R/RcppExports.R

In unmarked: Models for Data from Unmarked Animals

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

get_lik_trans <- function(I, I1) {
    .Call(`_unmarked_get_lik_trans`, I, I1)
}

get_mlogit <- function(lp_mat, type, S, guide) {
    .Call(`_unmarked_get_mlogit`, lp_mat, type, S, guide)
}

nll_distsamp <- function(y, lam, sig, scale, a, u, w, db, keyfun, survey) {
    .Call(`_unmarked_nll_distsamp`, y, lam, sig, scale, a, u, w, db, keyfun, survey)
}

nll_distsampOpen <- function(y, yt, X_lambda, X_gamma, X_omega, X_det, X_iota, beta, bi, offset_lambda, offset_gamma, offset_omega, offset_det, offset_iota, ytna, lk, mixture, first, last, first1, M, T, delta, dynamics, survey, fix, go_dims, immigration, I, I1, Ib, Ip, a, u, w, db, keyfun, lfac_k, kmyt, lfac_kmyt, fin, A) {
    .Call(`_unmarked_nll_distsampOpen`, y, yt, X_lambda, X_gamma, X_omega, X_det, X_iota, beta, bi, offset_lambda, offset_gamma, offset_omega, offset_det, offset_iota, ytna, lk, mixture, first, last, first1, M, T, delta, dynamics, survey, fix, go_dims, immigration, I, I1, Ib, Ip, a, u, w, db, keyfun, lfac_k, kmyt, lfac_kmyt, fin, A)
}

nll_gdistremoval <- function(beta, n_param, yDistance, yRemoval, ysum, mixture, keyfun, X_lambda, A, X_phi, X_rem, X_dist, db, a, u, w, pl, K, Kmin, threads) {
    .Call(`_unmarked_nll_gdistremoval`, beta, n_param, yDistance, yRemoval, ysum, mixture, keyfun, X_lambda, A, X_phi, X_rem, X_dist, db, a, u, w, pl, K, Kmin, threads)
}

nll_gdistsamp <- function(beta, n_param, y, mixture, keyfun, survey, X_lambda, offset_lambda, A, X_phi, offset_phi, X_det, offset_det, db, a, u, w, k, lfac_k, lfac_kmyt, kmyt, Kmin, threads) {
    .Call(`_unmarked_nll_gdistsamp`, beta, n_param, y, mixture, keyfun, survey, X_lambda, offset_lambda, A, X_phi, offset_phi, X_det, offset_det, db, a, u, w, k, lfac_k, lfac_kmyt, kmyt, Kmin, threads)
}

nll_gmultmix <- function(beta, n_param, y, mixture, pi_fun, X_lambda, offset_lambda, X_phi, offset_phi, X_det, offset_det, k, lfac_k, lfac_kmyt, kmyt, Kmin, threads) {
    .Call(`_unmarked_nll_gmultmix`, beta, n_param, y, mixture, pi_fun, X_lambda, offset_lambda, X_phi, offset_phi, X_det, offset_det, k, lfac_k, lfac_kmyt, kmyt, Kmin, threads)
}

nll_gpcount <- function(ym, X_lambda, X_phi, X_det, beta_lambda, beta_phi, beta_det, log_alpha, offset_lambda, offset_phi, offset_det, M, mixture, T, threads) {
    .Call(`_unmarked_nll_gpcount`, ym, X_lambda, X_phi, X_det, beta_lambda, beta_phi, beta_det, log_alpha, offset_lambda, offset_phi, offset_det, M, mixture, T, threads)
}

nll_multinomPois <- function(beta, pi_fun, Xlam, Xlam_offset, Xdet, Xdet_offset, y, navec, nP, nAP) {
    .Call(`_unmarked_nll_multinomPois`, beta, pi_fun, Xlam, Xlam_offset, Xdet, Xdet_offset, y, navec, nP, nAP)
}

