As such, it appears I would not have permissions to upload this article or any images from the article to this repository. As I cannot identify a green open-access version of the article, I will just be able to include cited text quotations.
10.38-10.47: Consensus on upload of code
RE: my uncertainty yesterday as to uploading code with commits more recent than the publication date, I discussed this with Tom, and we agreed that I should take a similar approach to as we do when we make environments for projects without them: start with the latest version of the code, and then if things don’t work, potentially go back in the commit history to help resolve it.
As such, I then uploaded a copy of the relevant branch of the repository to original_study/.
10.50-10.52: Update license
Switch to GNU General Public License version 3 to match original study. The requirements of this license are to:
Include a copy of the full license
State all significant changes made to the software
Make the original source code available when distributing binaries based on that work
Include a copy of the original copyright notice
It allows the code to be changed and distributed to others (as long as release under GPL v3 also).
10.53-11.01: Complete page about original study and license
As cannot upload anything from the study, just provided links.
11.09-11.22, 11.29-11.38, 12.04-12.24: Read the article and outline scope
Read through the article and identified scope as:
Table 3
Figure 3
Supp Appendix 6 (Figure)
Figure 4
Supp Appendix 7 (Figure)
There was one section of text not explicitly in the tables or figures, but it is an easy calculation from the values in Table 3, and so I feel the reproduction of Table 3 encompasses it. This was:
“This scenario (S1a) was associated with an incremental cost of $188 and an incremental effectiveness of 0.009 QALYs per eligible patient relative to the CDQ ≥ 16.5 points among ever smokers at 5-year intervals (S3b), resulting in an ICER of $22,044/QALY.”
This is just calculated from the table - $2438 - $2250 = $188
12.560 - 12.552 = 0.008 (likely rounding related)
ICER = 188 / 0.008 = $23,500/QALY
I outlined this on the scope.qmd page.
Tom later emailed to confirm he was likewise happy with this scope.
Timings
import syssys.path.append('../')from timings import calculate_times# Minutes used prior to todayused_to_date =32# Times from todaytimes = [ ('09.44', '09.48'), ('09.52', '09.56'), ('10.38', '10.47'), ('10.50', '10.52'), ('10.53', '11.01'), ('11.09', '11.22'), ('11.29', '11.38'), ('12.04', '12.24')]calculate_times(used_to_date, times)
Time spent today: 69m, or 1h 9m
Total used to date: 101m, or 1h 41m
Time remaining: 2299m, or 38h 19m
Used 4.2% of 40 hours max