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model-api/src/model-builder/code-blocks/derived-quantities/pred-site-means/_template_
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- LINK | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
#pred.site.sd[j.pred[i], k.pred[i]] <- sigma.ss[j.pred[i], k.pred[i]] | ||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
} |
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model-api/src/model-builder/code-blocks/derived-quantities/pred-site-means/_zi-template_
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
pred.site.mu.p[j.pred[i], x.pred.index[i], k.pred[i]] <- LINK | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
#pred.site.z[j.pred[i], x.pred.index[i], k.pred[i]] ~ dbern(p.zero[k.pred[i]]) | ||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
pred.site.mu.p[j.pred[i], x.pred.index[i], k.pred[i]] * (1 - p.zero[k.pred[i]]) | ||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
} |
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model-api/src/model-builder/code-blocks/derived-quantities/pred-site-means/beta-binomial
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- LINK | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
pred.site.p[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta + | ||
site.eps[j.pred[i], k.pred[i]] | ||
) | ||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
} |
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model-api/src/model-builder/code-blocks/derived-quantities/pred-site-means/gen-pois
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for(i in PRED_SITE_IDX) { | ||
pred.site.eta[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
B[j.pred[i], 1, k.pred[i]] + B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
pred.site.lambda[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
(1 - delta[k.pred[i]]) * exp(pred.site.eta[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
pred.site.lambda[j.pred[i], x.pred.index[i], k.pred[i]] / (1 - delta[k.pred[i]]) | ||
PRED_SITE_OOS_SWITCH | ||
} |
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...c/model-builder/code-blocks/derived-quantities/pred-site-means/hurdle-ordinal-latent-beta
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
phi.pred.site[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
G[j.pred[i], 1, k.pred[i]] + | ||
G[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Gamma | ||
) | ||
mu.pred.site[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
|
||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
pred.site.mean.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mu.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]] * | ||
(1 - phi.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean.01.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mean(phi.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean.gt0.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mean(mu.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
} |
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...-builder/code-blocks/derived-quantities/pred-site-means/hurdle-ordinal-latent-beta-b-drop
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
phi.pred.site[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
G[j.pred[i], 1, k.pred[i]] + | ||
G[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Gamma | ||
) | ||
mu.pred.site[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
B[j.pred[i], 1, k.pred[i]] | ||
) | ||
|
||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
pred.site.mean.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mu.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]] * | ||
(1 - phi.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean.01.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mean(phi.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean.gt0.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mean(mu.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
} |
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...builder/code-blocks/derived-quantities/pred-site-means/hurdle-ordinal-latent-beta-bg-drop
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
phi.pred.site[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
G[j.pred[i], 1, k.pred[i]] | ||
) | ||
mu.pred.site[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
B[j.pred[i], 1, k.pred[i]] | ||
) | ||
|
||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
pred.site.mean.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mu.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]] * | ||
(1 - phi.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean.01.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mean(phi.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean.gt0.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mean(mu.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
} |
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...-builder/code-blocks/derived-quantities/pred-site-means/hurdle-ordinal-latent-beta-g-drop
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
phi.pred.site[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
G[j.pred[i], 1, k.pred[i]] | ||
) | ||
mu.pred.site[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
|
||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
pred.site.mean.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mu.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]] * | ||
(1 - phi.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean.01.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mean(phi.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
pred.site.mean.gt0.oos[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
mean(mu.pred.site.oos[j.pred[i], x.pred.index[i], k.pred[i]]) | ||
} |
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model-api/src/model-builder/code-blocks/derived-quantities/pred-site-means/lognormal
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
pred.site.mean.log.y[j.pred[i], x.pred.index[i], k.pred[i]] <- log(pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]]) - | ||
1/2 * log((sigma.ss[j.pred[i], k.pred[i]]^2 + pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]]^2) / pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]]^2) | ||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- LINK | ||
B[j.pred[i], 1, k.pred[i]] + B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
} |
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model-api/src/model-builder/code-blocks/derived-quantities/pred-site-means/monomolecular
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
pred.site.lp[j.pred[i], x.pred.index[i], k.pred[i]] <- LINK | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
max(0.00001, maxR * (1 - exp(-pred.site.lp[j.pred[i], x.pred.index[i], k.pred[i]]))) | ||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
} |
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...src/model-builder/code-blocks/derived-quantities/pred-site-means/negative-binomial-DEPREC
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
pred.site.sigma.y[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
sigma.ss[j.pred[i], k.pred[i]] | ||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- LINK | ||
B[j.pred[i], 1, k.pred[i]] + B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
} |
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...pi/src/model-builder/code-blocks/derived-quantities/pred-site-means/ordinal-latent-normal
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for(i in PRED_SITE_IDX) { | ||
pred.site.mu[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
B[j.pred[i], 1, k.pred[i]] + B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
|
||
pred.site.pr[j.pred[i], x.pred.index[i], k.pred[i], 1] <- | ||
pnorm(theta[1], pred.site.mu[j.pred[i], x.pred.index[i], k.pred[i]] , | ||
tau.site[j.pred[i], k.pred[i]]) | ||
for (m in 2:(nYlevels - 1)) { | ||
pred.site.pr[j.pred[i], x.pred.index[i], k.pred[i], m] <- | ||
max(0, | ||
pnorm(theta[m] , pred.site.mu[j.pred[i], x.pred.index[i], k.pred[i]], | ||
tau.site[j.pred[i], k.pred[i]]) - | ||
pnorm(theta[m - 1] , pred.site.mu[j.pred[i], x.pred.index[i], k.pred[i]], | ||
tau.site[j.pred[i], k.pred[i]])) | ||
} | ||
pred.site.pr[j.pred[i], x.pred.index[i], k.pred[i], nYlevels] <- | ||
1 - pnorm(theta[nYlevels - 1], pred.site.mu[j.pred[i], x.pred.index[i], k.pred[i]], | ||
tau.site[j.pred[i], k.pred[i]]) | ||
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||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
inprod(pred.site.pr[j.pred[i], x.pred.index[i], k.pred[i], 1:nYlevels], 1:nYlevels) | ||
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PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
} |
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.../model-builder/code-blocks/derived-quantities/pred-site-means/zero-inflated-beta-binomial
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for(i in PRED_SITE_IDX) { | ||
## Site-level predictions at observed levels of any covariates. | ||
pred.site.mu.p[j.pred[i], x.pred.index[i], k.pred[i]] <- LINK | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta | ||
) | ||
pred.site.mean[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
pred.site.mu.p[j.pred[i], x.pred.index[i], k.pred[i]] * (1 - site.z[j.pred[i], k.pred[i]]) | ||
pred.site.p[j.pred[i], x.pred.index[i], k.pred[i]] <- ilogit( | ||
B[j.pred[i], 1, k.pred[i]] + | ||
B[j.pred[i], 2, k.pred[i]] * x.pred[i] + | ||
X.pred[i, ] %*% Beta + | ||
site.eps[j.pred[i], k.pred[i]] | ||
) | ||
pred.site.mean.extra[j.pred[i], x.pred.index[i], k.pred[i]] <- | ||
pred.site.p[j.pred[i], x.pred.index[i], k.pred[i]] * (1 - site.z[j.pred[i], k.pred[i]]) | ||
PRED_SITE_NEW_OBS_SWITCH | ||
PRED_SITE_OOS_SWITCH | ||
} |