nll_multmixOpen <- function(y, yt, X_lambda, X_gamma, X_omega, X_det, X_iota, beta, bi, offset_lambda, offset_gamma, offset_omega, offset_det, offset_iota, ytna, yna, lk, mixture, first, last, first1, M, T, J, R, delta, dynamics, fix, go_dims, immigration, I, I1, Ib, Ip, pi_fun, lfac_k, kmyt, lfac_kmyt, fin) {
    .Call(`_unmarked_nll_multmixOpen`, y, yt, X_lambda, X_gamma, X_omega, X_det, X_iota, beta, bi, offset_lambda, offset_gamma, offset_omega, offset_det, offset_iota, ytna, yna, lk, mixture, first, last, first1, M, T, J, R, delta, dynamics, fix, go_dims, immigration, I, I1, Ib, Ip, pi_fun, lfac_k, kmyt, lfac_kmyt, fin)
}

nll_nmixTTD <- function(beta, y, delta, X_state, X_det, pinds, mixture, tdist, N, J, K, naflag, threads) {
    .Call(`_unmarked_nll_nmixTTD`, beta, y, delta, X_state, X_det, pinds, mixture, tdist, N, J, K, naflag, threads)
}

nll_occu <- function(y, X, V, beta_psi, beta_p, nd, knownOcc, navec, X_offset, V_offset, link_psi) {
    .Call(`_unmarked_nll_occu`, y, X, V, beta_psi, beta_p, nd, knownOcc, navec, X_offset, V_offset, link_psi)
}

nll_occuCOP <- function(y, L, Xpsi, Xlambda, beta_psi, beta_lambda, removed) {
    .Call(`_unmarked_nll_occuCOP`, y, L, Xpsi, Xlambda, beta_psi, beta_lambda, removed)
}

nll_occuMS <- function(beta, y, dm_state, dm_phi, dm_det, sind, pind, dind, prm, S, T, J, N, naflag, guide) {
    .Call(`_unmarked_nll_occuMS`, beta, y, dm_state, dm_phi, dm_det, sind, pind, dind, prm, S, T, J, N, naflag, guide)
}

nll_occuMulti_loglik <- function(fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0) {
    .Call(`_unmarked_nll_occuMulti_loglik`, fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0)
}

nll_occuMulti <- function(fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0, penalty) {
    .Call(`_unmarked_nll_occuMulti`, fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0, penalty)
}

nll_occuPEN <- function(y, X, V, beta_psi, beta_p, nd, knownOcc, navec, X_offset, V_offset, penalty) {
    .Call(`_unmarked_nll_occuPEN`, y, X, V, beta_psi, beta_p, nd, knownOcc, navec, X_offset, V_offset, penalty)
}

nll_occuRN <- function(beta, n_param, y, X, V, X_offset, V_offset, K, Kmin, threads) {
    .Call(`_unmarked_nll_occuRN`, beta, n_param, y, X, V, X_offset, V_offset, K, Kmin, threads)
}

nll_occuTTD <- function(beta, y, delta, X_psi, X_det, X_col, X_ext, pind, dind, cind, eind, lpsi, tdist, N, T, J, naflag) {
    .Call(`_unmarked_nll_occuTTD`, beta, y, delta, X_psi, X_det, X_col, X_ext, pind, dind, cind, eind, lpsi, tdist, N, T, J, naflag)
}

nll_pcount <- function(beta, n_param, y, X, V, X_offset, V_offset, K, Kmin, mixture, threads) {
    .Call(`_unmarked_nll_pcount`, beta, n_param, y, X, V, X_offset, V_offset, K, Kmin, mixture, threads)
}

nll_pcountOpen <- function(ym, X_lambda, X_gamma, X_omega, X_det, X_iota, beta_lam, beta_gam, beta_om, beta_p, beta_iota, log_alpha, offset_lambda, offset_gamma, offset_omega, offset_det, offset_iota, ytna, ynam, lk, mixture, first, last, M, J, T, delta, dynamics, fix, go_dims, immigration, I, I1, Ib, Ip) {
    .Call(`_unmarked_nll_pcountOpen`, ym, X_lambda, X_gamma, X_omega, X_det, X_iota, beta_lam, beta_gam, beta_om, beta_p, beta_iota, log_alpha, offset_lambda, offset_gamma, offset_omega, offset_det, offset_iota, ytna, ynam, lk, mixture, first, last, M, J, T, delta, dynamics, fix, go_dims, immigration, I, I1, Ib, Ip)
}