I calculate the life expectancy of the Siler survival model, which involves an integral over the survival function via the R-native integrate(). For certain values of one parameter, this integral behaves weirdly when the upper bound is set to Inf The following plot crated by the reprex below shows the basic problem.
Plot: Integral value for different values of parameter l:
The weird jump at ca. 0.06 vanishes if I set the upper bound to a lesser value, e.g. 5000. What causes this behaviour?
Reproducible Example
library(purrr)
# Define the function to be integrated:
cumulative_hazard_siler = function(a, gamma, delta, A, R, alpha){
((gamma/delta) * ( 1 - exp(-delta * a))) + A*a + ((R/alpha) * ( exp(alpha * a) - 1))
}
survival_siler = function(a, gamma, delta, A, R, alpha){
exp(-cumulative_hazard_siler(a, gamma, delta, A, R, alpha))
}
# This is an interface to calculate the parameter R from the parameters l and s
LS_R = function(l, s){
1 / (s * exp(l/s))
}
# Standard Parameter values
gamma = 0.04687249
delta = 2.450284
A = 0.001597077
l = 76.37937
s = 11.18984
# A fine grid of changes which will be applied to parameter l
grid = (500:700)/10000
# Calculate the integral for all changes in l
estimates = map_dbl(grid,
~integrate(survival_siler,
lower = 0,
upper = Inf,
gamma,
delta,
A,
R = LS_R(l - .x, s),
1/s)$value)
# Visualisation
plot(x = grid, y = estimates, type = "line")
I have found no examples of neldermead() on the internet, so I figured I would post the following. That said, I cant figure out how to control the max number of iterations of the algorithm.
https://cran.r-project.org/web/packages/neldermead/neldermead.pdf
Which states the following:
optbase An object of class ’optimbase’, i.e. a list created by optimbase() and containing the following elements:
iterations The number of iterations.
Working example of using Nelder Mead to fit a parabola by minimizing the residuals
library(neldermead); library(nloptr);
## ========= Minimizing the residuals for a 2d quadrature =========== ##
x2d = seq(-4,6,length.out=50); ## x vector definition
ynoise = runif(n=50, min=-2, max = 2) ## noise
y2d = 1.3 + (x2d-2.1)^2 + ynoise ## y data for fitting
## Fitting with nelder-mead
quadmin <- function(x){ sum( (y2d - x[1] - (x2d - x[2])^2)^2 ) }
x000 <- c(1, 2)
sol2d <- neldermead(x0 = x000, fn = quadmin)
sol2d
yfit = sol2d[[1]][1] + (x2d - sol2d[[1]][2])^2 ## Fitted curve.
plot(x2d, y2d); lines(x2d, yfit) ## Plotting
But I'm looking to do something like:
sol2d <- neldermead(x0 = x000, fn = quadmin, iterations = 200)
^^^ which doesn't work. Neither does putting it into a list:
sol2d <- neldermead(x0 = x000, fn = quadmin, optbase = list(iterations = 200))
This is a basic question about how to use these arguments, so I apologize if this isn't the right title. In advance, thank you for your help.
There are at least tow neldermead functions available in R. One is from the package neldermead which correspond to the documentation you link.
I have not been able to make it work. It gives me back neither error or solution.
