frtm | R Documentation |
Function to fit the FRTM model of Cunningham, Hume et al (1991) to data.
frtm(
t_tac,
reftac,
roitac,
weights = NULL,
frameStartEnd = NULL,
R1.start = 1,
R1.lower = 0,
R1.upper = 10,
k2.start = 0.1,
k2.lower = 0,
k2.upper = 1,
bp.start = 1.5,
bp.lower = 0,
bp.upper = 15,
k4.start = 0.1,
k4.lower = 0,
k4.upper = 1,
multstart_iter = 1,
multstart_lower = NULL,
multstart_upper = NULL,
printvals = F
)
t_tac |
Numeric vector of times for each frame in minutes. We use the time halfway through the frame as well as a zero. If a time zero frame is not included, it will be added. |
reftac |
Numeric vector of radioactivity concentrations in the reference tissue for each frame. We include zero at time zero: if not included, it is added. |
roitac |
Numeric vector of radioactivity concentrations in the target tissue for each frame. We include zero at time zero: if not included, it is added. |
weights |
Optional. Numeric vector of the weights assigned to each frame in the fitting. We include zero at time zero: if not included, it is added. If not specified, uniform weights will be used. |
frameStartEnd |
Optional. This allows one to specify the beginning and final frame to use for modelling, e.g. c(1,20). This is to assess time stability. |
R1.start |
Optional. Starting parameter for fitting of R1. Default is 1. |
R1.lower |
Optional. Lower bound for the fitting of R1. Default is 0. |
R1.upper |
Optional. Upper bound for the fitting of R1. Default is 10. |
k2.start |
Optional. Starting parameter for fitting of k2. Default is 0.1. |
k2.lower |
Optional. Lower bound for the fitting of k2. Default is 0. |
k2.upper |
Optional. Upper bound for the fitting of k2. Default is 1. |
bp.start |
Optional. Starting parameter for fitting of bp. Default is 0.1. |
bp.lower |
Optional. Lower bound for the fitting of bp. Default is 0. |
bp.upper |
Optional. Upper bound for the fitting of bp. Default is 1. |
k4.start |
Optional. Starting parameter for fitting of k4. Default is 0.1. |
k4.lower |
Optional. Lower bound for the fitting of k4. Default is 0. |
k4.upper |
Optional. Upper bound for the fitting of k4. Default is 1. |
multstart_iter |
Number of iterations for starting parameters. Default
is 1. For more information, see |
multstart_lower |
Optional. Lower bounds for starting parameters. Defaults to the lower bounds. Named list of whichever parameters' starting bounds should be altered. |
multstart_upper |
Optional. Upper bounds for starting parameters. Defaults to the upper bounds. Named list of whichever parameters' starting bounds should be altered. |
printvals |
Optional. This displays the parameter values for each iteration of the model. This is useful for debugging and changing starting values and upper and lower bounds for parameters. |
A list with a data frame of the fitted parameters out$par
,
their percentage standard errors out$par.se
, the model fit object
out$fit
, the model weights out$weights
, and a dataframe
containing the TACs both of the data and the fitted values out$tacs
.
Granville J Matheson, mathesong@gmail.com
Cunningham, Vincent J., et al. "Compartmental analysis of diprenorphine binding to opiate receptors in the rat in vivo and its comparison with equilibrium data in vitro." Journal of Cerebral Blood Flow & Metabolism 11.1 (1991): 1-9.
data(simref)
t_tac <- simref$tacs[[2]]$Times
reftac <- simref$tacs[[2]]$Reference
roitac <- simref$tacs[[2]]$ROI1
weights <- simref$tacs[[2]]$Weights
fit1 <- frtm(t_tac, reftac, roitac)
fit2 <- frtm(t_tac, reftac, roitac, weights, frameStartEnd = c(1, 33))
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