Data_Fn | R Documentation |
Data_Fn
builds a tagged list of data inputs used by TMB for running the model
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 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)
|
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) |
Tagged list containing inputs to function Build_TMB_Fn()
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