Incorporated mean, rmst, q into dfns, Added missing exports

[jrdnmdhl]

• Added functions for mean/restricted mean for all distributions
• Renamed all existing mean functions so that roxygen2 didn't confuse them as S3 methods
• q/mean/rmst functions automatically included in dfns for all distributions
• implemented type="median" for summary.flexsurv
• Added missing exports
• Added extra tests

[chjackson]

Thanks. Looks good, just testing it out.

I think the default t in summary(..., type="rmst") should be a scalar, rather than the observation times. It's nicer in the situation where the calculation is slow - also I can't imagine someone wanting to know the "trajectory" of the RMST in the same way as the hazard or survival. What do you think of the default being the maximum follow up time in the data?

Also found a bug in mean_survspline, should have start=0 instead of start=start.

[jrdnmdhl]

Thanks Chris. Believe it or not, generating rmst over a sequence of observation times is a thing! I do a ton of curve fitting for economic evaluations. As part of this process, I often produce figures of RMST (and delta RMST) for time because they are quite good at showing the impact of extending/shortening the timeframe of a projection.

You are right though that the calculation is quite slow when CI=T and when t is a long vector. Sadly, I don't see a good way around this that wouldn't potentially compromise precision in certain cases. I defer to you on what to do with this.

I do like the idea of making the default maximum the maximum time in the data. Can implement that along w/ fixing the bug in mean_survspline.

[jrdnmdhl]

For using the max time as a default, I need to get a much better sense of what obj$data$Y looks like under the different ways that the Surv object can be defined. Not immediately obvious to me if I can safely take the max of one of the columns in order to cover all types of censoring/survival times.

[chjackson]

Merged now. max(obj$data$Y[,"time1"]) is fine I think - this is the event or right-censor time. "time2" is the left-censor time, so that interval censored events happen after time1 and before time2. So I think time1 is a good enough definition of the "follow-up time", for the purpose of this function.

Also I think mean_survspline (or any of the mean_ functions) shouldn't have a "start" argument - I just meant that start=0 should be set in the call to rmst_generic. I've made these changes now.

[jrdnmdhl]

Apologies, you are right.  Mean should not have a start parameter!  My initial implementation allowed for this, because it was always based on the numeric integral.  Here that gets more complicated/confusing since you couldn’t use the analytical means to calculate mean conditioned on start !=0. Must have gotten myself mixed up along the way... From: chjackson <notifications@github.com> Reply-To: chjackson/flexsurv-dev <reply@reply.github.com> Date: Saturday, February 18, 2017 at 5:44 PM To: chjackson/flexsurv-dev <flexsurv-dev@noreply.github.com> Cc: Jordan Amdahl <jrdnmdhl@gmail.com>, Author <author@noreply.github.com> Subject: Re: [chjackson/flexsurv-dev] Incorporated mean, rmst, q into dfns, Added missing exports (#27) Merged now. max(obj$data$Y[,"time1"]) is fine I think - this is the event or right-censor time. "time2" is the left-censor time, so that interval censored events happen after time1 and before time2. So I think time1 is a good enough definition of the "follow-up time", for the purpose of this function. Also I think mean_survspline (or any of the mean_ functions) shouldn't have a "start" argument - I just meant that start=0 should be set in the call to rmst_generic. I've made these changes now. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.