Nothing
example.optim.pcl = function() {
##
library(NBPSeq);
data(arab);
grp.ids = c(1, 1, 1, 2, 2, 2);
obj = prepare.nbp(arab, grp.ids);
## Fit a NBP model
par.init = c(log(0.1), 0);
par.lower = c(log(1e-20), -1.1);
par.upper = c(0, 0.1);
## debug(optim.pcl);
nbp = optim.pcl(obj, log.phi.nbp, par.init, par.lower, par.upper, print.level=5);
## Fit a NBQ model
par.init = c(log(0.1), 0, 0);
par.lower = c(log(1e-20), -1.0, -0.2);
par.upper = c(0, 1.0, 0.2);
nbq = optim.pcl(obj, log.phi.nbq, par.init, par.lower, par.upper, print.level=5);
## Fit a NB2 model
par.init = log(0.1);
par.lower = log(1e-20);
par.upper = log(10);
## debug(optim.pcl);
nb2 = optim.pcl(obj, log.phi.nb2, par.init, par.lower, par.upper, method="Brent", print.level=4);
pi = rowMeans(obj$pseudo.counts)/obj$pseudo.lib.sizes[1];
m = length(pi)
phi = matrix(0, m, 3);
phi[,1] = nb2$fun(nb2$par, pi);
phi[,2] = nbp$fun(nbp$par, pi);
phi[,3] = nbq$fun(nbq$par, pi);
matplot(pi, phi, log="x");
}
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