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 spatio-temporal 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 spatio-temporal variation (Default=TRUE) |
EncounterFunction, |
The link between density and encounter probability; 0=two-parameter logistic relationship; 1=two-parameter logistic relationship with less-than-one saturation; 2=one-parameter 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 spatio-temporal 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 among-species 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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