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| Original file line number | Diff line number | Diff line change |
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| paste_phi = function (nr, env = parent.frame()) { | ||
| vn <- env$.info$varname | ||
| ind <- env$.index | ||
| gk <- env$.isgk | ||
| paste0("phi( c_",vn,"[", nr, "] - eta_",vn,"[",ind, "] ) ") | ||
| } | ||
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| write_opm = function (info, index, isgk = FALSE, indent = 4L) { | ||
| .info <- info | ||
| .index <- index | ||
| .isgk <- isgk | ||
| probs <- cvapply(2L:(info$ncat - 1L), function(k, .info = info, .index = index, .isgk = isgk) { | ||
| paste0(tab(indent), paste_p(k), " <- ", (if (isTRUE(.info$rev)) { | ||
| paste0(paste_phi(k - 1L), " - ", paste_phi(k)) | ||
| } | ||
| else { | ||
| paste0(paste_phi(k), " - ", paste_phi(k - 1L)) | ||
| })) | ||
| }) | ||
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| paste0(tab(indent), paste_p(1L), " <- ", if (isTRUE(info$rev)) { | ||
| 1 - paste_phi(1L) | ||
| } else { | ||
| paste_phi(1L) | ||
| }, "\n", | ||
| paste(probs, collapse = "\n"), "\n", | ||
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| tab(indent), paste_p(info$ncat), " <- ", if (isTRUE(info$rev)) { | ||
| paste_phi(info$ncat) | ||
| } else { | ||
| paste0("1 - ", paste_phi(info$ncat - 1L)) | ||
| }) | ||
| } | ||
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| write_priors_opm = function (info) { | ||
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| # sign <- if (isTRUE(info$rev)) { | ||
| # " + " | ||
| # } else { | ||
| # " - " | ||
| # } | ||
| gammas <- cvapply(1L:(info$ncat - 1L), function(k) { | ||
| if (k == 1L) { | ||
| paste0(tab(), "gamma_", info$varname, "[", | ||
| k, "] ~ dnorm(mu_delta_ordinal, tau_delta_ordinal)") | ||
| } | ||
| else { | ||
| paste0(tab(), "gamma_", info$varname, "[", | ||
| k, "] ~ dgamma (0.001, 0.001)") | ||
| } | ||
| }) | ||
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| deltas <- cvapply(1L:(info$ncat - 1L), function(k) { | ||
| paste0(tab(), "c_", info$varname, "[", | ||
| k, "] <- sum( gamma_", info$varname, "[1:",k,"])") | ||
| }) | ||
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| paste0(c(gammas, "", deltas), collapse = "\n") | ||
| } | ||
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| jagsmodel_opm = function (info) { | ||
| if (info$ncat < 3L) { | ||
| errormsg("A cumulative logit mixed model is supposed to be fitted for the\n | ||
| variable %s but %s only has %s categories.", | ||
| dQuote(info$varname), dQuote(info$varname), info$ncat) | ||
| } | ||
| if (!is.null(info$hc_list)) { | ||
| errormsg("I found a random effects structure. Did you mean to use %s\n | ||
| instead of %s?", | ||
| dQuote("clmm"), dQuote("clm")) | ||
| } | ||
| indent <- 4L + 4L + nchar(info$varname) + 7L | ||
| index <- info$index[gsub("M_", "", info$resp_mat)] | ||
| linpred <- if (length(info$lp[[info$resp_mat]]) > 0L) { | ||
| paste_linpred(info$parname, info$parelmts[[info$resp_mat]], | ||
| matnam = info$resp_mat, index = index, cols = info$lp[[info$resp_mat]], | ||
| scale_pars = info$scale_pars[[info$resp_mat]]) | ||
| } | ||
| else { | ||
| "0" | ||
| } | ||
| linpred_nonprop <- if (!is.null(attr(info$parelmts[[info$resp_mat]], | ||
| "nonprop"))) { | ||
| rhs <- cvapply(attr(info$parelmts[[info$resp_mat]], "nonprop"), | ||
| function(par_elmts) { | ||
| add_linebreaks(paste_linpred(info$parname, par_elmts, | ||
| matnam = info$resp_mat, index = index, cols = attr(info$lp, | ||
| "nonprop")[[info$resp_mat]], scale_pars = info$scale_pars[[info$resp_mat]]), | ||
| indent = indent) | ||
| }) | ||
| paste0("\n\n", paste0(tab(4L), "eta_", info$varname, | ||
| "_", seq_along(rhs), "[", index, "] <- ", | ||
| rhs, collapse = "\n")) | ||
| } | ||
| dummies <- if (!is.null(info$dummy_cols)) { | ||
| paste0("\n", paste0(paste_dummies(resp_mat = info$resp_mat, | ||
| resp_col = info$resp_col, dummy_cols = info$dummy_cols, | ||
| index = index, refs = info$refs), collapse = "\n"), | ||
| "\n") | ||
| } | ||
| paste0("\r", tab(), add_dashes(paste0("# Cumulative logit model for ", | ||
| info$varname)), "\n", tab(), "for (", index, | ||
| " in 1:", info$N[gsub("M_", "", info$resp_mat)], | ||
| ") {", "\n", tab(4L), info$resp_mat, "[", | ||
| index, ", ", info$resp_col, "] ~ dcat(p_", | ||
| info$varname, "[", index, ", 1:", info$ncat, | ||
| "])", "\n", tab(4L), "eta_", info$varname, | ||
| "[", index, "] <- ", add_linebreaks(linpred, | ||
| indent = indent), linpred_nonprop, "\n\n", | ||
| write_opm(info, index), "\n\n", | ||
| #write_logits(info,index, nonprop = !is.null(linpred_nonprop)), "\n", | ||
| dummies, | ||
| info$trafos, tab(), "}", "\n\n", | ||
| tab(), "# Priors for the model for ", info$varname, | ||
| "\n", if (!is.null(info$lp[[info$resp_mat]])) { | ||
| paste0(tab(), "for (k in ", min(unlist(c(info$parelmts, | ||
| lapply(info$parelmts, attr, "nonprop")))), | ||
| ":", max(unlist(c(info$parelmts, lapply(info$parelmts, | ||
| attr, "nonprop")))), ") {", "\n", | ||
| get_priordistr(info$shrinkage, type = "ordinal", | ||
| parname = info$parname), tab(), "}", | ||
| "\n\n") | ||
| }, write_priors_opm(info)) | ||
| } | ||
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