In higgi13425/ggconsort: Creates CONSORT Diagrams for RCTs

options(htmltools.dir.version = FALSE)
library(xaringan)
library(xaringanthemer)
library(tidyverse)
source('create_status_tables.R')

library(xaringanthemer)
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What Are CONSORT diagrams?

To promote transparency

In clinical trials, a CONSORT diagram shows the flow of participants from screening to analysis, while identifying and providing reasons for dropout or exclusion of participants at each step along the way.

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CONSORT diagrams

Endorsed by most medical journals

.pull-left[ CONSORT = Consolidated Standards of Reporting Trials, developed by the CONSORT group, http://www.consort-statement.org, which started in 1993 to improve the quality of reporting of clinical trials. ] .pull-right[ ]

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An Artisanal Product

• CONSORT diagrams are now commonly used to report RCTs,
  but the template provided does not provide:
• An underlying data structure, or
• Best practices for building a diagram.
• The CONSORT diagram has become an artisanal product
• Usually built by counting categories and
• Copy/pasting results into templates.
• This leads to frequent errors in which the participant numbers don't add up.
• Most CONSORT diagrams are built from templates in
• MS Word
• Powerpoint, or
• Adobe Illustrator.
• Note: there is a way to do this in SAS, with PROC SGPLOT https://www.sas.com/content/dam/SAS/support/en/sas-global-forum-proceedings/2019/3149-2019.pdf

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{ggconsort} as an Idea

knitr::include_graphics("images/rpubs_consort.png")

- https://rpubs.com/phiggins/461686

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Limitations

• This is still being done by hand, not reproducible

• I would like to make this programmatic

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{ggconsort} Goal: One Function

draw_consort(status_table)

• any # of arms from 2 to 8 (or more)

• can control text wrap with \n or str_wrap(25)

• fits boxes to height, width of text

• creates lines and arrows to box center edges

• sets standard vertical and horizontal spacing between boxes, lines

• creates plot area sufficient to contain diagram

• then draws the diagram

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What is the Underlying Data Structure?

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Two Parts to CONSORT - N = 1 and N = n_arms

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Naming and labeling components

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Data Model: the Status Table

• One row per candidate participant, with their status at each step of the study

• Includes both:

• randomized participants, and

• candidate participants excluded (aka screen failures)

• (optional) column - studyid

• column randomized - Yes or NA
• column exc_reason - Text or NA
• column arm - Text per Arm or NA
• column recieved_int - Yes or NA
• column dnr_int_reason - Text or NA
• column completed - Yes or NA
• column discontinued_reason - Text or NA
• column analyzed - Yes or NA
• column not_an_reason - Text or NA

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Example Data - status_tables

• I built examples from actual clinical trials, numbered by # of arms

• status2 - (Indomethacin vs Placebo)

• status3 - (Aza vs IFX vs Aza/IFX combo)
• status4 - (Placebo vs 5,10,15 mg tofacitinib)
• status5 - (Placebo vs 4 doses of upadacitinib)
• status8 - (8 interventions to increase uptake of flu vaccine)

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Glimpse of a Status Table

glimpse(status2)

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Conceptual Model for Drawing CONSORT

• Build a top_tbl

- Then ggplot

ggplot(top_tbl) +
  geom_rect(aes(xmin = xmin, xmax=xmax, ymin=ymin, ymax=ymax)) +
  geom_text(aes(x=xcenter, y = ycenter, label= label)) +
  geom_segment(aes(x=x, xend=xend, y=y, yend=yend))

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Conceptual Model

• Build a bottom_n_tbl
• Shown here are just the assignment rows

- Then ggplot

ggplot(bottom_n_tbl) +
  geom_rect(aes(xmin = xmin, xmax=xmax, ymin=ymin, ymax=ymax)) +
  geom_text(aes(x=xcenter, y = ycenter, label= label)) +
  geom_segment(aes(x=x, xend=xend, y=y, yend=yend))

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Helper Functions in Place

• count_arms, list_arms

• for individual labels: filter and count #, glue to text for each box

• for complex labels: count exclusions, build mini-table, add total row, move to top line, collapse to text string with newlines

• Does not handle zeroes well (no discontinuations)

• build top_tbl

• (in progress) build bottom_n_tbl

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Problems

• I don't know enough about ggplot internals
• Hard to consistently convert char_width to x values on ggplot
• Hard to consistently convert lines to y values on ggplot
• Adding more rows of boxes = self-adjusting ggplot size shrinks previous boxes - labels no longer fit
• Would this be easier with the {ggtext} package?
• but lacks return values for box location
• Actually building a whole package with tests, roxygen documentation, pkgdown website
• This is way beyond what I have ever done

• There is no way I could maintain a package alone.

• Help needed

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Aspiration: Package / Repository

.center[ https://github.com/higgi13425/ggconsort ]

knitr::include_graphics("images/github-ggconsort.png")

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The Aspirational Hex Sticker

knitr::include_graphics("images/hex-ggconsort.png")

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Help (Collaborators) Needed!

• This is just a proof of concept, not a proper package.

Aspirational Goals

• Tests, especially on status_table input
• e.g. Actual software dev by people who know what they are doing
• Can this work across Graphics Devices (not just MacOS/RStudio)?
• Helper functions to take standard data formats and make a status_table from:
• SDTM data format?
• ADaM data format?
• Ability to work with data in the wild (1/0, "No"/Yes", "Completed")
• Not just carefully curated data
• Useful vignettes
• A proper package (roxygen2) and a useful {pkgdown} site
• More options, customization - currently like the original Model T.
• You can have any font or spacing that you want, as long as it is the default.

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Thanks for your Help!

higgi13425/ggconsort documentation built on June 14, 2024, 6:48 p.m.