R/RcppExports.R

In duncanplee/CARBayesST: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

linpredcompute <- function(X, nsites, p, beta, offset) {
    .Call(`_CARBayesST_linpredcompute`, X, nsites, p, beta, offset)
}

quadform <- function(Wtriplet, Wtripletsum, n_triplet, nsites, phi, theta, rho) {
    .Call(`_CARBayesST_quadform`, Wtriplet, Wtripletsum, n_triplet, nsites, phi, theta, rho)
}

gammaquadformcompute <- function(Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho) {
    .Call(`_CARBayesST_gammaquadformcompute`, Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho)
}

alphaquadformcompute <- function(Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho, tau2) {
    .Call(`_CARBayesST_alphaquadformcompute`, Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho, tau2)
}

tauquadformcompute <- function(Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho, gamma) {
    .Call(`_CARBayesST_tauquadformcompute`, Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho, gamma)
}

tauquadformcomputear2 <- function(Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho, alpha1, alpha2) {
    .Call(`_CARBayesST_tauquadformcomputear2`, Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho, alpha1, alpha2)
}

poissonbetaupdateMALA <- function(X, nsites, p, beta, offset, y, prior_meanbeta, prior_varbeta, nblock, beta_tune, block_list) {
    .Call(`_CARBayesST_poissonbetaupdateMALA`, X, nsites, p, beta, offset, y, prior_meanbeta, prior_varbeta, nblock, beta_tune, block_list)
}

poissonbetaupdateRW <- function(X, nsites, p, beta, offset, y, prior_meanbeta, prior_varbeta, nblock, beta_tune, block_list) {
    .Call(`_CARBayesST_poissonbetaupdateRW`, X, nsites, p, beta, offset, y, prior_meanbeta, prior_varbeta, nblock, beta_tune, block_list)
}

binomialbetaupdateMALA <- function(X, nsites, p, beta, offset, y, failures, trials, prior_meanbeta, prior_varbeta, nblock, beta_tune, block_list) {
    .Call(`_CARBayesST_binomialbetaupdateMALA`, X, nsites, p, beta, offset, y, failures, trials, prior_meanbeta, prior_varbeta, nblock, beta_tune, block_list)
}

binomialbetaupdateRW <- function(X, nsites, p, beta, offset, y, failures, prior_meanbeta, prior_varbeta, nblock, beta_tune, block_list) {
    .Call(`_CARBayesST_binomialbetaupdateRW`, X, nsites, p, beta, offset, y, failures, prior_meanbeta, prior_varbeta, nblock, beta_tune, block_list)
}

poissoncarupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, phi, tau2, y, phi_tune, rho, offset, ntime, mult_offset) {
    .Call(`_CARBayesST_poissoncarupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsites, phi, tau2, y, phi_tune, rho, offset, ntime, mult_offset)
}

poissonindepupdateRW <- function(nsites, theta, tau2, y, theta_tune, offset) {
    .Call(`_CARBayesST_poissonindepupdateRW`, nsites, theta, tau2, y, theta_tune, offset)
}

binomialindepupdateRW <- function(nsites, theta, tau2, y, failures, theta_tune, offset) {
    .Call(`_CARBayesST_binomialindepupdateRW`, nsites, theta, tau2, y, failures, theta_tune, offset)
}

binomialcarupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, phi, tau2, y, failures, phi_tune, rho, offset, ntime, mult_offset) {
    .Call(`_CARBayesST_binomialcarupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsites, phi, tau2, y, failures, phi_tune, rho, offset, ntime, mult_offset)
}

gaussiancarupdate <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, phi, tau2, nu2, offset, rho, ntime) {
    .Call(`_CARBayesST_gaussiancarupdate`, Wtriplet, Wbegfin, Wtripletsum, nsites, phi, tau2, nu2, offset, rho, ntime)
}

poissonar1carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, gamma, rho, ymat, phi_tune, offset, denoffset) {
    .Call(`_CARBayesST_poissonar1carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, gamma, rho, ymat, phi_tune, offset, denoffset)
}

