compute.tsme — compute.tsme • qrme

does the heavy lifting for computing nonlinear models with measurement error

Usage

compute.tsme(
  data,
  y_formula,
  t_formula,
  tau,
  t_values,
  x_data = NULL,
  me_distribution = "gaussian",
  copula = "gaussian",
  mcmc_method = "MH",
  n_copula_me_draws = 100L,
  report_transition_matrix = TRUE,
  report_spearman = TRUE,
  report_upward_mobility = TRUE,
  report_poverty = TRUE,
  pov_line = log(20000),
  report_quantiles = c(0.1, 0.5, 0.9),
  y_n_mix = 1,
  t_n_mix = 1,
  tol = NULL,
  conv_criterion = "params",
  loglik_draws = 100L,
  conv_patience = 1L,
  max_em_iters = 100L,
  mcmc_draws = 200,
  mcmc_burn_in = 100,
  proposal_sd = NULL,
  start_sigma_y = NULL,
  start_mu_y = NULL,
  start_pi_y = NULL,
  start_sigma_t = NULL,
  start_mu_t = NULL,
  start_pi_t = NULL,
  n_copula_draws = 100L,
  ignore_me = FALSE,
  verbose = FALSE
)

Arguments

data: data.frame
y_formula: formula for outcome model
t_formula: formula for treatment model
tau: values of tau to estimate first step quantile regressions for
t_values: values of the treatment to compute conditional distribution-type parameters for
x_data: matrix of values of covariates to average over for conditional distribution-type parameters. The default is NULL and in this case all covariates in the data will be averaged over. A main alternative would be to pass in a single row with particular values of covariates of interest.
me_distribution: the distribution of the measurement error. "gaussian" is the default and supports a mixture of normals. "laplace" is also supported
copula: what type of copula to use in second step. Options are "gaussian" (the default), "clayton", "gumbel", or "frank"
mcmc_method: simulation step to use in the EM algorithm. Currently only "MH" is supported.
n_copula_me_draws: Number of measurement-error draws used in the second-stage copula likelihood (default 100). Increase this for a less noisy copula likelihood at the cost of speed.
report_transition_matrix: whether or not to report a transition matrix
report_spearman: whether or not to report Spearman's rho (rank-rank correlation)
report_upward_mobility: whether or not to report upward mobility parameters
report_poverty: whether or not to report fraction of population below the poverty line as a function of parents' income
pov_line: value of the poverty line (default log(20000))
report_quantiles: quantiles of child's income as a function of parents' income to report (default is .1,.5,.9)
y_n_mix: Number of Gaussian mixture components for the outcome (Y) measurement error distribution. Default is 1 (single Gaussian). Use logLik(), AIC(), and BIC() on a fitted qrme() object to select the appropriate value. y_n_mix and t_n_mix can differ – it is valid and common to use different complexity for each equation.
t_n_mix: Number of Gaussian mixture components for the treatment (T) measurement error distribution. Default is 1. See y_n_mix.
tol: Convergence tolerance. When NULL (default), a value is chosen automatically based on conv_criterion. See em.algo for details.
conv_criterion: Convergence criterion passed to qrme: "params" (default) or "loglik". See em.algo.
loglik_draws: Number of Monte Carlo draws for the log-likelihood convergence check when conv_criterion = "loglik" (default 100). Ignored when conv_criterion = "params".
conv_patience: Integer. Consecutive iterations that must satisfy the convergence criterion before stopping (default 1).
max_em_iters: Maximum number of EM outer iterations per qrme call (default 100).
mcmc_draws: total number of MCMC draws per EM step (default 200)
mcmc_burn_in: number of MCMC draws to discard as burnin (default 100)
proposal_sd: Standard deviation of the MH proposal used in the two first-stage qrme calls. When NULL (default), each first stage uses its own automatic scale, sqrt(var(Y)) or sqrt(var(T)).
start_sigma_y: Starting value(s) for the ME standard deviation(s) in the outcome (Y) qrme call. A vector of length y_n_mix. When NULL (default), qrme chooses its own starting value.
start_mu_y: Starting value(s) for the ME mean(s) in the outcome (Y) qrme call. A vector of length y_n_mix. NULL uses the qrme default.
start_pi_y: Starting mixture weight(s) for the outcome (Y) qrme call. A vector of length y_n_mix that sums to 1. NULL uses the qrme default.
start_sigma_t: Starting value(s) for the ME standard deviation(s) in the treatment (T) qrme call. A vector of length t_n_mix. NULL uses the qrme default.
start_mu_t: Starting value(s) for the ME mean(s) in the treatment (T) qrme call. NULL uses the qrme default.
start_pi_t: Starting mixture weight(s) for the treatment (T) qrme call. NULL uses the qrme default.
n_copula_draws: Number of copula draws per covariate row used to compute mobility summaries such as transition matrices and rank correlations (default 100).
ignore_me: whether or not to ignore measurement error (this is primarily a way to get speedy calculations using copula-based approach)
verbose: Logical or nonnegative integer. If FALSE (default), suppresses progress output. If TRUE or 1, reports major computational stages, EM iteration numbers, and convergence diagnostics. If 2, also reports qrme-native details such as pi, mu, sigma, tolerance, finite-mixture summaries, and the no-measurement-error comparison copula step. If 3 or larger, also reports raw normalmixEM() output, which uses lambda for mixture probabilities.