[R-sig-eco] Predict on zero-inflated model using design matrix and parameter coefficients

[Peter Solymos]

Laura,

Depending on how you implement the ZIP model, the approach might be
slightly different. Using the pscl package you can do this:

r$> library(pscl)

r$> m <- zeroinfl(art ~ . | 1, data = bioChemists)

r$> cf0 <- coef(m, "zero")

r$> cf0
(Intercept)
  -1.681349

r$> cf1 <- coef(m, "count")

r$> cf1
 (Intercept)     femWomen   marMarried         kid5          phd
ment
 0.553995385 -0.231609021  0.131971507 -0.170473908  0.002525835
 0.021542720

r$> X0 <- model.matrix(m, "zero")

r$> head(X0)
  (Intercept)
1           1
2           1
3           1
4           1
5           1
6           1

r$> X1 <- model.matrix(m, "count")

r$> head(X1)
  (Intercept) femWomen marMarried kid5  phd ment
1           1        0          1    0 2.52    7
2           1        1          0    0 2.05    6
3           1        1          0    0 3.75    6
4           1        0          1    1 1.18    3
5           1        1          0    0 3.75   26
6           1        1          1    2 3.59    2

r$> pr <- drop((1 - plogis(X0 %*% cf0)) * exp(X1 %*% cf1))

r$> summary(pr - predict(m))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
      0       0       0       0       0       0

If you are predicting for a new data set, use model.matrix(~1, newdata) to
get X and make sure your inverse link functions are correct when using
probit or cloglog.

Cheers,

Péter Sólymos



On Tue, May 3, 2022 at 8:11 AM Lee, Laura <laura.lee using ncdenr.gov> wrote:

> Hi all,
>
> I am interested in predicting on a data set using a ZIP model without
> using the predict function. The reason is that I don't want to have to
> refit the model in the new script each time I want to do a prediction. I
> know I will have to specify the estimated coefficients and the design
> matrix, but I don't know what the code will look like. I would appreciate
> any assistance.
>
> Cheers,
>
> Laura
>
> Laura M. Lee
> Stock Assessment Program Manager
> Division of Marine Fisheries
> Department of Environmental Quality
>
> 252 808 8072    office
> Laura.Lee using ncdenr.gov
>
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> P.O. Box 769
> Morehead City, NC 28557-0769
>
>
>
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