A matrix filled with integers, for post hoc testing of differences in amongspecies correlations 
Tagged list containing inputs to function Build_TMB_Fn()
A tagged list of data inputs
A tagged list with input parameters
A character vector specifying which parameters are treated as random effects
A parameter map, used to turn off or mirror parameter values
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