poissonar2carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, alpha1, alpha2, rho, ymat, phi_tune, offset, denoffset) {
    .Call(`_CARBayesST_poissonar2carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, alpha1, alpha2, rho, ymat, phi_tune, offset, denoffset)
}

binomialar1carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, gamma, rho, ymat, failuresmat, phi_tune, offset, denoffset) {
    .Call(`_CARBayesST_binomialar1carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, gamma, rho, ymat, failuresmat, phi_tune, offset, denoffset)
}

binomialar2carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, alpha1, alpha2, rho, ymat, failuresmat, phi_tune, offset, denoffset) {
    .Call(`_CARBayesST_binomialar2carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, alpha1, alpha2, rho, ymat, failuresmat, phi_tune, offset, denoffset)
}

gaussianar1carupdate <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, nu2, gamma, rho, offset, denoffset) {
    .Call(`_CARBayesST_gaussianar1carupdate`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, nu2, gamma, rho, offset, denoffset)
}

gaussianar2carupdate <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, nu2, alpha1, alpha2, rho, offset, denoffset) {
    .Call(`_CARBayesST_gaussianar2carupdate`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, tau2, nu2, alpha1, alpha2, rho, offset, denoffset)
}

binomialmvar1carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha, rho, Sigmainv, ymat, failuresmat, innovations, offset, denoffset) {
    .Call(`_CARBayesST_binomialmvar1carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha, rho, Sigmainv, ymat, failuresmat, innovations, offset, denoffset)
}

binomialmvar2carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha1, alpha2, rho, Sigmainv, ymat, failuresmat, innovations, offset, denoffset) {
    .Call(`_CARBayesST_binomialmvar2carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha1, alpha2, rho, Sigmainv, ymat, failuresmat, innovations, offset, denoffset)
}

poissonmvar1carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha, rho, Sigmainv, ymat, innovations, offset, denoffset) {
    .Call(`_CARBayesST_poissonmvar1carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha, rho, Sigmainv, ymat, innovations, offset, denoffset)
}

poissonmvar2carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha1, alpha2, rho, Sigmainv, ymat, innovations, offset, denoffset) {
    .Call(`_CARBayesST_poissonmvar2carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha1, alpha2, rho, Sigmainv, ymat, innovations, offset, denoffset)
}

gaussianmvar1carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha, rho, Sigmainv, nu2, innovations, offset, denoffset) {
    .Call(`_CARBayesST_gaussianmvar1carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha, rho, Sigmainv, nu2, innovations, offset, denoffset)
}

gaussianmvar2carupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha1, alpha2, rho, Sigmainv, nu2, innovations, offset, denoffset) {
    .Call(`_CARBayesST_gaussianmvar2carupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsite, ntime, nvar, phi, alpha1, alpha2, rho, Sigmainv, nu2, innovations, offset, denoffset)
}

MVSTquadformcompute <- function(Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, nvar, phit, phij, rho, Sigmainv) {
    .Call(`_CARBayesST_MVSTquadformcompute`, Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, nvar, phit, phij, rho, Sigmainv)
}

MVSTrhoTAR1compute <- function(Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, ntime, nvar, phi, rho, Sigmainv) {
    .Call(`_CARBayesST_MVSTrhoTAR1compute`, Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, ntime, nvar, phi, rho, Sigmainv)
}

MVSTrhoTAR2compute <- function(Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, ntime, nvar, phi, rho, Sigmainv) {
    .Call(`_CARBayesST_MVSTrhoTAR2compute`, Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, ntime, nvar, phi, rho, Sigmainv)
}

MVSTrhoSAR1compute <- function(Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, ntime, nvar, phi, rho, alpha, Sigmainv) {
    .Call(`_CARBayesST_MVSTrhoSAR1compute`, Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, ntime, nvar, phi, rho, alpha, Sigmainv)
}

