Ngene code using constraints

[SuzannevD]

Dear reader,

For an international research project on Colorectal Cancer I am planning a DCE study. My team and I are researching what the preferences are for using AI in deciding on treatment options for patients. We have established the following attributes and levels:
AI involvement in selection treatment option:
1. Oncologists identify treatment options (No AI involvement)
2. Oncologists identify treatment options based on AI suggestions
3. Only AI identifies treatment options

Time Until Cancer Grows (Progression-free survival):
1. 3 months
2. 9 months
3. 12 months

Certainty of experienced severe side effects:
1. Yes, there is high certainty about the expected severe side effects from the treatment options.
2. No, there is no certainty about the expected severe side severe effects from the treatment options.

Risk of undertreatment:
(Restriction in design: should not be higher when AI is involved than when it is not)
The alternatives are:
1. High risk – 20%
2. Moderate risk – 10%
3. Low risk – 1%

Risk of overtreatment:
(restriction in design: should not be higher when AI is involved than when it is not)
1. High risk – 40%
2. Moderate risk – 20%
3. Low risk – 10%

Time until treatment decision is made:
1. 1 day
2. 1 week
3. 2 weeks

The levels constructed in Sawtooth in the same order as displayed here. I wrote a code (see below) to implement into Sawtooth. We want both the attributes Risk of undertreatment and Risk of overtreatment to have a restriction in the design. In the choice tasks; when the attribute on AI states that AI is not involved (level 1) the value of should of the 2 to risk attributes should always have a higher value (e.g. so level 1 20% and 40%) then when when AI is involved (e.g. level 2 and 3).

In addition, due to some of our expectations I have added some negative priors as we expect higher risk of under- and overtreatment and certainty of side effects to have a negative prior.

Could you please check our Ngene code below and if this is correctly formulated, especially the part for the constraints so we can import into sawtooth?


design
; alts = altA*, altB*
; eff = (mnl, d, mean)
; bdraws = halton(1000)
; rows = 36
; block = 3
; alg = mfederov
; cond:
if(altA.AIinvolvement. = [2,3], altA.RiskUndertreatment >= altB.RiskUndertreatment.), if(altA. AIinvolvement = [2,3], altA.RiskOvertreatment. >= altB.RiskOvertreatment.),
if(altB.AIinvolvement. = [2,3], altB.RiskUndertreatment >= altA.RiskUndertreatment),if(altB.AIinvolvement = [2,3], altB.RiskOvertreatment >= altA.RiskOvertreatment))
; model:
U(altA) = b1.dummy[(u, -0.1, -0.05)|(u, -0.15, -0.1)] * timecancergrows[2, 3, 1]
+ b2.dummy[0|0|0] * AIinvolvement[2, 3, 1]
+ b3.dummy[(u, -0.1, -0.15)] * CertaintySideEffects[1, 2]
+ b4.dummy[(u, -0.2, -0.1)|(u, -0.3, -0.2)] * RiskUndertreatment[2, 3, 1]
+ b5.dummy[(u, -0.1, -0.05)|(u, -0.15, -0.1)] * RiskOvertreatment[2, 3, 1]
+ b6.dummy[0|0|0] * TimeUntilDecision[1, 2, 3]
/
U(altB) = b1.dummy * timecancergrows[1, 2, 3]
+ b2.dummy * AIinvolvement
+ b3.dummy * CertaintySideEffects
+ b4.dummy * RiskUndertreatment
+ b5.dummy * RiskOvertreatment
+ b6.dummy * TimeUntilDecision
$


Kind regards,

Suzanne

[Michiel Bliemer]

I assume that you want to generate a design in Ngene and then import that design into Sawtooth?

There are numerous mistakes in your script that will prevent you from running it:
- You should remove the period behind attribute riskundertreatment in the conditional constraints
- You should remove the attribute levels behind timecancergrows as they are not in the same order as previously defined
- The number of dummy priors for AIinvolvement is too many, remove one of the zeros
- You cannot use ;cond together with the modified Federov algorithm, you need to specify ;reject constraints
- Priors (u,-0.1,-0.15) should be (u,-0.15,0.1) since the format is (u,lower,upper)

I am not sure I understand the constraints you defined, based on the text I would expect something like:
;reject:
altA.AIinvolvement = 1 and altA.riskundertreatment = 1,
altB.AIinvolvement = 1 and altB.riskundertreatment = 1

Michiel

[SuzannevD]

Dear Michiel,

Thank you for your response! I changed the comments you made about the code in the bullets and indeed I want to upload the design into Sawtooth.