The code:
library(neldermead)
library(nloptr)
## ========= Minimizing the residuals for a 2d quadrature =========== ##
x2d = seq(-4,6,length.out=50); ## x vector definition
ynoise = runif(n=50, min=-2, max = 2) ## noise
y2d = 1.3 + (x2d-2.1)^2 + ynoise ## y data for fitting
## Fitting with nelder-mead
quadmin <- function(x){
sum(y2d - x[1] - (x2d - x[2])^2)^2 }
x000 <- c(1, 2)
opt <- optimbase(x0 = as.matrix(x000),fx0 = -1000,maxiter = 200,fopt = quadmin,verbose=T)
sol2d <- neldermead::neldermead(opt)
On the other hand, package nloptr also provides a neldermedad function which sintax looks closer to you code and I have been able to run:
library(neldermead)
library(nloptr)
## ========= Minimizing the residuals for a 2d quadrature =========== ##
x2d = seq(-4,6,length.out=50); ## x vector definition
ynoise = runif(n=50, min=-2, max = 2) ## noise
y2d = 1.3 + (x2d-2.1)^2 + ynoise ## y data for fitting
## Fitting with nelder-mead
quadmin <- function(x){
sum(y2d - x[1] - (x2d - x[2])^2)^2 }
x000 <- c(1, 2)
sol2d <- nloptr::neldermead(x0 = x000,fn =quadmin,control =list(maxeval=200))
yfit = sol2d[[1]][1] + (x2d - sol2d[[1]][2])^2 ## Fitted curve.
plot(x2d, y2d); lines(x2d, yfit)
As you can see, the only issue with you code was the control part.
Best!
I first want to sample 100 gamma distributed numbers where shape = 2 and scale = 1/2. I wrote down the log-likelyhood function and negated it since I'm using a minimization tool to maximize. I also tried using optim but to no avail. both optim and nlm gave me different answers. This is my code thus far:
N = 100
shape = 2
scale = 1/2
Data <- rgamma(SampSize, shape, scale)
LogL = function (x){
k = x[1]
gamma = x[2]
(-1)*(N*x[1]*log(x[2])+(x[1]-1)*sum(log(Data))-x[2]*sum(Data))
}
nlm(LogL,c(1.5,1))
logL <- function (x) -sum(dgamma(Data, x[1], x[2], log = TRUE))
N = 100
shape = 2
scale = 1/2
Data <- rgamma(N, shape, scale)
optim(c(1.5, 1), logL)$par
nlm(logL, c(1.5, 1))$estimate
Some background: the nlm function in R is a general purpose optimization routine that uses Newton's method. To optimize a function, Newton's method requires the function, as well as the first and second derivatives of the function (the gradient vector and the Hessian matrix, respectively). In R the nlm function allows you to specify R functions that correspond to calculations of the gradient and Hessian, or one can leave these unspecified and numerical solutions are provided based on numerical derivatives (via the deriv function). More accurate solutions can be found by supplying functions to calculate the gradient and Hessian, so it's a useful feature.
My problem: the nlm function is slower and often fails to converge in a reasonable amount of time when the analytic Hessian is supplied. I'm guessing this is some sort of bug in the underlying code, but I'd be happy to be wrong. Is there a way to make nlm work better with an analytic Hessian matrix?
Example: my R code below demonstrates this problem using a logistic regression example, where
log(Pr(Y=1)/Pr(Y=0)) = b0 + Xb
where X is a multivariate normal of dimension N by p and b is a vector of coefficients of length p.
library(mvtnorm)
# example demonstrating a problem with NLM
expit <- function(mu) {1/(1+exp(-mu))}
mk.logit.data <- function(N,p){
set.seed(1232)
U = matrix(runif(p*p), nrow=p, ncol=p)
S = 0.5*(U+t(U)) + p*diag(rep(1,p))
X = rmvnorm(N, mean = runif(p, -1, 1), sigma = S)
Design = cbind(rep(1, N), X)
beta = sort(sample(c(rep(0,p), runif(1))))
y = rbinom(N, 1, expit(Design%*%beta))
list(X=X,y=as.numeric(y),N=N,p=p)
}
# function to calculate gradient vector at given coefficient values
logistic_gr <- function(beta, y, x, min=TRUE){
