Basics: How do I enter quantitative/numerical covariates?

questions concerning analysis/theory using program PRESENCE

Re: Basics: How do I enter quantitative/numerical covariates

Postby jhines » Tue Oct 30, 2018 4:53 pm

I'm not sure what you meant by "both ways", but if you enter the seasonal covariates as survey covariates with each column repeated 5 times, then Presence will use the SST covariates for season 1 for the 1st 5 seasons, since you repeated the covariate 5 times. Presence will only read the 1st 16 columns for colonization and extinction, so do not repeat the columns. Instead, enter each season's SST values in the 1st 16 columns of the survey covariate input matrix. The remaining columns will be ignored, so you don't have to change them. The only other way would be to create 16 site covariates, named SST1, SST2, SST3,...SST16, and use those in the design matrix.

Example design matrix using SST as survey covariates:

gam1 1 SST
gam2 1 SST
gam3 1 SST
:
gam16 1 SST

Example using SST as site covariates:

gam1 1 SST1
gam2 1 SST2
gam3 1 SST3
:
gam16 1 SST16

The first method is a little easier since you can let Presence fill in SST to all rows of the design matrix using the "initial" menu. With the 2nd method, you need to manually enter a different value into each row of the design matrix (unless you use Excel and paste).
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Re: Basics: How do I enter quantitative/numerical covariates

Postby jhines » Tue Oct 30, 2018 4:58 pm

Those two design matrices should give the same results. If the results differ, I suspect it's because you repeated the SST covariate, instead of just using each value in 1 column. If that's not the case, I'd be happy to look at it and diagnose.
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Re: Basics: How do I enter quantitative/numerical covariates

Postby darryl » Tue Oct 30, 2018 4:58 pm

Hi Jim,
Note this is a multi-state multi-season application not regular multi-season, so the design matrix set up is quite different. Does PRESENCE just use the row number in the DM to correspond to the column number in the survey-specific covariate? How does it handle having multiple parameter types in one DM?

Given the values are constant across all sites each season, then it's fine to enter the values directly into the DM.

Cheers
Darryl
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Re: Basics: How do I enter quantitative/numerical covariates

Postby jhines » Tue Oct 30, 2018 5:23 pm

Hi Darryl,

Presence uses the row number in the design matrix to figure out which parameter is to be computed, based on the model. So, for a single-season model, it knows row i corresponds to season i. For multi-state, it knows which parameters are in which rows. Having multiple parameters in the same DM (eg., psi/phi/R, p/delta) allows you to build models where those parameters can be set equal, different, or additive of each other.

Since the covariate values don't change by site, I think the easiest way would be to enter directly into the DM, as you suggest (maybe into Excel, then paste into Presence).

Cheers,

Jim
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Re: Basics: How do I enter quantitative/numerical covariates

Postby kbrunk » Tue Oct 30, 2018 5:43 pm

Awesome. I have a massive excel spreadsheet with all my design matrices and covariates...someday I'll sit down with RPresence, but until then...

Thanks to you both for clarifying!

KB
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