NEWS

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MetaboDynamics 2.1.104

• bug fix in estimates_dynamics

MetaboDynamics 2.1.103

• bug fix in estimates_dynamics

MetaboDynamics 2.1.101

• bug fix in fit_dynamics_model()
• new message in diagnostics_dynamics

MetaboDynamics 2.1.100

• bug fix in plot_PPC for raw_plus_counts_model
• estimates_dynamics does not return 'sigma' or 'lambda' anymore

MetaboDynamics 2.1.99

• added model_option in fit_dynamics_model(): either "sd_per_time_point" (only option before) or "sd_per_condition" (less sigmas, more robust with few replicates)

MetaboDynamics 2.1.2

• bug fix in plot_cluster: correct sorting of time points

MetaboDynamics 2.1.1

• cluster_dynamics bug fix: can handle all metabolite names

MetaboDynamics 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

MetaboDynamics 1.0.2

Minor bug fix in vignette that caused errors in package checks

MetaboDynamics 1.0.1

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

MetaboDynamics 1.0.0

Bioconductor Release 3_21

MetaboDynamics 0.99.26

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

MetaboDynamics 0.99.25

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

MetaboDynamics 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

MetaboDynamics 0.99.22

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

MetaboDynamics 0.99.20

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

MetaboDynamics 0.99.18

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

MetaboDynamics 0.99.0

• Initial Bioconductor submission.