mu = beta[1] + x %*% beta[-1]
p = length(beta)
n = length(y)
D = cbind(rep(1,n), x)
gri = matrix(nrow=n, ncol=p)
for(j in 1:p){
gri[,j] = D[,j]*(exp(-mu)*y-1+y)/(1+exp(-mu))
}
gr = apply(gri, 2, sum)
if(min) gr = -gr
gr
}
# function to calculate Hessian matrix at given coefficient values
logistic_hess <- function(beta, y, x, min=TRUE){
# allow to fail with NA, NaN, Inf values
mu = beta[1] + x %*% beta[-1]
p = length(beta)
n = length(y)
D = cbind(rep(1,n), x)
h = matrix(nrow=p, ncol=p)
for(j in 1:p){
for(k in 1:p){
h[j,k] = -sum(D[,j]*D[,k]*(exp(-mu))/(1+exp(-mu))^2)
}
}
if(min) h = -h
h
}
# function to calculate likelihood (up to a constant) at given coefficient values
logistic_ll <- function(beta, y,x, gr=FALSE, he=FALSE, min=TRUE){
mu = beta[1] + x %*% beta[-1]
lli = log(expit(mu))*y + log(1-expit(mu))*(1-y)
ll = sum(lli)
if(is.na(ll) | is.infinite(ll)) ll = -1e16
if(min) ll=-ll
# the below specification is required for using analytic gradient/Hessian in nlm function
if(gr) attr(ll, "gradient") <- logistic_gr(beta, y=y, x=x, min=min)
if(he) attr(ll, "hessian") <- logistic_hess(beta, y=y, x=x, min=min)
ll
}
First example, with p=3:
dat = mk.logit.data(N=100, p=3)
The glm function estimates are for reference. nlm should give the same answer, allowing for small errors due to approximation.
(glm.sol <- glm(dat$y~dat$X, family=binomial()))$coefficients
> (Intercept) dat$X1 dat$X2 dat$X3
> 0.00981465 0.01068939 0.04417671 0.01625381
# works when correct analytic gradient is specified
(nlm.sol1 <- nlm(p=runif(dat$p+1), f=logistic_ll, gr=TRUE, y=dat$y, x=dat$X))$estimate
> [1] 0.009814547 0.010689396 0.044176627 0.016253966
# works, but less accurate when correct analytic hessian is specified (even though the routine notes convergence is probable)
(nlm.sol2 <- nlm(p=runif(dat$p+1), f=logistic_ll, gr=TRUE, he=TRUE, y=dat$y, x=dat$X, hessian = TRUE, check.analyticals=TRUE))$estimate
> [1] 0.009827701 0.010687278 0.044178416 0.016255630
But the problem becomes apparent when p is larger, here it is 10
dat = mk.logit.data(N=100, p=10)
Again, glm solution for reference. nlm should give the same answer, allowing for small errors due to approximation.
(glm.sol <- glm(dat$y~dat$X, family=binomial()))$coefficients
> (Intercept) dat$X1 dat$X2 dat$X3 dat$X4 dat$X5 dat$X6 dat$X7
> -0.07071882 -0.08670003 0.16436630 0.01130549 0.17302058 0.03821008 0.08836471 -0.16578959
> dat$X8 dat$X9 dat$X10
> -0.07515477 -0.08555075 0.29119963
# works when correct analytic gradient is specified
(nlm.sol1 <- nlm(p=runif(dat$p+1), f=logistic_ll, gr=TRUE, y=dat$y, x=dat$X))$estimate
> [1] -0.07071879 -0.08670005 0.16436632 0.01130550 0.17302057 0.03821009 0.08836472
> [8] -0.16578958 -0.07515478 -0.08555076 0.29119967
# fails to converge in 5000 iterations when correct analytic hessian is specified
(nlm.sol2 <- nlm(p=runif(dat$p+1), f=logistic_ll, gr=TRUE, he=TRUE, y=dat$y, x=dat$X, hessian = TRUE, iterlim=5000, check.analyticals=TRUE))$estimate
> [1] 0.31602065 -0.06185190 0.10775381 -0.16748897 0.05032156 0.34176104 0.02118631
> [8] -0.01833671 -0.20364929 0.63713991 0.18390489
Edit: I should also add that I have confirmed I have the correct Hessian matrix through multiple different approaches
I tried the code, but at first it seemed to be using a different rmvnorm than I can find on CRAN. I found one rmvnorm in dae package, then one in the mvtnorm package. The latter is the one to use.
nlm() was patched about the time of the above posting. I'm currently trying to verify the patches and it now seems to work OK. Note that I am author of a number of R's optimization codes, including 3/5 in optim().
nashjc at uottawa.ca
Code is below.
