I am trying to solve for the parameters of a gamma distribution that is convolved with both normal and lognormal distributions. I can experimentally derive parameters for both the normal and lognormal components, hence, I just want to solve for the gamma params.
I have attempted 3 approaches to this problem:
1) generating convolved random datasets (i.e. rnorm()+rlnorm()+rgamma()) and using least-squares regression on the linear- or log-binned histograms of the data (not shown, but was very biased by RNG and didn't optimize well at all.)
2) "brute-force" numerical integration of the convolving functions (example code #1)
3) numerical integration approaches w/ the distr package. (example code #2)
I have had limited success with all three approaches. Importantly, these approaches seem to work well for "nominal" values for the gamma parameters, but they all begin to fail when k(shape) is low and theta(scale) is high—which is where my experimental data resides. please find the examples below.
Straight-up numerical Integration
# make the functions
f.N <- function(n) dnorm(n, N[1], N[2])
f.L <- function(l) dlnorm(l, L[1], L[2])
f.G <- function(g) dgamma(g, G[1], scale=G[2])
# make convolved functions
f.Z <- function(z) integrate(function(x,z) f.L(z-x)*f.N(x), -Inf, Inf, z)$value # L+N
f.Z <- Vectorize(f.Z)
f.Z1 <- function(z) integrate(function(x,z) f.G(z-x)*f.Z(x), -Inf, Inf, z)$value # G+(L+N)
f.Z1 <- Vectorize(f.Z1)
# params of Norm, Lnorm, and Gamma
N <- c(0,5)
L <- c(2.5,.5)
G <- c(2,7) # this distribution is the one we ultimately want to solve for.
# G <- c(.5,10) # 0<k<1
# G <- c(.25,5e4) # ballpark params of experimental data
# generate some data
set.seed(1)
rN <- rnorm(1e4, N[1], N[2])
rL <- rlnorm(1e4, L[1], L[2])
rG <- rgamma(1e4, G[1], scale=G[2])
Z <- rN + rL
Z1 <- rN + rL + rG
# check the fit
hist(Z,freq=F,breaks=100, xlim=c(-10,50), col=rgb(0,0,1,.25))
hist(Z1,freq=F,breaks=100, xlim=c(-10,50), col=rgb(1,0,0,.25), add=T)
z <- seq(-10,50,1)
lines(z,f.Z(z),lty=2,col="blue", lwd=2) # looks great... convolution performs as expected.
lines(z,f.Z1(z),lty=2,col="red", lwd=2) # this works perfectly so long as k(shape)>=1
# I'm guessing the failure to compute when shape 0 < k < 1 is due to
# numerical integration problems, but I don't know how to fix it.
integrate(dgamma, -Inf, Inf, shape=1, scale=1) # ==1
integrate(dgamma, 0, Inf, shape=1, scale=1) # ==1
integrate(dgamma, -Inf, Inf, shape=.5, scale=1) # !=1
integrate(dgamma, 0, Inf, shape=.5, scale=1) # != 1
# Let's try to estimate gamma anyway, supposing k>=1
optimFUN <- function(par, N, L) {
print(par)
-sum(log(f.Z1(Z1[1:4e2])))
}
f.G <- function(g) dgamma(g, par[1], scale=par[2])
fitresult <- optim(c(1.6,5), optimFUN, N=N, L=L)
par <- fitresult$par
lines(z,f.Z1(z),lty=2,col="green3", lwd=2) # not so great... likely better w/ more data,
# but it is SUPER slow and I observe large step sizes.
Attempting convolving via distr package
# params of Norm, Lnorm, and Gamma
N <- c(0,5)
L <- c(2.5,.5)
G <- c(2,7) # this distribution is the one we ultimately want to solve for.
# G <- c(.5,10) # 0<k<1
# G <- c(.25,5e4) # ballpark params of experimental data
# make the distributions and "convolvings'
dN <- Norm(N[1], N[2])
dL <- Lnorm(L[1], L[2])
dG <- Gammad(G[1], G[2])
d.NL <- d(convpow(dN+dL,1))
d.NLG <- d(convpow(dN+dL+dG,1)) # for large values of theta, no matter how I change
# getdistrOption("DefaultNrFFTGridPointsExponent"), grid size is always wrong.
# Generate some data
set.seed(1)
rN <- r(dN)(1e4)
rL <- r(dL)(1e4)
rG <- r(dG)(1e4)
r.NL <- rN + rL
r.NLG <- rN + rL + rG
# check the fit
hist(r.NL, freq=F, breaks=100, xlim=c(-10,50), col=rgb(0,0,1,.25))
hist(r.NLG, freq=F, breaks=100, xlim=c(-10,50), col=rgb(1,0,0,.25), add=T)
z <- seq(-10,50,1)
lines(z,d.NL(z), lty=2, col="blue", lwd=2) # looks great... convolution performs as expected.
lines(z,d.NLG(z), lty=2, col="red", lwd=2) # this appears to work perfectly
# for most values of K and low values of theta
# this is looking a lot more promising... how about estimating gamma params?
optimFUN <- function(par, dN, dL) {
tG <- Gammad(par[1],par[2])
d.NLG <- d(convpow(dN+dL+tG,1))
p <- d.NLG(r.NLG)
p[p==0] <- 1e-15 # because sometimes very low probabilities evaluate to 0...
# ...and logs don't like that.
-sum(log(p))
}
fitresult <- optim(c(1,1e4), optimFUN, dN=dN, dL=dL)
fdG <- Gammad(fitresult$par[1], fitresult$par[2])
fd.NLG <- d(convpow(dN+dL+fdG,1))
lines(z,fd.NLG(z), lty=2, col="green3", lwd=2) ## this works perfectly when ~k>1 & ~theta<100... but throws
## "Error in validityMethod(object) : shape has to be positive" when k decreases and/or theta increases
## (boundary subject to RNG).
Can i speed up the integration in example 1? can I increase the grid size in example 2 (distr package)? how can I address the k<1 problem? can I rescale the data in a way that will better facilitate evaluation at high theta values? Is there a better way all-together? Help!
