This function calculates the time to suppress HIV below a specified threshold.
get_TTS(model_output = NULL, data = NULL, suppression_threshold = 20,
uppertime = 365, decline_buffer = 500, parametric = TRUE,
ARTstart = FALSE, npoints = 1000)output from fitting model. Only required if parametric = TRUE.
raw data set. Must be a data frame with the following columns: 'id' - stating the unique identifier for each subject; 'vl'- numeric vector stating the viral load measurements for each subject; 'time' - numeric vector stating the time at which each measurement was taken. Only required if parametric = FALSE.
suppression threshold: measurements below this value will be assumed to represent viral suppression. Typically this would be the detection threshold of the assay. Default value is 20.
the maximum time interval to search for the time to suppression. Default value is 365.
the maximum allowable deviation of values away from a strictly decreasing sequence in viral load. This allows for e.g. measurement noise and small fluctuations in viral load. Default value is 500.
logical TRUE/FALSE indicating whether time to suppression should be calculated using the parametric (TRUE) or non-parametric (FALSE) method. If TRUE, a fitted model object is required. If FALSE, the raw data frame is required. Defaults to TRUE.
logical TRUE/FALSE indicating whether the time to suppression should be represented as time since ART initiation. Default = FALSE. If TRUE, ART initiation times must be included as a data column named 'ART'.
numeric value of the number of interpolation points to be considered. Default is 1000.
a data frame containing all individuals who fit the inclusion criteria, along with their TTS estimates, and a column indicating whether the parametric or nonparametric approach was used.
Options include: parametric (i.e. using the fitted model) or non-parametric (i.e. interpolating the processed data).
# NOT RUN {
set.seed(1234567)
simulated_data <- simulate_data(nsubjects = 20)
get_TTS(data = simulated_data, parametric = FALSE)
# }
Run the code above in your browser using DataCamp Workspace