Converting Choosing a PK Metric into a PMX Tools page
Working specification
Converted on 2026-09-02. One figure is missing. The page is live at Selecting an Exposure Metric and linked from the Scoping section of PMX Tools. Section 4 holds what remains.
1. Goal
PK_Choosing_Metric_public.Rmd becomes a page on this site, so that the four questions it holds are readable in a browser, linkable from PMX Tools, and open on a network that blocks the original host.
The prose is Andy’s and stays his. The conversion changes the container and repairs the debris; it does not rewrite the argument.
2. What the source holds
An R Markdown file, 111 lines, with a Background section and four question-headed sections. It carries no computation: the only code chunk loads ggplot2, dplyr, stringr and xgxr, sets a seed and a theme, and nothing downstream uses any of it. The one figure is a PNG at Figures/Dumortier15_Tacrolimus_Concentration.png.
Two sources are cited inline, both by link rather than through the declared Bibliography.bib, which was not in the upload. They are listed in references.qmd.
3. What changed in the conversion
| Change | Why |
|---|---|
| The setup chunk is dropped | Nothing in the document computes anything, so the page renders without R and the site build stays free of a dependency |
bibliography: Bibliography.bib is dropped |
The file was not supplied, and both citations are inline links |
| Headings numbered and put in title case | The document is organized around four numbered questions, and the source headings were full sentences |
| E-R, NCA, PFS, OS, CRS and TMDD expanded at first use | The page is public and reaches readers outside pharmacometrics |
| An out-of-scope statement added at the top | The page chooses a metric; it does not run the analysis or build the PK model |
| The Dumortier figure replaced by prose | The image was not in the upload. Section 4. |
Four repairs, all of them debris from editing rather than changes of meaning:
A useful reference is from a [a comprehensive...]carried a doubled article.- The Dumortier sentence opened a parenthesis it never closed.
- Under chronic effects, the efficacy example read “Tumor reduction of a chemotherapy or liver toxicity that develops from prolonged exposure”. The second half is the safety example from the line above, pasted in. Cut.
- Under response affecting exposure, the PD-1 example had a stray closing parenthesis and then said the same thing twice in consecutive sentences. Merged into one.
4. What remains
The Dumortier figure. The source references Figures/Dumortier15_Tacrolimus_Concentration.png, which was not in the upload. The page currently describes in prose what the figure shows: daily tacrolimus concentration with organ rejection events drawn on it in black, most of them below the median. The description carries the argument, so the page is not broken without it, but the figure is the better version. Drop the PNG into files/ and it can go back in.
The two citations are unchecked. Neither paper has been read against what the page says about it. Both are marked ❌ in references.qmd.