Comments (5)
OK, I've partially addressed this request in two ways:
- I've added a new function
Summary( Obj )
, which will be expanded to
output a battery of useful and interpretable results, which are documented
using?SpatialDeltaGLMM::Summary
. Right now, it containsD_xt
(density
at each knot and year), which I imagine is most important for plotting. - I've changed
PlotResultsOnMap_Fn
to invisibly return the object that
it's plotting last for a givenplot_set
input (and have also added
documentation for what these mean). So e.g.,
PlotResultsOnMap_Fn( plot_set=c(3,10), ... )
will plot predicted log-density and the CV of density, but it will return
the CV of density in matrix form.
- I earlier added a new feature
plot_set=10
which plots the predicted
CV of density, which will only run if
Data_Fn(...,Options=c('SD_site_logdensity'=1,...))
.
Jim
On Fri, Sep 9, 2016 at 1:02 PM, Paul Dolder [email protected]
wrote:
Jim,
In addition to the functionality to produce maps, it would be good to be
able to extract the spatial density estimates into a dataframe for external
plotting.Thanks,
Paul—
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from vast.
Great, thanks! Will test and let you know any issues
from vast.
Jim,
Think (1) (Summarize not Summary ??) is not working correctly. Haven't tested on Obj, as I hadn't saved this from the run...but should this extract D_xct from the Report (which I had saved) not D_xt ?
from vast.
Sorry, I'll need more details here...
But yes, I changed it to Summarize
(avoid namespace conflicts with base and utils). And yes it currently only extracts D_xct
(Summarize
in the single species package SpatialDeltaGLMM
extracts D_xt
)
.. are you saying you get an error when using the function?
from vast.
No, sorry - I haven't an Obj to test it on at the moment (only saved Report, ParHat etc.. ) so haven't tested the function directly. I had assumed the D_xct / D_xt issue was a typo....as it is not I've no doubt it will work fine.... will confirm
from vast.
Related Issues (20)
- Example Code Model Structure Errors
- Effect.fit_model new error on latest version of VAST HOT 19
- (www.github.com/james-thorson/VAST/examples)is not working HOT 2
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- SE of EOF factor loadings HOT 3
- Index units changed HOT 2
- Plot_maps function error HOT 3
- project_model function HOT 1
- Spatially varying Day of the year as catchability covariate HOT 1
- Poisson-link model application HOT 5
- New version of R may be causing issues with making extrapolation grid HOT 10
- Creating extrapolation grid: shifted south HOT 4
- Pink salmon time structure HOT 3
- Effect.fit_model or pdp do not work very well for binomial model
- Model crashes when e_i not equal to c_iz HOT 1
- INLA issue HOT 8
- Error running seasonal model example HOT 2
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from vast.