Main Model FunctionsMain interface for fitting models and returning model objects |
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Interface to fit pibble models |
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Interface to fit basset models |
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Interface to fit orthus models |
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Interface to fit maltipoo models |
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Rcpp Model InterfacesLow level interfaces for fitting models |
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Function to Optimize the Collapsed Pibble Model |
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Function to Optimize the Collapsed Maltipoo Model |
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Solve Bayesian Multivariate Conjugate Linear Model |
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Uncollapse output from optimPibbleCollapsed to full pibble Model |
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Calculations for the Collapsed Pibble Model |
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Calculations for the Collapsed Maltipoo Model |
Multivariate RBF Kernel |
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Object MethodsMethods for working with model objects |
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Generic method for accessing model fit dimensions |
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Convert object of class orthusfit to a list |
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Convert object of class pibblefit to a list |
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Generic method to convert to list |
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convert list to orthusfit |
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convert list to pibblefit |
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Return regression coefficients of orthus object |
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Return regression coefficients of pibblefit object |
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Return regression coefficients of pibblefit or orthusfit object |
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Create maltipoofit object |
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S3 for orthusfit apply names to orthusfit object |
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S3 for pibblefit apply names to pibblefit object |
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Generic method for applying names to an object |
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Generic method for getting and setting dimension names of fit object |
Generic method for fitting model from passed model fit object |
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Create orthusfit object |
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Create pibblefit object |
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Generic method for visualizing posterior predictive checks |
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Visualization of Posterior Predictive Check of fit model |
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Generic Method to Plot Posterior Predictive Summaries |
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Predict using basset |
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Predict response from new data |
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Predict response from new data |
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Plot Summaries of Posterior Distribution of pibblefit Parameters |
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Print dimensions and coordinate system information for an orthusfit or pibblefit object. |
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Print dimensions and coordinate system information for pibblefit object. |
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Print dimensions and coordinate system information for orthusfit object. |
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Sample from the prior distribution of pibblefit object |
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Generic method for sampling from prior distribution of object |
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Transform Fit fido Parameters to other representations |
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require elements to be non-null in pibblefit or throw error |
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require elements to be non-null in orthusfit or throw error |
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require elements to be non-null in pibblefit or throw error |
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Generic method for ensuring object contains required elements |
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Summarise pibblefit or orthusfit object and print posterior quantiles |
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Summarise pibblefit object and print posterior quantiles |
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Summarise orthusfit object and print posterior quantiles |
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Simple verification of passed bassetfit object |
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Simple verification of passed multipoo object |
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Simple verification of passed orthusfit object |
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Simple verification of passed pibblefit object |
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Generic method for verifying new objects |
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Helpful Utility MethodsJust that, mostly support other package functions |
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Compute the ALR of a matrix |
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Compute the inverse ALR of a matrix |
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Compute the ALR of an array |
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Compute the ALR of an array |
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Check vector/matrix/data.frame for expected dimensions or throw error |
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Compute the CLR of an array |
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Create a default ILR base |
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Gather Multidimensional Array to Tidy Tibble |
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Transform Lambda into IQLR (Inter-Quantile Log-Ratio) |
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Closure operator |
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Closure Operation applied to array on margin |
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Simulate simple orthus dataset and priors (for testing) |
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Convert orthus samples of Eta Lambda and Sigma to tidy format |
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Simulate simple pibble dataset and priors (for testing) |
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Convert pibble samples of Eta Lambda and Sigma to tidy format |
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Provide random initialization for pibble model |
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Holds information on coordinates system to later be reapplied |
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Shortcut for summarize variable with quantiles and mean |
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Utility Math FunctionsFast, C++, mostly for internal use |
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Convert orthus covariance matricies between representations |
Log of Multivarate Gamma Function - Gamma_p(a) |
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Derivative of Log of Multivariate Gamma Function - Gamma_p(a) |
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Log-Ratio transforms for orthus objects |
DatasetsExample Datasets |
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Data from Silverman et al. (2018) Microbiome |
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Data from Silverman et al. (2018) Microbiome |
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Data from Silverman et al. (2019) bioRxiv |
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Data from Silverman et al. (2019) bioRxiv |