dsp <- function(dsp_data,
n_samp = 10000L,
nBurn = 5000L,
nThin = 1L,
hypGam = NULL,
tuningGam = NULL,
hypPhi = NULL,
tuningPhi = 0.3,
trackProg = "percent",
progQuants = seq(0.1, 1.0, 0.1)) {
# stub functions for gamma and phi specs
gamma_hyper_list <- get_gamma_specs(dsp_data)
phi_specs <- get_phi_specs()
# TODO: need to insert a way to add priors for UGen
# start timer
start_time <- proc.time()
out <- dsp_(u_rcpp = dsp_data$U,
x_rcpp = dsp_data$intercourse$X,
w_day_blocks = dsp_data$w_day_blocks,
w_to_days_idx = dsp_data$w_to_days_idx,
w_cyc_to_subj_idx = dsp_data$w_cyc_to_subj_idx,
subj_day_blocks = dsp_data$subj_day_blocks,
day_to_subj_idx = dsp_data$day_to_subj_idx,
gamma_specs = gamma_hyper_list,
phi_specs = phi_specs,
# x_miss_cyc = dsp_data$intercourse$miss_cyc,
x_miss = dsp_data$x_miss,
# x_miss_day = dsp_data$intercourse$miss_day,
sex_miss_to_w = dsp_data$sex_miss_to_w,
utau_rcpp = dsp_data$utau,
tau_coefs = dsp_data$tau_fit,
u_miss_info = dsp_data$u_miss_info,
u_miss_type = dsp_data$u_miss_type,
u_preg_map = dsp_data$cov_miss_w_idx,
u_sex_map = dsp_data$cov_miss_x_idx,
fw_len = 5L,
n_burn = 0L,
n_samp = n_samp)
# end timer
run_time <- proc.time() - start_time
# transpose data
coefs_trans <- matrix(out$coefs,
nrow = n_samp,
ncol = ncol(dsp_data$U),
byrow = TRUE,
dimnames = list(NULL, colnames(dsp_data$U)))
xi_trans <- matrix(out$xi,
nrow = n_samp,
byrow = TRUE)
list(coefs = coefs_trans,
xi = xi_trans,
phi = out$phi,
ugen = out$ugen,
run_time = run_time)
}
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