Estimating Infection Rates from Serological Data
kinetics of the antibody (ab) response (power function decay)
Analyze simulation results
Load antibody decay curve parameter
Load noise parameters
Load a cross-sectional antibody survey data set
Load longitudinal seroresponse parameters
Graph antibody decay curves by antigen isotype
Plot distribution of antibodies
Plot seroincidence.by log-likelihoods
Plot the log-likelihood curve for the incidence rate estimate
Plot simulation results autoplot() method for sim_results objects
Plot method for summary.seroincidence.by objects
Substitute baseline values
Check the formatting of a cross-sectional antibody survey dataset.
Count observations by stratum
Convert a data.frame (or tibble) into a multidimensional array
Convert a data.frame (or tibble) into a multidimensional array
Calculate negative log-likelihood
Estimate Seroincidence
Find the maximum likelihood estimate of the incidence rate parameter
Estimate Seroincidence
Estimate Seroincidence
Snapshot testing for data.frame s
Calculate negative log-likelihood (deviance) for one antigen:isotype p...
Calculate negative log-likelihood (deviance) for one antigen:isotype p...
Calculate negative log-likelihood (deviance)
Extract biomarker levels
Get biomarker variable name
Extract biomarker names column
Extract antibody measurement values
Get antibody measurement values
Graph log-likelihood of data
graph antibody decay curves by antigen isotype
Graph estimated antibody decay curves
Get person ID variable name
Get person IDs
extract a row from longitudinal parameter set
Calculate log-likelihood
Load antibody decay curve parameter samples
Load noise parameters
Load a cross-sectional antibody survey data set
Load longitudinal seroresponse parameter samples
Calculate log-likelihood
generate random sample from baseline distribution
Graph an antibody decay curve model
Print Method for seroincidence.by Object
Print Method for seroincidence Class
Print Method for Seroincidence Summary Object
Objects exported from other packages
Get path to an example file
serocalculator: Estimating Infection Rates from Serological Data
Specify person ID column
Simulate multiple data sets
Simulate a cross-sectional serosurvey with noise
Simulate multiple data sets
Simulate a cross-sectional serosurvey with noise
collect cross-sectional data
simulate antibody kinetics of y over a time interval
Barplot method for summary.seroincidence.by objects
Scatterplot method for summary.seroincidence.by objects
Extract the Strata attribute from an object, if present
Extract Strata metadata from an object
Split data by stratum
Extract or replace parts of a seroincidence.by object
Summarize cross-sectional antibody survey data
Summary Method for "seroincidence.by" Objects
Summarizing fitted seroincidence models
Warn about missing stratifying variables in a dataset
Translates antibody levels measured in cross-sectional population samples into estimates of the frequency with which seroconversions (infections) occur in the sampled populations. Replaces the previous `seroincidence` package.
Useful links