run_options: Design options
In DanChaltiel/nih.joinpoint: R Interface for NIH's Joinpoint Regression Software

View source: R/options_run.R

run_options

R Documentation

Design options

Description

Create a character representation of the .ini file needed for run options.

Usage

run_options(
  model = c("linear", "ln"),
  data_shift = 0,
  min_joinpoints = 0,
  max_joinpoints = 4,
  pairwise = NULL,
  pairwise_signif_lvl = 0.05,
  pairwise_n_permut = 4499,
  method = c("grid", "hudsons"),
  min_obs_end = 2,
  min_obs_between = 2,
  n_obs_between = 0,
  model_selection_method = c("permutation test", "bic", "mbic",
    "data dependent selection", "wbic", "wbic-alt"),
  permutation_signif_lvl = 0.05,
  n_permutations = 4499,
  early_stopping = c("b-value", "curtailed", "fixed"),
  run_type = c("calculated", "provided"),
  rates_per_n = 1e+05,
  dependent_variable_type = c("count", "crude rate", "age-adjusted rate", "proportion",
    "percent"),
  het_error = c("constant variance", "standard error", "poisson rate", "poisson count"),
  het_error_var_location = NULL,
  ci_method = c("parametric", "empirical quantile method 1",
    "empirical quantile method 2"),
  n_cores = 1,
  delay_type = c("delay", "non-delay", "both"),
  autocorr_errors = c("number", "estimated"),
  jump_model = FALSE,
  comparability_ratio = FALSE,
  include_std_analysis = FALSE,
  jump_location = 9999,
  comparability_ratio_value = 0,
  cr_variance = 0,
  joinpoint_alpha_lvl = 0.05,
  apc_alpha_lvl = 0.05,
  aapc_alpha_lvl = 0.05,
  jump_cr_alpha_lvl = 0.05,
  random_seed = 7160,
  empirical_quantile_seed = 10000,
  empirical_quantile_seed_type = c("constant", "varying"),
  n_resample = 1000,
  madwd = FALSE,
  madwd_psi = 0
)

Arguments

`model`	one of `c("linear", "ln")`
`data_shift`	data_shift
`min_joinpoints`	min_joinpoints
`max_joinpoints`	max_joinpoints
`pairwise`	pairwise
`pairwise_signif_lvl`	pairwise_signif_lvl
`pairwise_n_permut`	pairwise_n_permut
`method`	method
`min_obs_end`	min_obs_end
`min_obs_between`	min_obs_between
`n_obs_between`	n_obs_between
`model_selection_method`	model_selection_method
`permutation_signif_lvl`	permutation_signif_lvl
`n_permutations`	n_permutations
`early_stopping`	early_stopping
`run_type`	run_type
`rates_per_n`	rates_per_n
`dependent_variable_type`	dependent_variable_type
`het_error`	het_error
`het_error_var_location`	het_error_var_location
`ci_method`	ci_method
`n_cores`	n_cores
`delay_type`	delay_type
`autocorr_errors`	autocorr_errors
`jump_model`	jump_model
`comparability_ratio`	comparability_ratio
`include_std_analysis`	include_std_analysis
`jump_location`	jump_location
`comparability_ratio_value`	comparability_ratio_value
`cr_variance`	cr_variance
`joinpoint_alpha_lvl`	joinpoint_alpha_lvl
`apc_alpha_lvl`	apc_alpha_lvl
`aapc_alpha_lvl`	aapc_alpha_lvl
`jump_cr_alpha_lvl`	jump_cr_alpha_lvl
`random_seed`	random_seed
`empirical_quantile_seed`	empirical_quantile_seed
`empirical_quantile_seed_type`	empirical_quantile_seed_type
`n_resample`	n_resample
`madwd`	madwd
`madwd_psi`	madwd_psi