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 at ncdenr.gov 3441 Arendell Street P.O. Box 769 Morehead City, NC 28557-0769 Email correspondence to and from this address is subject to the North Carolina Public Records Law and may be disclosed to third parties.
Predict on zero-inflated model using design matrix and parameter coefficients
2 messages · Lee, Laura, 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,
P?ter S?lymos
On Tue, May 3, 2022 at 8:11 AM Lee, Laura <laura.lee at 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 at ncdenr.gov 3441 Arendell Street P.O. Box 769 Morehead City, NC 28557-0769 Email correspondence to and from this address is subject to the North Carolina Public Records Law and may be disclosed to third parties.
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