NEWS
glmmSeq 0.5.6
17/01/2025
- Now returns variance of the random effect term as an additional column in the
@predict slot.
glmmSeq 0.5.5 (2022-10-08)
29/09/2022
- Improve error handling if all genes give errors
glmmSeq 0.5.4
25/09/2022
- Add option for likelihood ratio test (LRT) in
glmmSeq() and lmmSeq()
- Enable changing of model formula, family and control parameters when refitting
model for a single gene in
glmmRefit()
glmmSeq 0.5.2
19/09/2022
- Fix passing of
... in parallelisation on windows in glmmSeq() & lmmSeq()
glmmSeq 0.5.1 (2022-09-12)
02/09/2022
- Add option to
glmmSeq() to use glmmTMB package for fitting negative
binomial GLMM (or other GLM family) models
- Add
plab argument to modelPlots to customise p-value labels
- Add mean expression column
meanExp to results in @stats$res slot
glmmSeq 0.4.0 (2022-08-12)
10/08/2022
- Further speed enhancements to
lmmSeq() using lme4::modular code. Speed
increase of around 25%.
glmmSeq 0.3.0
05/08/2022
- Significant update including output of standard error on fitted coefficients
for both
glmmSeq and lmmSeq
- Add
summary function for glmmSeq and lmmSeq to display results for an
individual gene
- Reorganised
@stats slot in output objects to include more information
including DF
- Added option of using Saiterthwaite's DF method with ANOVA type III tables as
option for
lmmSeq using the lmerTest package
- Added
lmmRefit function to fit an identical (g)lmer model. This can then be
passed to the emmeans package for visualisation of more complex models.
- Separated
modelPlots (base graphics) and ggmodelPlots (ggplot2)
- Streamlined
modelPlots to allow for simplest case gene ~ Time + (1 | ID)
glmmSeq 0.2.2
16/07/2022
- Fast version of
lmmSeq(). Improves speed of calculation of type 2 Wald test.
Overall speed increase of 25-50%.
- Faster version of
glmmSeq()
- Automatically detects
id column name from the RE term in the formula
glmmSeq 0.2.1
11/07/2022
- Add
... option to fcPlot which is passed to plotly() or ggplot()
- set
annotationPosition=FALSE in fcPlot so arrows/connectors are not moved
glmmSeq 0.2.0 (2022-07-11)
09/07/2022
- Add lmmSeq function for gaussian linear mixed models
glmmSeq 0.1.2
08/07/2022
glmmSeq 0.1.1
18/04/2021
Bug Fixes
- Fix colours in pairedPlots and modelPlots
glmmSeq 0.1.0 (2021-03-30)
16/03/2021
Features
- Add progress bars to glmmSeq functions
- Add option
returnList to return glmmSeq output as list (to make error
catching easier)
Bug Fixes
- Fix missing plots in vignette
glmmSeq 0.0.1 (2021-03-11)
05/03/2021
- This is the initial build of
glmmSeq