pedmod_profile_nleq | R Documentation |
Computes Profile Likelihood Based Confidence Intervals for a Nonlinear Transformation of the Variables
pedmod_profile_nleq( ptr, par, maxvls, minvls = -1L, alpha = 0.05, abs_eps, rel_eps, heq, heq_bounds = c(-Inf, Inf), delta, indices = NULL, maxvls_start = max(100L, as.integer(ceiling(maxvls/5))), minvls_start = if (minvls < 0) minvls else minvls/5, do_reorder = TRUE, use_aprx = FALSE, n_threads = 1L, cluster_weights = NULL, method = 0L, seed = 1L, verbose = FALSE, max_step = 15L, use_tilting = FALSE, vls_scales = NULL, control.outer = list(itmax = 100L, method = "BFGS", kkt2.check = FALSE, trace = FALSE), control.optim = list(fnscale = get_n_terms(ptr)), ... )
ptr |
object from |
par |
numeric vector with the maximum likelihood estimator e.g. from
|
maxvls |
maximum number of samples in the approximation for each marginal likelihood term. |
minvls |
minimum number of samples for each marginal likelihood term. Negative values provides a default which depends on the dimension of the integration. |
alpha |
numeric scalar with the confidence level required. |
abs_eps |
absolute convergence threshold for
|
rel_eps |
rel_eps convergence threshold for
|
heq |
function that returns a one dimensional numerical vector which should be profiled. It does not need to evaluate to zero at the maximum likelihood estimator. |
heq_bounds |
two dimensional numerical vector with bounds for
|
delta |
numeric scalar with an initial step to take. Subsequent steps
are taken by |
indices |
zero-based vector with indices of which log marginal
likelihood terms to include. Use |
maxvls_start, minvls_start |
number of samples to use when finding the initial values for the optimization. |
do_reorder |
|
use_aprx |
|
n_threads |
number of threads to use. |
cluster_weights |
numeric vector with weights for each cluster. Use
|
method |
integer with the method to use. Zero yields randomized Korobov lattice rules while one yields scrambled Sobol sequences. |
seed |
seed to pass to |
verbose |
logical for whether output should be printed to the console during the estimation of the profile likelihood curve. |
max_step |
integer scalar with the maximum number of steps to take in either directions. |
use_tilting |
|
vls_scales |
can be a numeric vector with a positive scalar for each
cluster. Then |
control.outer, control.optim, ... |
arguments passed to
|
pedmod_opt
, pedmod_sqn
,
pedmod_profile
, and pedmod_profile_prop
.
# similar examples to that in help("pedmod_profile_prop") K <- matrix(c( 0.5 , 0 , 0.25 , 0 , 0.25 , 0 , 0.125 , 0.125 , 0.125 , 0.125 , 0 , 0.5 , 0.25 , 0 , 0.25 , 0 , 0.125 , 0.125 , 0.125 , 0.125 , 0.25 , 0.25 , 0.5 , 0 , 0.25 , 0 , 0.25 , 0.25 , 0.125 , 0.125 , 0 , 0 , 0 , 0.5 , 0 , 0 , 0.25 , 0.25 , 0 , 0 , 0.25 , 0.25 , 0.25 , 0 , 0.5 , 0 , 0.125 , 0.125 , 0.25 , 0.25 , 0 , 0 , 0 , 0 , 0 , 0.5 , 0 , 0 , 0.25 , 0.25 , 0.125, 0.125, 0.25 , 0.25, 0.125, 0 , 0.5 , 0.25 , 0.0625, 0.0625, 0.125, 0.125, 0.25 , 0.25, 0.125, 0 , 0.25 , 0.5 , 0.0625, 0.0625, 0.125, 0.125, 0.125, 0 , 0.25 , 0.25, 0.0625, 0.0625, 0.5 , 0.25 , 0.125, 0.125, 0.125, 0 , 0.25 , 0.25, 0.0625, 0.0625, 0.25 , 0.5 ), 10) C <- matrix(c( 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1 ), 10L) # simulates a data set. # # Args: # n_fams: number of families. # beta: the fixed effect coefficients. # sig_sq: the scale parameters. sim_dat <- function(n_fams, beta = c(-1, 1, 2), sig_sq = c(3, 1)){ # setup before the simulations Cmat <- 2 * K n_obs <- NROW(K) Sig <- diag(n_obs) + sig_sq[1] * Cmat + sig_sq[2] * C Sig_chol <- chol(Sig) # simulate the data out <- replicate( n_fams, { # simulate covariates X <- cbind(`(Intercept)` = 1, Continuous = rnorm(n_obs), Binary = runif(n_obs) > .5) # assign the linear predictor + noise eta <- drop(X %*% beta) + drop(rnorm(n_obs) %*% Sig_chol) # return the list in the format needed for the package list(y = as.numeric(eta > 0), X = X, scale_mats = list(genetic = Cmat, environment = C)) }, simplify = FALSE) # add attributes with the true values and return attributes(out) <- list(beta = beta, sig_sq = sig_sq) out } # simulate the data set.seed(1) dat <- sim_dat(200L) # fit the model ptr <- pedigree_ll_terms(dat, max_threads = 2L) start <- pedmod_start(ptr = ptr, data = dat, n_threads = 2L) fit <- pedmod_opt(ptr = ptr, par = start$par, use_aprx = TRUE, n_threads = 2L, maxvls = 5000L, minvls = 1000L, abs_eps = 0, rel_eps = 1e-3) fit$par # the estimate # 90% likelihood ratio based confidence interval for the proportion of variance # of the genetic effect heq <- function(par){ vars <- exp(tail(par, 2)) vars[1] / (1 + sum(vars)) } heq(fit$par) prof_out_nleq <- pedmod_profile_nleq( ptr = ptr, fit$par, maxvls = 2500L, minvls = 500L, alpha = .1, abs_eps = 0, rel_eps = 1e-3, verbose = TRUE, use_aprx = TRUE, heq = heq, heq_bounds = c(0, Inf), delta = .2, n_threads = 2L) prof_out_nleq$confs # the confidence interval for the proportion # plot the log profile likelihood plot(prof_out_nleq$xs, prof_out_nleq$p_log_Lik, pch = 16, xlab = "proportion of variance", ylab = "log profile likelihood") abline(v = prof_out_nleq$confs, lty = 2)
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