Changes in version 1.99.12                       

  - contains a vignette describing the package workflow with a data
    frame input
  - altered plot_cluster and plot_ORA visualization for patchwork option
    enabling easier visualization
  - all functions require columns names "metabolite","condition","time"
    for consistency throughout the package
  - get_ORA_annotations() function (retrieving KEGG IDs hierarchies)
    added back to package
  - no more samples in estimates dynamics as probability of clustering
    solution is implemented now as bootstrapping from model posterior in
    function cluster_dynamics
  - estimates_dynamics() now returns a list with: estimated metabolite
    abundance (mu), estimated standard deviation of metabolite abundance
    (sigma), estimated pooled standard deviation per metabolite and dose
    (lambda), differences in metabolite abundances between time points,
    euclidean distance between metabolite dynamics of different
    conditions
  - plot_estimates() additionally visualizes the euclidean distance
    between conditions of metabolite specific dynamics
  - cluster_dynamics() provides clustering solution of mean estimates of
    mu as well as bootstraps clustering solutions
  - plot_cluster provides bubbletree, cluster identity, dynamics plots
    as well as patchwork plot (combining bubbletree, cluster identity
    and dynamics plots)
  - plot_ORA() has now option to be added to bubbletree obtained by
    plot_cluster
  - ORA_hypergeometric() requires now a data frame annotationg
    metabolites to KEGG IDs (column names "metabolite" and "KEGG")
  - internal adding of ANOVA model with euclidean distance estimation
    between doses and ANOVA model that integrates cell count uncertainty
  - internal adding of simulated cell counts to
    data("longitudinalMetabolomics")
  - differences between time points are now ordered and return is a list
    of plots

                        Changes in version 1.0.2                        

Minor bug fix in vignette that caused errors in package checks

                        Changes in version 1.0.1                        

bug fix: fit_dynamics_model() can now correctly handle provided variable
names

                        Changes in version 1.0.0                        

Bioconductor Release 3_21

                       Changes in version 0.99.26                       

  - deprecate function get_ORA_annotations, needed data for
    ORA_hypergeometric is included in package ("modules_compounds")

                       Changes in version 0.99.25                       

  - comparison of clusters including visualization now handles number of
    clusters >10 correctly
  - altered vignette including new clustering functions

                       Changes in version 0.99.24                       

  - Bug fix: estimates_dynamics handles now differences between
    timepoints correctly
  - added functions: cluster_dynamics: convenient clustering function
    wrapper using dynamictreecut package plot_cluster: cluster
    visualization

                       Changes in version 0.99.22                       

  - Bug fix: fit_dynamics allows number of time points that are not
    equal to 4

                       Changes in version 0.99.20                       

  - Bug fix: can now handle tibbles as input (along with data frames and
    summarizedExperiments)

                       Changes in version 0.99.18                       

  - Accepted to Bioconductor
    https://www.bioconductor.org/packages/devel/bioc/html/MetaboDynamics.html

                       Changes in version 0.99.0                        

  - Initial Bioconductor submission.