fix_cluster: adjust cluster ids by specification

In zhenkewu/rewind: Reconstructing Etiology with Binary Decomposition

Description

adjust cluster ids by specification

Usage

fix_cluster(cluster_list, z, N, t, mylist)

Arguments

cluster_list	a list of clusters, each comprised of subject ids known to fall in the same cluster.
z, N, t, mylist	cluster ids for all subjects, cluster sizes, total # clusters, unique cluster ids (includes 0).

Value

z,N,t,mylist,c_next

Examples

# simulate data:
L0 <- 100   # dimension of measurements.
M0 <- 3     # true dimension of latent states.
K0 <- 2^M0     # true number of clusters.
options_sim0  <- list(N = 100,    # sample size.
                      M = M0,     # true number of machines.
                      L = L0,     # number of antibody landmarks.
                      K = K0,     # number of true components.
                      theta = rep(0.8,L0),  # true positive rates.
                      psi   = rep(0.15,L0), # false positive rates.
                      #alpha1 = 1, # half of the people have the first machine.
                      frac = 0.2, # fraction of positive dimensions (L-2M) in Q.
                      #pop_frac = rep(1/K0,K0) # population prevalences.
                      #pop_frac = (1:K0)/sum(1:K0) # population prevalences.
                      pop_frac = c(rep(2,4),rep(1,4)) # population prevalences.
                      #pop_frac = c(rep(0.75/4,4),rep(0.25/4,4))
)

simu     <- simulate_data(options_sim0, SETSEED=TRUE)

dat <- simu$datmat
t_max <- 40
n <- options_sim0$N
hc <- hclust(dist(dat),"complete")
t  <- floor(t_max/4)
z  <- cutree(hc,k = t)
mylist <- rep(0,t_max+3); mylist[1:t] <- 1:t  # mylist[1:t] is the list of active cluster IDs.
c_next <- t+1
N <- rep(0,t_max+3); N[1:t] <- table(z)
log_p <- rep(0,n+1)
zs <- z
S  <- rep(0,n)

# before forcing clusters:
list(z=z,N=N,t=t,mylist=mylist,c_next=c_next)

cl_list <- list(c(1:(rle(simu$Z)$lengths[1])), 
                c((1+rle(simu$Z)$lengths[1]):(rle(simu$Z)$lengths[2])))
cl_list
fix_cluster(cl_list,z,N,t,mylist)

zhenkewu/rewind documentation built on Sept. 9, 2020, 3:40 p.m.