Add workflow vignette

_pkgdown.yml

@@ -68,3 +68,4 @@ articles:
   - modestWLRTVignette
   - pvalue_maxcomboVignette
   - simtrialroutines
+  - workflow

vignettes/workflow.Rmd

@@ -0,0 +1,109 @@
+---
+title: "TTE simulation data manipulations"
+author: "Keaven Anderson"
+output: rmarkdown::html_vignette
+bibliography: simtrial.bib
+vignette: >
+  %\VignetteIndexEntry{TTE simulation data manipulations}
+  %\VignetteEngine{knitr::rmarkdown}
+---
+
+```{r, include=FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+## Overview
+
+We attempt to provide a big picture view of what is involved in a clinical trial
+simulation with individual time-to-event data generated for each patient.
+Primary interest is in group sequential trials, usually with a single endpoint.
+However extensions could be made.
+
+## Results data table
+
+At the time of simulation planning an analysis plan for the trial is needed.
+For a group sequential design, a data table to store results is generated.
+Generally, the dimensions and variables planned for storage would be
+planned up front. As a simple example, if there is a group sequential design
+with 3 analyses planned, 15 data items for each analysis and 10,000 simulations
+planned, a data table with 30,000 rows and 15 columns has been used to store
+summary results. As each trial simulation proceeds, a row is updated with
+results for each analysis.
+
+## Simulated trial dataset generation
+
+For each simulated trial, an initial table is generated with information at a
+patient level. If trials are generated sequentially, the space needed for this
+data table could be re-used, never requiring allocation of more space.
+Each row contains data for a single patient. As an example, we could simulate
+a trial with 500 patients and 10 data items per patients.
+The data items would be in columns, the patients in rows.
+
+## Dataset manipulations for analysis
+
+Simulated trial data need to be manipulated to do any individual analysis
+(interim or final) for a clinical trial. The following operations are needed:
+
+1. Ordering data
+1. Selecting a subset for analysis
+1. Calculating individual patient results for the subset at the time of analysis.
+1. Performing statistical tests and computing treatment effect estimates
+   as well as other summaries that will included in the results summary dataset
+   described above. Types of computations needed are
+   1. Number of subjects by treatment group
+   1. Number of events by treatment group
+   1. Kaplan-Meier estimation of survival curves
+   1. Observed minus expected computations as well as weighting for logrank, weighted logrank calculations.
+   1. Using the survival package to compute hazard ratio estimates.
+
+## Flow for simulating group sequential: one scenario algorithm
+
+Group sequential design simulation flow:
+
+- Generate a trial.
+- Analyze repeatedly.
+- Summarize across simulated trials.
+
+```{r, echo=FALSE, fig.align="center", out.width="85%"}
+knitr::include_graphics("workflow.png")
+```
+
+```{r, echo=FALSE, eval=FALSE}
+g <- DiagrammeR::grViz("
+digraph boxes_and_diamonds {
+
+  # a 'graph' statement
+  graph [ordering = 'in']
+
+  # several 'node' statements
+  node [fontsize = '14', fontname = 'Arial']
+
+  node [shape = box, style = filled, fillcolor = '#d9d2e9'] 'Save analysis\n summary'; 'Cut data\n for analysis'; 'Analyze data';
+
+  node [shape = diamond, style = filled, fillcolor = '#fff2cc'] 'Final analysis?'
+  node [shape = diamond, style = filled, fillcolor = '#fff2cc'] 'Finished with\n all trials?'
+
+  node [shape = box, style = filled, fillcolor = '#e6b8af', label = 'Summarize across\n trials'] summarize
+
+  node [shape = box, style = filled, fillcolor = '#d9ead3', label = 'Scenario'] scenario
+  node [shape = box, style = filled, fillcolor = '#cfe2f3', label = 'Generate enrollment\n times'] enrollment
+  node [shape = box, style = filled, fillcolor = '#cfe2f3', label = 'Generate strata'] strata
+  node [shape = box, style = filled, fillcolor = '#cfe2f3', label = 'Randomize patients'] randomize 
+  node [shape = box, style = filled, fillcolor = '#cfe2f3', label = 'Generate outcomes'] outcomes
+  node [shape = box, style = filled, fillcolor = '#cfe2f3', label = 'Generate next\n trial'] next
+
+  scenario -> enrollment -> strata -> randomize -> outcomes
+  outcomes -> 'Cut data\n for analysis' -> 'Analyze data'->'Save analysis\n summary'
+  'Save analysis\n summary' -> 'Final analysis?'
+  'Final analysis?' -> 'Cut data\n for analysis' [label = 'No', fontname = 'Arial']
+  'Final analysis?' -> 'Finished with\n all trials?' [label = 'Yes', fontname = 'Arial']
+  'Finished with\n all trials?' -> summarize [label = 'Yes', fontname = 'Arial']
+  'Finished with\n all trials?' -> next [label = 'No', fontname = 'Arial']
+}
+")
+
+rsvg::rsvg_png(charToRaw(DiagrammeRsvg::export_svg(g)), file = "vignettes/workflow.png")
+```