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Tips to speed up computation

Source: vignettes/fast.Rmd
fast.Rmd

Go faster

Analyses can slow to a crawl when models need hours to run. In this article you will find a few tricks to prevent this bottleneck when using orsf().

Don’t specify a control

The default control for orsf() is NULL because, if unspecified, orsf() will pick the fastest possible control for you depending on the type of forest being grown. The default control run-time compared to other approaches can be striking. For example:


time_fast <- system.time(
 expr = orsf(pbc_orsf, 
             formula = time+status~. -id, 
             n_tree = 5)
)

time_net <- system.time(
 expr = orsf(pbc_orsf, 
             formula = time+status~. -id, 
             control = orsf_control_survival(method = 'net'), 
             n_tree = 5)
)

# unspecified control is much faster
time_net['elapsed'] / time_fast['elapsed']
#>  elapsed 
#> 45.59091

Use n_thread

The n_thread argument uses multi-threading to run aorsf functions in parallel when possible. If you know how many threads you want, e.g. you want exactly 5, set n_thread = 5. If you aren’t sure how many threads you have available but want to use a feasible amount, using n_thread = 0 (the default) tells aorsf to do that for you.


# automatically pick number of threads based on amount available

orsf(pbc_orsf, 
     formula = time+status~. -id, 
     n_tree = 5,
     n_thread = 0)

Note: sometimes multi-threading is not possible. For example, because R is a single threaded language, multi-threading cannot be applied when orsf() needs to call R functions from C++, which occurs when a customized R function is used to find linear combination of variables or compute prediction accuracy.

Do less

There are some inputs in orsf() that can be adjusted to make it run faster:

  • set n_retry to 0

  • set oobag_pred_type to 'none'

  • set importance to 'none'

  • increase split_min_events, split_min_obs, leaf_min_events, or leaf_min_obs to make trees stop growing sooner

  • increase split_min_stat to enforce more strict requirements for growing deeper trees.

Applying these tips:


orsf(pbc_orsf, 
     formula = time+status~., 
     n_thread = 0, 
     n_tree = 5, 
     n_retry = 0,
     oobag_pred_type = 'none', 
     importance = 'none',
     split_min_events = 20, 
     leaf_min_events = 10,
     split_min_stat = 10)

While modifying these inputs can make orsf() run faster, they can also impact prediction accuracy.

Show progress

Setting verbose_progress = TRUE doesn’t make anything run faster, but it can help make it feel like things are running less slow.


verbose_fit <- orsf(pbc_orsf, 
                    formula = time+status~. -id, 
                    n_tree = 5, 
                    verbose_progress = TRUE)
#> Growing trees: 100%. 
#> Computing predictions: 100%.

Don’t wait. Estimate!

Instead of running a model and hoping it will be fast, you can estimate how long a specification of that model will take by using no_fit = TRUE in the call to orsf().


fit_spec <- orsf(pbc_orsf, 
                 formula = time+status~. -id, 
                 control = orsf_control_survival(method = 'net'), 
                 n_tree = 2000,
                 no_fit = TRUE)

# how much time it takes to estimate training time:
system.time(
 time_est <- orsf_time_to_train(fit_spec, n_tree_subset = 5)
)
#>    user  system elapsed 
#>   0.283   0.000   0.282

# the estimated training time:
time_est
#> Time difference of 112.619 secs