Manuscript export workflow • dynasimR

This vignette shows how to get from raw simulation output to a publication-quality document with automatically filled [XX_*] placeholders.

1. LaTeX tables

library(dynasimR)
sim <- load_example_data()
pol <- policy_effect(sim,
  policy_a_scenario = "A-S08",
  policy_b_scenario = "A-S07")

export_latex_table(
  data     = pol$effect_sizes,
  filename = "table_policy.tex",
  caption  = "Policy effect sizes (Cohen's d and risk difference).",
  label    = "policy",
  note     = "n = 50 replications per scenario."
)

The generated .tex uses \botrule and escapes </> in character cells for compatibility with common publisher templates.

2. Figures at publication dimensions

km <- km_estimate(sim, endpoint = "stage2")
export_figure(
  plot      = plot_km(km),
  filename  = "figure_km.pdf",
  width_mm  = 174,          # single column
  height_mm = 110
)

3. Placeholder substitution in the .tex body

Given a source manuscript.tex with placeholders like [XX_POLICY_DELTA_EVENT], substitute them in one call:

reps <- fill_placeholders(
  sim_data          = sim,
  tex_file          = "manuscript.tex",
  output_file       = "manuscript_filled.tex",
  policy_a_scenario = "A-S08",
  policy_b_scenario = "A-S07",
  baseline_scenario = "A-S00"
)
reps          # named character vector of substitutions performed

Complete placeholder list

Placeholder	Source
`[XX_POLICY_DELTA_EVENT]`	`policy_effect()`
`[XX_POLICY_DELTA_CI_LO]`	`policy_effect()`
`[XX_POLICY_DELTA_CI_HI]`	`policy_effect()`
`[XX_COMPLIANCE_A]`	`compute_compliance_index()`
`[XX_COMPLIANCE_B]`	`compute_compliance_index()`
`[XX_OPTIMAL_AL]`	`al_efficiency()`
`[XX_EVENT_BASELINE]`	median event rate at baseline scenario
`[XX_EVENT_BEST]`	min median event rate across all scenarios