add new descriptive error to qgcomp.cox.boot for missing data
(resolve https://github.com/alexpkeil1/qgcomp/issues/14)
Documentation: changed example in
mice.impute.leftcenslognorm function to accomodate breaking
change in mice package
Bug fixes
none
qgcomp v2.18.7
Major changes
None
Minor changes
export .qgcomp_object function and .qgcomp_object_add function.
These function facilitate transportable methods that can be used in
external extensions to qgcomp (.e.g)
Bug fixes
bug fix for weights, cluster in Cox models
qgcomp v2.18.4
Major changes
Added modelbound.ee function to generate confidence intervals for
regression lines with estimating equation fits
Revamped underlying code to plots to facilitate
integration/overlays
Minor changes
Implementing a few functions from qgcompint package to
support consistency across packages
Documentation fixes (cch functions and missing plots/formulae in
vignettes)
Bug fixes
fix bug in df.residual function that impacted integration with
mice package
qgcomp v2.17.3
Major changes
Added glm.tobit.noboot function to fit a Tobit model with
qgcomp
Minor changes
Documentation improvements
Code hygeine to prevent issues with edge cases
Bug fixes
None
qgcomp v2.16.4
Major changes
Added glm.ee function to use estimating equations approach (allows
non-linear and longitudinal models without bootstrapping)
Minor changes
Split vignette into two vignettes and added examples
Bug fixes
Mice function (mice.impute.leftcenslognorm) to allow empty
prediction sets: fixed a bug that led to hidden failures resulting in
very low values for imputations
Fixed glm.ee for Tibbles, non-linear models (which never made it to
CRAN release)
qgcomp v2.15.2
Major changes
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)
Bug fixes
Fixed major bug in qgcomp.partials:
https://github.com/alexpkeil1/qgcomp/issues/28
qgcomp v2.9.0
Major changes
None
Minor changes
Replace qgcomp.partials with re-factored version with new
quantization defaults
Clarifed error message in
https://github.com/alexpkeil1/qgcomp/issues/14
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.qgcompfit
function 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 via
qgcomp.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() and
pointwisebound.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() and
qgcomp.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 the
mice 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 in
qgcomp.boot
MCsize parameter caused intermittent error when used in
qgcomp.boot
vcov() didn’t yield a covariance matrix when applied to
qgcomp.*.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 on
pscl 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 of
qgcomp.cox.boot when model was adjusted for covariates
Fixed variable typing issue that arose when fitting
qgcomp.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 model
that 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 and
qgcomp.cox.noboot functions.
Added (semi-)Bayesian approaches to linear,
logistic models via the arm package. Available for
qgcomp.boot, qgcomp.noboot, and
qgcomp functions
Allow parallel processing of bootstrap variance estimation via the
future and future.apply packages
Added default plotting of survival curves for the
qgcomp.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 if
q 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 using
qgcomp.boot when q = NULL, rather than causing a fatal
error (rare, minor)
v0.8.13: Fixed error if specifying nonlinear fit in
qgcomp.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 using
qgcomp.boot when q = NULL, rather than causing a fatal
error
v0.8.13: Fixed error if specifying nonlinear fit in
qgcomp.boot when q = NULL by specifying fixed values for
“interventions” and warning users