Man pages for serocalculator
Estimating Infection Rates from Serological Data
| ab | kinetics of the antibody (ab) response (power function decay) |
| as_curve_params | Load antibody decay curve parameter |
| as_noise_params | Load noise parameters |
| as_pop_data | Load a cross-sectional antibody survey data set |
| autoplot.curve_params | graph antibody decay curves by antigen isotype |
| autoplot.pop_data | Plot distribution of antibodies |
| autoplot.seroincidence | Plot the log-likelihood curve for the incidence rate estimate |
| autoplot.seroincidence.by | Plot 'seroincidence.by' log-likelihoods |
| autoplot.summary.seroincidence.by | Plot method for 'summary.seroincidence.by' objects |
| check_pop_data | Check the formatting of a cross-sectional antibody survey... |
| df.to.array | Convert a data.frame (or tibble) into a multidimensional... |
| dot-nll | Calculate negative log-likelihood |
| est.incidence | Find the maximum likelihood estimate of the incidence rate... |
| est.incidence.by | Estimate Seroincidence |
| example_noise_params_pk | Small example of noise parameters for typhoid |
| fdev | Calculate negative log-likelihood (deviance) |
| f_dev | Calculate negative log-likelihood (deviance) for one... |
| f_dev0 | Calculate negative log-likelihood (deviance) for one... |
| graph.curve.params | Graph estimated antibody decay curve |
| graph_loglik | Graph log-likelihood of data |
| ldpar | extract a row from longitudinal parameter set |
| llik | Calculate log-likelihood |
| load_curve_params | Load antibody decay curve parameter samples |
| load_noise_params | Load noise parameters |
| load_pop_data | Load a cross-sectional antibody survey data set |
| log_likelihood | Calculate log-likelihood |
| mkbaseline | generate random sample from baseline distribution |
| mk_baseline | generate random sample from baseline distribution |
| plot_curve_params_one_ab | Graph an antibody decay curve model |
| print.seroincidence | Print Method for 'seroincidence' Object |
| print.seroincidence.by | Print Method for 'seroincidence.by' Object |
| print.summary.seroincidence.by | Print Method for Seroincidence Summary Object |
| reexports | Objects exported from other packages |
| row_longitudinal_parameter | extract a row from longitudinal parameter set |
| sees_pop_data_pk_100 | Small example cross-sectional data set |
| sees_pop_data_pk_100_old_names | Small example cross-sectional data set |
| serocalculator | Estimating Infection Rates from Serological Data |
| serocalculator_example | Get path to an example file |
| sim.cs | Simulate a cross-sectional serosurvey with noise |
| sim.cs.multi | Simulate multiple data sets |
| simcs.tinf | collect cross-sectional data |
| simresp.tinf | simulate antibody kinetics of y over a time interval |
| strata | Extract strata from an object |
| strata.seroincidence.by | Extract the 'Strata' attribute from an object, if present |
| stratify_data | Split data by stratum |
| sub-.seroincidence.by | Extract or replace parts of a 'seroincidence.by' object |
| summary.pop_data | Summarize cross-sectional antibody survey data |
| summary.seroincidence | Summarizing fitted seroincidence models |
| summary.seroincidence.by | Summary Method for '"seroincidence.by"' Objects |
| typhoid_curves_nostrat_100 | Small example of antibody response curve parameters for... |
| warn.missing.strata | Warn about missing stratifying variables in a dataset |
