Man pages for AurMad/STOCfree
STOC free model: prediction of probability of freedom from longitudinal data
| add_risk_factor | Adds a risk factor to a new infection dataset |
| date_from_lag | Generates an initial date from a reference date and a time... |
| dnorm_logit | The normal distribution on the logit scale |
| ess_STOCfree_param | Effective sample sizes of STOC free model parameters |
| extract_herd_from_status_id | Extract data from a STOCfree_data object based on status ids |
| extract_STOCfree_month_prev | Extracting draws from the posterior distributions for monthly... |
| extract_STOCfree_param | Extracting parameter MCMC samples from the results of a STOC... |
| extract_STOCfree_pred | Extracting MCMC samples for the predicted probabilities of... |
| herdBTM | Bulk tank milk ELISA test results for 100 herds |
| herd_summary | Summary of herd level probabilities of infection generated by... |
| intro | Date and number of animals introduced in the tested farms |
| invlogit | Inverse logit function |
| logit | logit function |
| logit_nwinf | Logistic regression for the probability of new infection |
| logit_nwinf_lagged | Modelling of all possible lagged relationships between risk... |
| make_month_id | Creates a data.frame with first date of month and... |
| make_nwinf_data | Creates a dataset with new infection events from herd level... |
| param_summary | Summary quantiles for the STOC free model parameters |
| plot_priors_rf | Plotting prior distributions for the risk factors of new... |
| plot_priors_status_dyn | Plots the prior distributions for the parameters related to... |
| plot_priors_tests | Plot the distribution for the prior distributions on test... |
| plot.STOCfree_month_prev | Boxplot of monthly prevalences predicted by the STOC free... |
| plot.STOCfree_param | plot method for STOCfree parameters |
| plot.STOCfree_pred | plot method for herd-level predicted probabilities of being... |
| print.STOCfree_param | print method for STOCfree parameters |
| print.STOCfree_pred | print method for predicted probabilities of status positive |
| read_STOCfree_month_prev | Importing output files for predicted monthly prevalences... |
| read_STOCfree_param | Importing MCMC samples for model parameters from the results... |
| read_STOCfree_pred | Importing MCMC samples for the predicted probabilities of... |
| set_priors_rf | Set priors associated with risk factors of new infection |
| set_priors_status_dyn | Sets the parameters associated with priors related to... |
| set_priors_tests | Set parameters for the Beta distributions used to represent... |
| sf_add_risk_factor | Add a risk factor to STOCfree_data |
| sf_remove_risk_factor | Remove risk factor from STOCfree_data |
| show_priors_status_dyn | Shows the parameters associated with priors related to... |
| show_rf | List of risk factors of new infection in a STOCfree_data |
| show_tests | Shows parameter of the Beta distributions used to represent... |
| STOCfree_data | STOCfree_data class |
| STOCfree_JAGS | JAGS implementation of the STOC free model |
| STOCfree_JAGS_data | Creates the JAGS model input data |
| STOCfree_Stan | Stan implementation of the STOC free model |
| summary.STOCfree_param | summary method for the STOCfree_param class |
| summary.STOCfree_pred | summary method for herd-level predicted probabilities of... |
| write_JAGS_model | Writes a text file with the JAGS model. For internal use. |
| write_Stan_model | Writes the code for the Stan model. For internal use. |
