Cyclops
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OHDSI
Cyclops (Cyclic coordinate descent for logistic, Poisson and survival analysis) is an R package for performing large scale regularized regressions.
As part of our suite of study diagnostics, it would be good to evaluate whether the proportionality assumption holds when performing a Cox regression. Could we add something like Schoenfeld...
Not a Cyclops bug, but did encounter it while running Cyclops. The error `Rcpp_precious_remove' not provided by package 'Rcpp'` is thrown when calling `convertToCyclopsData()` with certain versions of Rcpp. Oddly,...
From the release [package documentation](https://cran.r-project.org/web/packages/Cyclops/Cyclops.pdf) ``` These columns are expected in the outcome object: - stratumId (integer) (optional) Stratum ID for conditional regression models - rowId (integer) Row ID is...
Tasks (this is the usual contract): - [ ] Refactor message-level check into `*Logger` class. May address this later, since `Cyclops` only constructs strings if message-level
Large covariate values ( > 1 ) can lead to numeric overflow errors. We currently solve this by dividing the covariate value by the max value for that covariate before...
The `selectorType` option allows you to specify what the unit of sampling is for cross-validation: rows or strata. We could implement a simple heuristic that can automatically make a choice...
Cyclops is currently lacking support for Efron's method (default behavior in R as @schuemie brought to my attention). Default Cyclops behavior for ties in Cox regression is Breslow's method, which...
In long running jobs we are finding that Cyclops `getCyclopsProfileLogLikelihood` runs for many hours and often produces the warning: > WARN Cyclops getCyclopsProfileLogLikelihood Coefficient drift detected. Resetting Cyclops object and...
