questions regarding initial configurations

[dvarkey]

1. What is the difference between FieldConfig and RhoConfig? These seem to have similar arguments and values but unclear on the spatial/spatio-temporal correlation.

2. Which parameters in the model govern covariance in distribution between the different species in a multispecies example (the parameters that produce figure 2 in Thorson and Barnett 2017)?

3. I wish to run the model with and without covariates – for example version 1 which does not use any covariates versus other versions which uses one or more covariates? The covariates I have are depth and temperature. Am I expected to do a spatial extrapolation for the covariate values at the knots? Or can I provide the sample depth in X_xj?

4. I have survey data for different fish ages – the function PlotIndex_Fn produces nice maps – but legends vary between plots and it is difficult to determine visually if one age is more or less abundant in any given area – Will it be possible that these maps have the same legend?

[James-Thorson]

1. You've seen the help file ?Data_Fn...? Please tell me what remaining questions you have regarding these inputs, so I can figure out how to expand that description there.

2. I've sorry to do this, but have you looked at the User Manual (https://github.com/James-Thorson/VAST/blob/master/examples/VAST_user_manual.docx)...? It points out that the covariance is from L1_omega, L1_epsilon, L2_omega, and L2_epsilon, and uses similar notation to the function outputs. Again, please tell me how I can make this more clear in the general documentation if you have remaining questions after skimming that.

3. Yes, X_xj is deprecated and you're expected to provide values at knots via input X_xtp. You can do this many different ways, but extrapolating from field measurements, taking the nearest, taking the average of nearest, etc., are standard approaches.

4. SpatialDeltaGLMM::PlotResultsOnMap_Fn produces the maps, and passes ... to SpatialDeltaGLMM::PlotMap_Fn. The latter function has an optional input zlim that is used to control the lower and upper bounds for the density-scale. Maybe give that a try and report back if it doesn't work the way you want?

Finally, if these answers are sufficient please close the issue thread. You can always reopen it later if you want.