Man pages for fido
Bayesian Multinomial Logistic Normal Regression
| access_dims | Generic method for accessing model fit dimensions |
| alr | Compute the ALR of a matrix |
| alr_array | Compute the ALR of an array |
| alrInv | Compute the inverse ALR of a matrix |
| alrInv_array | Compute the ALR of an array |
| as.list.orthusfit | Convert object of class orthusfit to a list |
| as.list.pibblefit | Convert object of class pibblefit to a list |
| as.orthusfit | convert list to orthusfit |
| as.pibblefit | convert list to pibblefit |
| basset_fit | Interface to fit basset models |
| check_dims | Check vector/matrix/data.frame for expected dimensions or... |
| clr_array | Compute the CLR of an array |
| coef.orthusfit | Return regression coefficients of orthus object |
| coef.pibblefit | Return regression coefficients of pibblefit object |
| conjugateLinearModel | Solve Bayesian Multivariate Conjugate Linear Model |
| convert_orthus_covariance | Convert orthus covariance matricies between representations |
| create_default_ilr_base | Create a default ILR base |
| fido_package | fido: Fitting and Analysis of Multinomial Logistic Normal... |
| fido_transforms | Transform Fit fido Parameters to other representations |
| gather_array | Gather Multidimensional Array to Tidy Tibble |
| kernels | Multivariate RBF Kernel |
| lambda_to_iqlr | Transform Lambda into IQLR (Inter-Quantile Log-Ratio) |
| lmvgamma | Log of Multivarate Gamma Function - Gamma_p(a) |
| lmvgamma_deriv | Derivative of Log of Multivariate Gamma Function - Gamma_p(a) |
| loglikPibbleCollapsed | Calculations for the Collapsed Pibble Model |
| mallard | Data from Silverman et al. (2018) Microbiome |
| mallard_family | Data from Silverman et al. (2018) Microbiome |
| metadata | Data from Silverman et al. (2019) bioRxiv |
| miniclo | Closure operator |
| miniclo_array | Closure Operation applied to array on margin |
| mongrel-deprecated | mongrel |
| name | Generic method for applying names to an object |
| name_dims | Generic method for getting and setting dimension names of fit... |
| name.orthusfit | S3 for orthusfit apply names to orthusfit object |
| name.pibblefit | S3 for pibblefit apply names to pibblefit object |
| optimPibbleCollapsed | Function to Optimize the Collapsed Pibble Model |
| orthusfit | Create orthusfit object |
| orthus_fit | Interface to fit orthus models |
| orthus_lr_transforms | Log-Ratio transforms for orthus objects |
| orthus_sim | Simulate simple orthus dataset and priors (for testing) |
| orthus_tidy_samples | Convert orthus samples of Eta Lambda and Sigma to tidy format |
| pcrbias_mock | Data from Silverman et al. (2019) bioRxiv |
| pibblefit | Create pibblefit object |
| pibble_fit | Interface to fit pibble models |
| pibble_sim | Simulate simple pibble dataset and priors (for testing) |
| pibble_tidy_samples | Convert pibble samples of Eta Lambda and Sigma to tidy format |
| plot.pibblefit | Plot Summaries of Posterior Distribution of pibblefit... |
| ppc | Generic method for visualizing posterior predictive checks |
| ppc.pibblefit | Visualization of Posterior Predictive Check of fit model |
| ppc_summary | Generic Method to Plot Posterior Predictive Summaries |
| predict.bassetfit | Predict using basset |
| predict.pibblefit | Predict response from new data |
| print.orthusfit | Print dimensions and coordinate system information for... |
| print.pibblefit | Print dimensions and coordinate system information for... |
| r2 | Generic Method to Calculate R2 for Fitted Model |
| random_pibble_init | Provide random initialization for pibble model |
| refit | Generic method for fitting model from passed model fit object |
| req | Generic method for ensuring object contains required elements |
| req.orthusfit | require elements to be non-null in orthusfit or throw error |
| req.pibblefit | require elements to be non-null in pibblefit or throw error |
| RISK_CCFA | Data from Gevers et al. (2014) |
| RISK_CCFA_otu | Data from Gevers et al. (2014) |
| RISK_CCFA_sam | Data from Gevers et al. (2014) |
| RISK_CCFA_tax | Data from Gevers et al. (2014) |
| sample_prior | Generic method for sampling from prior distribution of object |
| sample_prior.pibblefit | Sample from the prior distribution of pibblefit object |
| store_coord | Holds information on coordinates system to later be reapplied |
| summarise_posterior | Shortcut for summarize variable with quantiles and mean |
| summary.orthusfit | Summarise orthusfit object and print posterior quantiles |
| summary.pibblefit | Summarise pibblefit object and print posterior quantiles |
| uncollapsePibble | Uncollapse output from optimPibbleCollapsed to full pibble... |
| uncollapsePibble_sigmaKnown | Uncollapse output from optimPibbleCollapsed to full pibble... |
| verify | Generic method for verifying new objects |
| verify.bassetfit | Simple verification of passed bassetfit object |
| verify.orthusfit | Simple verification of passed orthusfit object |
| verify.pibblefit | Simple verification of passed pibblefit object |
| Y | Data from Silverman et al. (2019) bioRxiv |