What I mean with the constraints is that the attributes risk of undertreatment and risk of overtreatment can have level 1 when there is AI involvement in the treatment. But as soon as one of the 2 options in the choice tasks consist of NO AI involvement then the other choice option that does consist AI involvement should always have a lower risk of under- and overtreatment (levels 2 and 3). I hope this is a more clear explanation of what we need.

I have added the code again with the changes I made. Is this correct now and do we need to change the conditions still?

design
; alts = altA*, altB*
; eff = (mnl, d, mean)
; bdraws = halton(1000)
; rows = 36
; block = 3
; reject constraints
; cond:
if(altA.AIinvolvement = [2,3], altA.RiskUndertreatment >= altB.RiskUndertreatment), if(altA. AIinvolvement = [2,3], altA.RiskOvertreatment >= altB.RiskOvertreatment),
if(altB.AIinvolvement = [2,3], altB.RiskUndertreatment >= altA.RiskUndertreatment),if(altB.AIinvolvement = [2,3], altB.RiskOvertreatment >= altA.RiskOvertreatment))
; model:
U(altA) = b1.dummy[(u, -0.1, -0.05)|(u, -0.15, -0.1)] * timecancergrows[2, 3, 1]
+ b2.dummy[0|0] * AIinvolvement[2, 3, 1]
+ b3.dummy[(u, -0.15,-0.1)] * CertaintySideEffects[1, 2]
+ b4.dummy[(u, -0.2, -0.1)|(u, -0.3, -0.2)] * RiskUndertreatment[2, 3, 1]
+ b5.dummy[(u, -0.1, -0.05)|(u, -0.15, -0.1)] * RiskOvertreatment[2, 3, 1]
+ b6.dummy[0|0|0] * TimeUntilDecision[1, 2, 3]
/
U(altB) = b1.dummy * timecancergrows[1, 2, 3]
+ b2.dummy * AIinvolvement
+ b3.dummy * CertaintySideEffects
+ b4.dummy * RiskUndertreatment
+ b5.dummy * RiskOvertreatment
+ b6.dummy * TimeUntilDecision
$

[Michiel Bliemer]

Please run the script yourself, Ngene will tell you if there are any further mistakes. If you would have run it, you would have noticed that no design cannot be generated using the default swapping algorithm because your design is highly constrained because of the presence of many dominant alternatives. So you MUST use the modified Federov algorithm, which only works with reject constraints.

Michiel

[SuzannevD]

Dear Michiel,

Thank you for the fast response. I think that based on your comment this is what you mean, am i correct?

design
; alts = altA*, altB*
; eff = (mnl, d, mean)
; bdraws = halton(1000)
; rows = 36
; block = 3
; alg = mfederov
; reject:
if(altA.AIinvolvement = [2,3], altA.RiskUndertreatment >= altB.RiskUndertreatment),
if(altA.AIinvolvement = [2,3], altA.RiskOvertreatment >= altB.RiskOvertreatment),
if(altB.AIinvolvement = [2,3], altB.RiskUndertreatment >= altA.RiskUndertreatment),
if(altB.AIinvolvement = [2,3], altB.RiskOvertreatment >= altA.RiskOvertreatment)
; model:
U(altA) = b1.dummy[(u, -0.1, -0.05)|(u, -0.15, -0.1)] * timecancergrows[2, 3, 1]
+ b2.dummy[0|0] * AIinvolvement[2, 3, 1]
+ b3.dummy[(u, -0.15,-0.1)] * CertaintySideEffects[1, 2]
+ b4.dummy[(u, -0.2, -0.1)|(u, -0.3, -0.2)] * RiskUndertreatment[2, 3, 1]
+ b5.dummy[(u, -0.1, -0.05)|(u, -0.15, -0.1)] * RiskOvertreatment[2, 3, 1]
+ b6.dummy[0|0|0] * TimeUntilDecision[1, 2, 3]
/
U(altB) = b1.dummy * timecancergrows
+ b2.dummy * AIinvolvement
+ b3.dummy * CertaintySideEffects
+ b4.dummy * RiskUndertreatment
+ b5.dummy * RiskOvertreatment
+ b6.dummy * TimeUntilDecision
$

Kind regards,

Suzanne

[Michiel Bliemer]

There are still several mistakes in your script, when you run it Ngene will point out where the mistakes are.
The reject constraints are also not properly specified, please have a look at the manual for examples.

Michiel