samOptiPro/NAMESPACE at main · DIASPARAproject/samOptiPro · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
# Generated by roxygen2: do not edit by hand

export(.compile_mcmc_with_build)
export(as_mcmc_list)
export(as_mcmc_list_sop)
export(assess_performance)
export(assess_performance_vect)
export(build_conf_with_monitors)
export(checkInits)
export(checkInitsAndRun)
export(compute_WAIC)
export(compute_diag_from_mcmc)
export(compute_diag_from_mcmc_alt)
export(configure_hmc_safely)
export(configure_hmc_safely_bis)
export(configure_hmc_safely_parallel)
export(configure_hmc_safely_parallel_bis)
export(diagnose_model_structure)
export(diagnostics_by_target)
export(ensure_monitors_exist)
export(generate_all_convergence_and_metric_plots)
export(identify_bottlenecks_family)
export(merge_mcmc_samples)
export(monitors_sampled_from_conf)
export(monitors_sampled_safe)
export(normalize_constants_generic)
export(plot_bottlenecks)
export(plot_bottlenecks_fast)
export(plot_bottlenecks_index)
export(plot_convergence_checks)
export(plot_convergence_rhat_sampled_fast)
export(plot_family_ess_bar)
export(plot_family_rhat_bar)
export(plot_mcmc_histograms)
export(plot_strategies_from_test_result_hmc_fast)
export(profile_sampler_times)
export(proxy_step_sd)
export(run_baseline_coda)
export(run_baseline_config)
export(run_baseline_config_parallel)
export(run_baseline_config_parallel_bis)
export(run_custom_mcmc_parallel)
export(run_hmc_all_nodes)
export(run_hmc_all_nodes_parallel)
export(run_only_slice_parallel)
export(run_structure_and_hmc_test)
export(samOptiPro_options)
export(sampler_df_from_conf)
export(sampler_env_dump)
export(sampler_env_numeric_fields)
export(sampler_functions_from_conf)
export(sampler_scale)
export(sampler_scales_after_run)
export(sampler_scales_from_run)
export(sampler_targets)
export(test_strategy)
export(test_strategy_family)
importFrom(coda,as.mcmc)
importFrom(coda,mcmc)
importFrom(coda,mcmc.list)
importFrom(data.table,":=")
importFrom(ggplot2,aes_string)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_x_continuous)
importFrom(nimble,buildMCMC)
importFrom(nimble,compileNimble)
importFrom(nimble,nimbleOptions)
importFrom(stats,aggregate)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(stats,reorder)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(stats,start)
importFrom(utils,capture.output)
importFrom(utils,sessionInfo)
importFrom(utils,tail)