Added multinomial models (qgcomp.multinomial.noboot and qgcomp.multinomial.boot)
Plot for multinomial models (qgcomp.multinomial.noboot only)
Changed qgcomp.boot to qgcomp.glm.boot and qgcomp.noboot to qgcomp.glm.noboot for clarity. The old functions still work (for now).
Minor changes
Mice function (mice.impute.leftcenslognorm) to allow empty prediction sets
mice.impute.leftcenslognorm has been given an alias mice.impute.tobit
Added simulation of multinomial outcomes
Code-base hygiene
Bug fixes
Fixed some miscellaneous bugs in the print function for non-standard link functions.
Fixing bug in model pointwisebound.noboot that gave non-sense confidence intervals
qgcomp v2.10.0
Major changes
None
Minor changes
qgcomp.partials now allows quantile definitions based on the training and validation data, which treats the quantiles as fixed values across both datasets and leads to more stable results in small samples (set via .globalbreaks = TRUE in qgcomp.partials)
Created new hidden functions for testing that will eventually replace qgcomp.partials
qgcomp v2.8.6
Major changes
None
Minor changes
None
Bug fixes
Fixed misuse of “all.equal” in tests
qgcomp v2.8.5
Major changes
None
Minor changes
Handling of parallel processing through futures: bringing in line with package recommendations and planned deprecations.
Documentation changes
qgcomp v2.8.0
Major changes
Exposed simulation functions to the user
Enabled no-intercept models in qgcomp.boot and qgcomp.noboot
Minor changes
Parallel code now enables external setting of if(parplan) future::plan to facilitate broader parallelization schemes
Documentation improvements
Included FAQs in vignette
qgcomp v2.7.0
Major changes
None
Minor changes
Changed underlying parallel code to adapt to deprecations from future package
Documentation improvements
Enabled by-observation limit of detection/right censoring point for mice.impute.leftcensorlognorm
Bug fixes
None
qgcomp v2.6.0
Major changes
Added cox.survcurve.boot function to estimate survival curves from a qgcomp.cox.boot fit
Refactored plot code (changes should be invisible to users except bug fixes)
Minor changes
documentation improvements
Changed “pointwisebound.*” and “modelbounds.*” to give more sensible output
Bug fixes
Fix bug in tidy when using Cox model
Bug fixes in bounds calculation with binomial outcomes, which lead to incorrect bounds on plots
Fixed long running harmless and annoying print bug that confused “t” with “z”
qgcomp v2.5.0
Major changes
Documentation improvements
Added split_data function to assist with inference from data adaptive procedures (such as qgcomp.partials) and model selection
Minor changes
Removed “experimental” tags on Poisson family, Zero inflated models
Added smarter “expnms” default to predict.qgcompfitfunction with new data
qgcomp v2.4.0
Major changes
Documentation improvements
Added hurdle models (qgcomp.hurdle.*boot functions), which address the excess in zeroes in a distribution slightly differently from zero inflated models (based on pscl package functions.)
Bug fixes
Package broom deprecates a dependency in an upcoming release. This dependency was removed
Bug with pointwisebound.noboot when non-exposure variables are encoded as factors
fixed bug in .split.cluster.data function that failed with most ID variable types
fixed R 4.0.0 bug where MCsize was ignored
fixed rare bug in hurdle/zi methods with non-quantized exposures, resulted in ridiculous runtimes if not errors
qgcomp v2.3.0
Major changes
Documentation improvements
Added ability to perform weighted analysis for glm, survival, and zero inflated objects
Implement sample splitting to estimate partial effects viaqgcomp.partials.
Bug fixes
Fixed bug in print function that missed linear fits
Fixed visual bug in plots introduced after updating ggplot 3.3.0 (instituted forced update of ggplot2 for users, sorry!)
qgcomp v2.2.2
Major changes
Documentation improvements
Added pointwisebound.boot() andpointwisebound.noboot() function to get confidence intervals for pointwise comparisons (e.g. mean outcome at all exposures below first quartile compared to mean outcome at all exposures above the third quartile. Used after qgcomp fits.
