News
glmmSeq 0.5.7
29/09/2025
- Fixing broken links in documetation and adding kableExtra to
Imports.
glmmSeq v0.5.6
17/01/2025
- Now returns variance of the random effect term as an additional
column in the
@predict slot.
glmmSeq v0.5.5
29/09/2022
- Improve error handling if all genes give errors
glmmSeq v0.5.4
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 v0.5.2
19/09/2022
- Fix passing of
... in parallelisation on windows in
glmmSeq() & lmmSeq()
glmmSeq v0.5.1
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 v0.4.0
10/08/2022
- Further speed enhancements to
lmmSeq() using
lme4::modular code. Speed increase of around 25%.
glmmSeq v0.3.0
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 v0.2.2
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 v0.2.1
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 v0.2.0
09/07/2022
- Add lmmSeq function for gaussian linear mixed models
glmmSeq v0.1.2
08/07/2022
glmmSeq v0.1.1
18/04/2021
Bug Fixes
- Fix colours in pairedPlots and modelPlots
glmmSeq v0.1.0
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 v0.0.1
05/03/2021
- This is the initial build of
glmmSeq