SummarizedExperiment Infrastructure for Microbial Growth Phenotyping

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Documentation for package ‘growkar’ version 0.99.2

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

as_tidy_growth_data	Import Growth Data into Canonical Tidy Format
augment_growth_fit	Augment Observed Data with Fitted Values
augment_growth_fit-method	Augment Observed Data with Fitted Values
coef-method	Model Components of a 'GrowthFit' Object
compute_doubling_time	Compute Doubling Time
compute_growth_rate	Compute Growth Rate
detect_exponential_phase	Detect Candidate Exponential-Phase Windows
extract_params	Extract Fitted Growth Parameters
extract_params-method	Extract Fitted Growth Parameters
fitted-method	Model Components of a 'GrowthFit' Object
fit_converged	Accessors for 'GrowthFit' Objects
fit_converged-method	Accessors for 'GrowthFit' Objects
fit_data	Accessors for 'GrowthFit' Objects
fit_data-method	Accessors for 'GrowthFit' Objects
fit_growth_curve	Fit a Parametric Growth Model
fit_growth_models	Fit and Store Growth Models
fit_growth_plate	Fit Growth Models Across a Plate
fit_model	Accessors for 'GrowthFit' Objects
fit_model-method	Accessors for 'GrowthFit' Objects
fit_sample	Accessors for 'GrowthFit' Objects
fit_sample-method	Accessors for 'GrowthFit' Objects
fit_status	Accessors for 'GrowthFit' Objects
fit_status-method	Accessors for 'GrowthFit' Objects
GrowthExperiment	Construct a 'GrowthExperiment'
GrowthExperiment-class	Growth Assay Experiment
GrowthExperiment-coerce	Coerce to a 'GrowthExperiment'
GrowthFit-accessors	Accessors for 'GrowthFit' Objects
GrowthFit-model-methods	Model Components of a 'GrowthFit' Object
growth_assay	Growth Assay Matrix
growth_metrics	Compute and Store Growth Metrics
growth_model_fits	Stored Growth Model Fits
nobs-method	Model Components of a 'GrowthFit' Object
phase_windows	Compute and Store Exponential-Phase Windows
plot_doubling_time	Plot Doubling Time Summary
plot_fitted_curve	Plot a Fitted Growth Curve
plot_growth_curve	Plot Growth Curves
plot_growth_curve_facets	Plot Growth Curves as Facets
residuals-method	Model Components of a 'GrowthFit' Object
sample_data	Sample Metadata
show-method	Display a 'GrowthFit' Object
summarize_growth_metrics	Summarize Growth Metrics
summary-method	Summarize a 'GrowthFit' Object
timepoints	Timepoint Metadata
validate_growth_data	Validate Canonical Growth Data
validate_growth_experiment	Validate a Growth 'SummarizedExperiment'
yeast_growth_data	Optical Density (OD600) of growing yeast cells