Added support for Poisson link in qgcomp.boot() andqgcomp.noboot() functions to fit quantile g-computation for count data
Added generics and tibble package dependencies and optional installs of broom
Added functions to facilitate multiple imputation through themice package.
Added weight parameters to base, zi, and cox (not yet used) in preparation for v2.3.0, which will implement weighting
Added vc_comb() to better calculate covariance matrices.
Bug fixes
Fixed an error in confidence bounds in plot functions introduced in v2.0.0 (binary outcomes in qgcomp.boot).
id parameter caused intermittent error when used inqgcomp.boot
MCsize parameter caused intermittent error when used inqgcomp.boot
vcov() didn’t yield a covariance matrix when applied toqgcomp.*.noboot objects
qgcomp v2.1.2
Major changes
Documentation improvements
Added qgcomp.zi.boot function to fit non-linear/non-additive versions of quantile g-computation for zero-inflated Poisson or negative binomial models
Added two functions to estimate confidence intervals for regression line fits and pointwise comparisons: modelbound.boot, pointwisebound.boot
Bug fixes
MAJOR: Fixed error in confidence bounds in plot functions introduced in v2.0.0
qgcomp v2.0.0
Major changes
Documentation improvements
Added qgcomp.zi.noboot function to fit (linear/additive only) versions of quantile g-computation for zero-inflated Poisson or negative binomial models (adds additional dependency onpscl package)
Major version change to account for possible breaking of old code in v.1.3.0
Bug fixes
MAJOR: Fixed error in print function that printed incorrect confidence intervals introduced in v1.3.0
qgcomp v1.3.0
Major changes
Documentation improvements
Improved error messages
Added intercept to main output (this may break some code that depends on qgcomp)
Added pointwise confidence bounds and better control over plot output for qgcomp.boot fits.
Bug fixes
Fixed fatal error for plotting output ofqgcomp.cox.boot when model was adjusted for covariates
Fixed variable typing issue that arose when fittingqgcomp.boot with a single exposure variable with non-linear fit
qgcomp v1.2.0
Major changes
Added bootstrapped version of Cox proportional hazards model, which estimates parameters of a marginal structural Cox modelthat uses a simulation-based approach to characterize the population average effect of increasing all exposures of interest by one quantile. Survival analysis now available from qgcomp.cox.boot andqgcomp.cox.noboot functions.
Added (semi-)Bayesian approaches to linear, logistic models via the arm package. Available forqgcomp.boot, qgcomp.noboot, andqgcomp functions
Allow parallel processing of bootstrap variance estimation via thefuture and future.apply packages
Added default plotting of survival curves for theqgcomp.cox.boot function
Miscellaneous error checking to improve readability of error messages
Bug fixes
Better guessing for qgcomp function
qgcomp v1.1.0
Major changes
Added bootstrap covariance matrix to output of qgcomp.boot, which allows plotting of MSM intervals
Plots now include confidence bands, when appropriate, and offer more control
Fixed standardization in data
Added Cox proportional hazards variants of qgcomp models
Allow tibbles to be used as data objects
Bug fixes
Fixed issue where MSM fit would default to 4 levels ifq is unspecified and breaks are user defined (rare, major)
Fixed error that occurred when a tibble was used as the data object, rather than a data frame (common, minor)
qgcomp v1.0.0
Major changes
First release on CRAN, benchmark v0.8.14 as release version 1.0
Bug fixes
v0.8.12: Breaks now properly reported as NULL usingqgcomp.boot when q = NULL, rather than causing a fatal error (rare, minor)
v0.8.13: Fixed error if specifying nonlinear fit inqgcomp.boot when q = NULL by specifying fixed values for “interventions” and warning users (rare, minor)
v0.8.14: Documentation fixes for CRAN release
qgcomp v0.8.13
Major changes
Bug fixes
v0.8.12: Breaks now properly reported as NULL usingqgcomp.boot when q = NULL, rather than causing a fatal error
v0.8.13: Fixed error if specifying nonlinear fit inqgcomp.boot when q = NULL by specifying fixed values for “interventions” and warning users