Changes in version 0.5.7 (2025-10-02)                  

29/09/2025

  - Fixing broken links in documetation and adding kableExtra to
    Imports.

                        Changes in version 0.5.6                        

17/01/2025

  - Now returns variance of the random effect term as an additional
    column in the @predict slot.

                 Changes in version 0.5.5 (2022-10-08)                  

29/09/2022

  - Improve error handling if all genes give errors

                        Changes in version 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()

                        Changes in version 0.5.2                        

19/09/2022

  - Fix passing of ... in parallelisation on windows in glmmSeq() &
    lmmSeq()

                 Changes in version 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

                 Changes in version 0.4.0 (2022-08-12)                  

10/08/2022

  - Further speed enhancements to lmmSeq() using lme4::modular code.
    Speed increase of around 25%.

                        Changes in version 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)

                        Changes in version 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

                        Changes in version 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

                 Changes in version 0.2.0 (2022-07-11)                  

09/07/2022

  - Add lmmSeq function for gaussian linear mixed models

                        Changes in version 0.1.2                        

08/07/2022

  - Fix CMD check errors

                        Changes in version 0.1.1                        

18/04/2021

Bug Fixes

  - Fix colours in pairedPlots and modelPlots

                 Changes in version 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

                 Changes in version 0.0.1 (2021-03-11)                  

05/03/2021

  - This is the initial build of glmmSeq