MVSTrhoSAR2compute <- function(Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, ntime, nvar, phi, rho, alpha1, alpha2, Sigmainv) {
    .Call(`_CARBayesST_MVSTrhoSAR2compute`, Wtriplet, Wtripletsum, n_triplet, den_offset, nsite, ntime, nvar, phi, rho, alpha1, alpha2, Sigmainv)
}

qform <- function(Qtrip, phi) {
    .Call(`_CARBayesST_qform`, Qtrip, phi)
}

qform_asym <- function(Qtrip, phi1, phi2) {
    .Call(`_CARBayesST_qform_asym`, Qtrip, phi1, phi2)
}

qformSPACETIME <- function(Qtrip, phi, ntime, nsite) {
    .Call(`_CARBayesST_qformSPACETIME`, Qtrip, phi, ntime, nsite)
}

SPTICARphiGaussian <- function(W, nsites, ntimes, phi, nneighbours, tau, lik_var, y, alpha, XB) {
    .Call(`_CARBayesST_SPTICARphiGaussian`, W, nsites, ntimes, phi, nneighbours, tau, lik_var, y, alpha, XB)
}

qform_difference_ST <- function(Qtrip, Qtime, phi, nsites) {
    .Call(`_CARBayesST_qform_difference_ST`, Qtrip, Qtime, phi, nsites)
}

qform_ST <- function(Qspace, Qtime, phi, nsites) {
    .Call(`_CARBayesST_qform_ST`, Qspace, Qtime, phi, nsites)
}

qform_ST_asym <- function(Qspace, Qtime, phi1, phi2, nsites) {
    .Call(`_CARBayesST_qform_ST_asym`, Qspace, Qtime, phi1, phi2, nsites)
}

update_Qtime <- function(Qtime, alpha, rowNumberLastDiag) {
    .Call(`_CARBayesST_update_Qtime`, Qtime, alpha, rowNumberLastDiag)
}

updatetriplets_rho <- function(trips, nsites, rho_old, rho_new, fixedridge) {
    .Call(`_CARBayesST_updatetriplets_rho`, trips, nsites, rho_old, rho_new, fixedridge)
}

updatetripList2 <- function(trips, vold, vnew, nedges, nsites, block, block_length, rho, fixedridge) {
    .Call(`_CARBayesST_updatetripList2`, trips, vold, vnew, nedges, nsites, block, block_length, rho, fixedridge)
}

SPTICARphiBinomial <- function(W, nsites, ntimes, phi, nneighbours, tau, y, alpha, XB, phiVarb_tune, trials) {
    .Call(`_CARBayesST_SPTICARphiBinomial`, W, nsites, ntimes, phi, nneighbours, tau, y, alpha, XB, phiVarb_tune, trials)
}

SPTICARphiVarb <- function(W, nsites, ntimes, phiVarb, nneighbours, tau, y, E, phiVarb_tune, alpha, XB) {
    .Call(`_CARBayesST_SPTICARphiVarb`, W, nsites, ntimes, phiVarb, nneighbours, tau, y, E, phiVarb_tune, alpha, XB)
}

Zupdatesqbin <- function(Z, Offset, Y, delta, lambda, nsites, ntime, G, SS, prioroffset, Gstar, failures) {
    .Call(`_CARBayesST_Zupdatesqbin`, Z, Offset, Y, delta, lambda, nsites, ntime, G, SS, prioroffset, Gstar, failures)
}

Zupdatesqpoi <- function(Z, Offset, Y, delta, lambda, nsites, ntime, G, SS, prioroffset, Gstar) {
    .Call(`_CARBayesST_Zupdatesqpoi`, Z, Offset, Y, delta, lambda, nsites, ntime, G, SS, prioroffset, Gstar)
}

Zupdatesqgau <- function(Z, Offset, delta, lambda, nsites, ntime, G, SS, prioroffset, Gstar, nu2) {
    .Call(`_CARBayesST_Zupdatesqgau`, Z, Offset, delta, lambda, nsites, ntime, G, SS, prioroffset, Gstar, nu2)
}

tau2compute <- function(tau2, temp, tau2_shape, prior_tau2, N) {
    .Call(`_CARBayesST_tau2compute`, tau2, temp, tau2_shape, prior_tau2, N)
}

rhoquadformcompute <- function(Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho, tau2) {
    .Call(`_CARBayesST_rhoquadformcompute`, Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho, tau2)
}

binomialsrecarupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, rho, ymat, failuresmat, phi_tune, offset, denoffset, tau2) {
    .Call(`_CARBayesST_binomialsrecarupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, rho, ymat, failuresmat, phi_tune, offset, denoffset, tau2)
}

poissonsrecarupdateRW <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, rho, ymat, phi_tune, offset, denoffset, tau2) {
    .Call(`_CARBayesST_poissonsrecarupdateRW`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntime, phi, rho, ymat, phi_tune, offset, denoffset, tau2)
}

tauquadformcompute2 <- function(Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho) {
    .Call(`_CARBayesST_tauquadformcompute2`, Wtriplet, Wtripletsum, n_triplet, nsites, ntime, phi, rho)
}

tempupdate <- function(Nchains, dt) {
    .Call(`_CARBayesST_tempupdate`, Nchains, dt)
}

matcomp <- function(X, beta, prop, p, Nchains) {
    .Call(`_CARBayesST_matcomp`, X, beta, prop, p, Nchains)
}

offsetcompute <- function(w, gamma, time, Nchains, nsites, Ntrends, begin) {
    .Call(`_CARBayesST_offsetcompute`, w, gamma, time, Nchains, nsites, Ntrends, begin)
}

matN <- function(x, nsites, Nchains) {
    .Call(`_CARBayesST_matN`, x, nsites, Nchains)
}

linpredcomputeNchains <- function(X, nsites, p, beta, Nchains) {
    .Call(`_CARBayesST_linpredcomputeNchains`, X, nsites, p, beta, Nchains)
}

gammaproposal <- function(Nchains, gamma, gamma_tune, prior_vargamma, Wareas, trend, knots) {
    .Call(`_CARBayesST_gammaproposal`, Nchains, gamma, gamma_tune, prior_vargamma, Wareas, trend, knots)
}

lambdaupdate <- function(Nchains, temp) {
    .Call(`_CARBayesST_lambdaupdate`, Nchains, temp)
}

tau2quadform <- function(Wtriplet, Wtripletsum, n_triplet, nsites, phi, theta, rho, Nchains) {
    .Call(`_CARBayesST_tau2quadform`, Wtriplet, Wtripletsum, n_triplet, nsites, phi, theta, rho, Nchains)
}

tau2computeNchains <- function(temp, tau2_shape, prior_tau2, Nchains) {
    .Call(`_CARBayesST_tau2computeNchains`, temp, tau2_shape, prior_tau2, Nchains)
}

rhoquadformcomputeNchains <- function(Wtriplet, Wtripletsum, n_triplet, nsites, Nchains, phi, rho, tau2) {
    .Call(`_CARBayesST_rhoquadformcomputeNchains`, Wtriplet, Wtripletsum, n_triplet, nsites, Nchains, phi, rho, tau2)
}

Qdet <- function(Nchains, rho, Wstar_val) {
    .Call(`_CARBayesST_Qdet`, Nchains, rho, Wstar_val)
}

poissondevfit <- function(y, fitted, nsites, Nchains) {
    .Call(`_CARBayesST_poissondevfit`, y, fitted, nsites, Nchains)
}

poissonbetablockupdate <- function(nsites, beta, betaprop, lp_beta, lp_betaprop, offset, y, prior_meanbeta, prior_varbeta, Nchains, temps, p) {
    .Call(`_CARBayesST_poissonbetablockupdate`, nsites, beta, betaprop, lp_beta, lp_betaprop, offset, y, prior_meanbeta, prior_varbeta, Nchains, temps, p)
}

poissongammaupdate <- function(nsites, gamma, proposal, offset, offset_proposal, y, prior_meangamma, prior_vargamma, Nchains, temps) {
    .Call(`_CARBayesST_poissongammaupdate`, nsites, gamma, proposal, offset, offset_proposal, y, prior_meangamma, prior_vargamma, Nchains, temps)
}

