Description Usage Arguments Value Examples
q_mv_gr2
calculates the gradient of q_mv2
.
q_mv_gr2
calculates the target function for each k
instead of all k.
1 | q_mv_gr2(pars, X, E, L, k)
|
pars |
a vector of length 2. c(v[k], m[k]) |
X |
a list of vectors of observed states x |
E |
a vector of normalizing constant for each observed chain in X |
L |
a list of matrix L from |
k |
a scalar indicating which state is calculated |
A vector of length 2, the gradient for q_mv2.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | df <- uORF[1:10]
X <- L <- list()
E <- c()
for (i in 1:length(df)){
X[[i]] <- df[[i]]$x
RNA[[i]] <- df[[i]]$RNA
E[i]=df[[i]]$E; trans=df[[i]]$trans;
a=df[[i]]$v; b=df[[i]]$v/df[[i]]$m
la <- forwardAlg(X[[i]], RNA[[i]], trans, a, b, E[i])
lb <- backwardAlg(X[[i]], RNA[[i]], trans, a, b, E[i])
L[[i]] <- computeL(la, lb)
}
pars <- c(df[[1]]$v, df[[1]]$m)
# check by comparing with numeric approximation
require(numDeriv)
D1 <- rep(0,42)
for (k in 1:21){
D1[c(k,21+k)] <- grad(function(u) q_mv2(u,X,E,L,k) , pars[c(k,21+k)])
}
D2 <- rep(0,42)
for (k in 1:21){
D2[c(k,21+k)] <- q_mv_gr2(pars[c(k,21+k)], X, E, L, k)
}
print(round(D1-D2, 10))
|
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