PACE trial TSC and TMG minutes released

Lucibee said:
I think Graham's already done that. But I'm not sure it helps without knowing what they did.
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I did it anyway, just in case, and for my own amusement.

fitness_pace-png.2521

fitness_pace_calculated.png

There are 4 measurements for each data point on the graph.
 
Luther Blissett said:
I did it anyway, just in case, and for my own amusement
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I had done the same thing about three years ago, but I also captured the error bar ranges for both the fitness and Borg/% max HR. I would have used some open source graph digitising software like http://markummitchell.github.io/engauge-digitizer/ but I know longer know exactly which one I used. I would have attached spreadsheet files but the forum software doesn't seem to allow that.

In both cases, the data is extracted from Figure 2 of Chalder et al, Lancet Psychiatry 2015; 2: 141-52, Rehabilitative therapies for chronic fatigue syndrome: a secondary mediation analysis of the PACE trial. I extracted the image directly from the pdf at high resolution using Gimp before digitising.

Columns Upper and Lower are the upper and lower extent of the error bar respectively. Any difference with Graham or Luther's values should give an indication of the error involved in this sort of digitising from the published graph.
Code: 
Fitness:

APT
   Time
  (weeks)  Mean  Upper  Lower
     0     1.60   1.74   1.46
    12     1.52   1.64   1.41
    24     1.67   1.79   1.54
    52     1.99   2.34   1.63

CBT
   Time
  (weeks)  Mean  Upper  Lower
     0     1.75   1.97   1.55
    12     1.65   1.81   1.49
    24     1.72   1.90   1.55
    52     1.85   2.11   1.59

GET
   Time
  (weeks)  Mean  Upper  Lower
     0     1.73   2.01   1.46
    12     1.86   2.13   1.59
    24     1.90   2.16   1.64
    52     1.84   2.02   1.66

SMC
   Time
  (weeks)  Mean  Upper  Lower
     0     1.84   2.05   1.62
    12     1.90   2.13   1.67
    24     1.83   1.99   1.66
    52     2.01   2.34   1.67

Code: 
Borg/% max HR reached

APT
   Time
  (weeks)  Mean   Upper  Lower
     0     0.203  0.211  0.194
    12     0.197  0.204  0.190
    24     0.194  0.203  0.185
    52     0.195  0.205  0.185

CBT
   Time
  (weeks)  Mean   Upper  Lower
     0     0.195  0.203  0.188
    12     0.190  0.197  0.182
    24     0.184  0.193  0.175
    52     0.184  0.193  0.175

GET
   Time
  (weeks)  Mean   Upper  Lower
     0     0.197  0.205  0.190
    12     0.193  0.201  0.185
    24     0.186  0.194  0.178
    52     0.179  0.188  0.170

SMC
   Time
  (weeks)  Mean   Upper  Lower
     0     0.205  0.213  0.197
    12     0.200  0.209  0.190
    24     0.200  0.208  0.192
    52     0.197  0.207  0.186
 
Lucibee said:
Please be aware that taking the values from the graphs printed in The Lancet is not going to be accurate. All graphs are redrawn, so are at best an approximation.
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I'm not sure exactly what you mean by this. In my day (20 years ago) in physics we would supply a graph in digital format (usually postscript) and the reproduction in the journal would be generated from that. I'm pretty sure the method I used would reliably reproduce data from graphs I published. Do they do something different in medicine?
 
BruceInOz said:
I'm not sure exactly what you mean by this. In my day (20 years ago) in physics we would supply a graph in digital format (usually postscript) and the reproduction in the journal would be generated from that. I'm pretty sure the method I used would reliably reproduce data from graphs I published. Do they do something different in medicine?
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Granted. In my day was 20 years ago, so I would hope things have changed by now!

Update: I've checked the Lancet Illustrators guide. As long as they get the graphs in eps (or another vector-based) format, they can reproduce them fairly accurately. But I know from experience that mistakes still get made. And we don't know what they were sent. If they were saved as png or tiff, then that info will have been lost.
 
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My feeling is that if this the only way they have chosen to publish their data then digitising in this way to make comparisons and draw conclusions is legitimate, providing that a description of how the data was obtained from the published graph is provided. If the graph is wrong, that's their problem.
 
Someone mentioned a link to a Powerpoint set of slides of the graphs, and they were in much higher resolution. I copied them into Photoshop, and constructed a grid to the appropriate size so that I could read the values more accurately, which I did.

Then, while asking an editor if it was acceptable to use data from the graphs in another analysis, I was given this link to baseline and 52 week data on a wide range of items. (http://www.thelancet.com/cms/attachment/2044286192/2056345919/mmc1.pdf): it is an appendix to Chalder's paper on moderating factors.

Comparing the two, I was only out by a few percent (i.e. for 1.75 I would be out by about 0.02), which was remarkable. I assumed therefore that my intermediate values were fine.

In the end though, I only used the baseline and 52 week data.

Sorry to be so slow in responding! I was struggling to remember what had happened.
 