poissonwupdate <- function(nsites, ntimes, w, offset, offset_proposal, w_proposal, y, lambda, Nchains, temps, begin, regbegin, Ntrends) {
    .Call(`_CARBayesST_poissonwupdate`, nsites, ntimes, w, offset, offset_proposal, w_proposal, y, lambda, Nchains, temps, begin, regbegin, Ntrends)
}

poissonphiupdate <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntimes, phi, offset, y, tau2, rho, Nchains, temps, phi_tune, regbegin) {
    .Call(`_CARBayesST_poissonphiupdate`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntimes, phi, offset, y, tau2, rho, Nchains, temps, phi_tune, regbegin)
}

poissoncouplingAllupdate <- function(nsites, K, p, w, offset, beta, gamma, lambda, phi, rho, tau2, Wtripletsum, Wtriplet, Wbegfin, y, prior_meanbeta, prior_varbeta, prior_meantrends, prior_vartrends, prior_lambda, prior_tau2, swap, temps, begin, Ntrends, TrendSel) {
    .Call(`_CARBayesST_poissoncouplingAllupdate`, nsites, K, p, w, offset, beta, gamma, lambda, phi, rho, tau2, Wtripletsum, Wtriplet, Wbegfin, y, prior_meanbeta, prior_varbeta, prior_meantrends, prior_vartrends, prior_lambda, prior_tau2, swap, temps, begin, Ntrends, TrendSel)
}

binomialdevfit <- function(y, trials, probs, nsites, Nchains) {
    .Call(`_CARBayesST_binomialdevfit`, y, trials, probs, nsites, Nchains)
}

binomialbetablockupdate <- function(nsites, beta, betaprop, lp_beta, lp_betaprop, offset, y, failures, prior_meanbeta, prior_varbeta, Nchains, temps, p) {
    .Call(`_CARBayesST_binomialbetablockupdate`, nsites, beta, betaprop, lp_beta, lp_betaprop, offset, y, failures, prior_meanbeta, prior_varbeta, Nchains, temps, p)
}

binomialgammaupdate <- function(nsites, gamma, proposal, offset, offset_proposal, y, failures, prior_meangamma, prior_vargamma, Nchains, temps) {
    .Call(`_CARBayesST_binomialgammaupdate`, nsites, gamma, proposal, offset, offset_proposal, y, failures, prior_meangamma, prior_vargamma, Nchains, temps)
}

binomialwupdate <- function(nsites, ntimes, w, offset, offset_proposal, w_proposal, y, failures, lambda, Nchains, temps, begin, regbegin, Ntrends) {
    .Call(`_CARBayesST_binomialwupdate`, nsites, ntimes, w, offset, offset_proposal, w_proposal, y, failures, lambda, Nchains, temps, begin, regbegin, Ntrends)
}

binomialphiupdate <- function(Wtriplet, Wbegfin, Wtripletsum, nsites, ntimes, phi, offset, y, failures, tau2, rho, Nchains, temps, phi_tune, regbegin) {
    .Call(`_CARBayesST_binomialphiupdate`, Wtriplet, Wbegfin, Wtripletsum, nsites, ntimes, phi, offset, y, failures, tau2, rho, Nchains, temps, phi_tune, regbegin)
}

binomialcouplingAllupdate <- function(nsites, K, p, w, offset, beta, gamma, lambda, phi, rho, tau2, Wtripletsum, Wtriplet, Wbegfin, y, failures, prior_meanbeta, prior_varbeta, prior_meantrends, prior_vartrends, prior_lambda, prior_tau2, swap, temps, begin, Ntrends, TrendSel) {
    .Call(`_CARBayesST_binomialcouplingAllupdate`, nsites, K, p, w, offset, beta, gamma, lambda, phi, rho, tau2, Wtripletsum, Wtriplet, Wbegfin, y, failures, prior_meanbeta, prior_varbeta, prior_meantrends, prior_vartrends, prior_lambda, prior_tau2, swap, temps, begin, Ntrends, TrendSel)
}

optimise_graph <- function(adj, data, add = FALSE, remove = TRUE, remove_first = FALSE) {
    .Call(`_CARBayesST_optimise_graph`, adj, data, add, remove, remove_first)
}