BruceInOz said:
My feeling is that if this the only way they have chosen to publish their data then digitising in this way to make comparisons and draw conclusions is legitimate, providing that a description of how the data was obtained from the published graph is provided. If the graph is wrong, that's their problem.
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I would be inclined to agree. If they are unwilling to release the data or fully disclose the methods they used to obtain it, then we are forced to take it at face value, and forced to make assumptions about it. That's why transparency is so much more advisable than trying to hide the data.

And if we do take it at face value, then those in the APT and SMC groups improved their 'fitness' more than those in the CBT and GET groups, albeit non-significantly. Oops.
 
Just noticed that the appendix to the Chalder et al Lancet Psychiatry 2015 paper linked to by Graham above does have the fitness data at 0 and 12 weeks in Table D. My digitised values agree to within +/- 1 in the third significant figure for the mean and upper and lower bounds. I think this verifies that the digitisation method is pretty reliable.

ETA. cross posted
 
BruceInOz said:
Just noticed that the appendix to the Chalder et al Lancet Psychiatry 2015 paper linked to by Graham above does have the fitness data at 0 and 12 weeks in Table D. My digitised values agree to within +/- 1 in the third significant figure for the mean and upper and lower bounds. I think this verifies that the digitisation method is pretty reliable.

ETA. cross posted
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The frustration is that it doesn't let us quote them which I suspect is why they won't publish numbers and why the I suspect they also dropped it as a secondary outcome.

From the published protocol list of secondary outcomes.

9. The self-paced step test of fitness [43].
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Its not mentioned as a secondary outcome in the stats plan and so the question is whether they got approval for this protocol change or if it was just implied in an approval of the stats plan (even though explicit approval of that is not mentioned in the TSC minutes).

I believe a stats plan is not a replacement for a protocol (they even suggest this in their own stats plan) but a more detailed plan of how to conduct the analysis. So I can't see from the evidence we have around the TSC minutes that they had permission to drop this measure as a secondary outcome of the trial.
 
janice said:
Yes Invisible Woman I get worse HR values if in PEM.

Although I wonder if anyone could recommend a precise and accurate wrist HR monitor for continuous use in day ? My cheap £30 one seems to show some v high rate which I'm not sure are accurate or precise.

I'd love to be able to use an objective measure so that I can stop tipping into that poisoned PEM state?
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I’ve found the Wahoo Tickr Fit to be helpful: 30 Hour battery life, can set wise wrists of audio announcements & programme HR bands. Needs to be near smartphone & all info displayed & managed via App.
 
Trish said:
The graph shows values around 1.5 to 2. This can be easily obtained with a different assumption about the heart rate part of the formula.

For example, take a 30 year old male with a resting heart rate of 70, a predicted max heart rate of 190 and an actual max heart rate in the test of 110.

This would give the %HRR as
(110 - 70 ) / (190 - 70 ) = 40 / 120 = 0.33 = 33%

This leads to a result for the step test of:
6593 / (125 x 33) = 1.6

What we need is a few people to try it!
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When should the resting heart rate be measured? E.g. over the day, my resting heart rate is relatively high, at night and in the morning it's around 50.

How long should the test last? 120s? Does it include going downstairs or only upstairs?
Short: I would try it, but I wouldn't do maximum strength (I don't know where that would lead - well, I do now that I think about it), i.e. I would rest as soon as the knees burn and the heart rate goes up too high - would that be ok? And I don't know every detail, so a brief how-to would be helpful.
 
Inara said:
When should the resting heart rate be measured? E.g. over the day, my resting heart rate is relatively high, at night and in the morning it's around 50.

How long should the test last? 120s? Does it include going downstairs or only upstairs?
Short: I would try it, but I wouldn't do maximum strength (I don't know where that would lead - well, I do now that I think about it), i.e. I would rest as soon as the knees burn and the heart rate goes up too high - would that be ok? And I don't know every detail, so a brief how-to would be helpful.
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You know what? I really wouldn't, unless you can normally cope going up and down 3 flights of stairs. Because that's what it's equivalent to.
 
Why not? They have published a graph. We quote the numbers obtained from the graph, perhaps with a footnote that the numbers were requested but denied.
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I actually wrote to the editor and explained what I wanted to do - to extract the data from the graphs and use them in an article on CBT and CFS - and explained that I had tried to get hold of the data from the authors and had been refused - "vexatious". The editor, who I will leave as anonymous, was clearly sympathetic and wrote " We publish data precisely so that researchers, clinicians, and other readers (including patients) can read it and interpret it. So it’s not really for me to give or deny permission for you to use the data from the paper however you see fit. " The editor also gave me the link to that appendix, commenting that it was there to be used, and that only if I wanted to reproduce the graphs themselves would I need to ask for permission. I also got some useful writing tips. My interpretation was that the editor was sympathetic, but subject to higher powers.

In fact, in my article in the JHoP, I said something almost exactly along the lines suggested by Bruce within the main text, including "vexatious".
 
Keela Too said:
Interesting too that Resting HR affects the score.

I notice that now I've got ME I have a higher resting HR than I used to have.
Also if I go somewhere (eg going for a test like this) my HR stays higher again just from being out and about.
So, I wonder, how they ensure they have a sound Resting HR measure.

And putting a higher resting HR into this equation would decrease the %HRR score. Hmmmm
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Presumably this is because the observation is change of HR commensurate with change of applied power (change of energy conversion rate)?
 
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