Revised code:
# example demonstrating a problem with NLM
expit <- function(mu) {1/(1+exp(-mu))}
mk.logit.data <- function(N,p){
set.seed(1232)
U = matrix(runif(p*p), nrow=p, ncol=p)
S = 0.5*(U+t(U)) + p*diag(rep(1,p))
X = rmvnorm(N, mean = runif(p, -1, 1), sigma = S)
Design = cbind(rep(1, N), X)
beta = sort(sample(c(rep(0,p), runif(1))))
y = rbinom(N, 1, expit(Design%*%beta))
list(X=X,y=as.numeric(y),N=N,p=p)
}
# function to calculate gradient vector at given coefficient values
logistic_gr <- function(beta, y, x, min=TRUE){
mu = beta[1] + x %*% beta[-1]
p = length(beta)
n = length(y)
D = cbind(rep(1,n), x)
gri = matrix(nrow=n, ncol=p)
for(j in 1:p){
gri[,j] = D[,j]*(exp(-mu)*y-1+y)/(1+exp(-mu))
}
gr = apply(gri, 2, sum)
if(min) gr = -gr
gr
}
# function to calculate Hessian matrix at given coefficient values
logistic_hess <- function(beta, y, x, min=TRUE){
# allow to fail with NA, NaN, Inf values
mu = beta[1] + x %*% beta[-1]
p = length(beta)
n = length(y)
D = cbind(rep(1,n), x)
h = matrix(nrow=p, ncol=p)
for(j in 1:p){
for(k in 1:p){
h[j,k] = -sum(D[,j]*D[,k]*(exp(-mu))/(1+exp(-mu))^2)
}
}
if(min) h = -h
h
}
# function to calculate likelihood (up to a constant) at given coefficient values
logistic_ll <- function(beta, y,x, gr=FALSE, he=FALSE, min=TRUE){
mu = beta[1] + x %*% beta[-1]
lli = log(expit(mu))*y + log(1-expit(mu))*(1-y)
ll = sum(lli)
if(is.na(ll) | is.infinite(ll)) ll = -1e16
if(min) ll=-ll
# the below specification is required for using analytic gradient/Hessian in nlm function
if(gr) attr(ll, "gradient") <- logistic_gr(beta, y=y, x=x, min=min)
if(he) attr(ll, "hessian") <- logistic_hess(beta, y=y, x=x, min=min)
ll
}
##!!!! NOTE: Must have this library loaded
library(mvtnorm)
dat = mk.logit.data(N=100, p=3)
(glm.sol <- glm(dat$y~dat$X, family=binomial()))$coefficients
# works when correct analytic gradient is specified
(nlm.sol1 <- nlm(p=runif(dat$p+1), f=logistic_ll, gr=TRUE, y=dat$y, x=dat$X))$estimate
# works, but less accurate when correct analytic hessian is specified (even though the routine notes convergence is probable)
(nlm.sol2 <- nlm(p=runif(dat$p+1), f=logistic_ll, gr=TRUE, he=TRUE, y=dat$y, x=dat$X, hessian = TRUE, check.analyticals=TRUE))$estimate
dat = mk.logit.data(N=100, p=10)
# Again, glm solution for reference. nlm should give the same answer, allowing for small errors due to approximation.
(glm.sol <- glm(dat$y~dat$X, family=binomial()))$coefficients
# works when correct analytic gradient is specified
(nlm.sol1 <- nlm(p=runif(dat$p+1), f=logistic_ll, gr=TRUE, y=dat$y, x=dat$X))$estimate
# fails to converge in 5000 iterations when correct analytic hessian is specified
(nlm.sol2 <- nlm(p=runif(dat$p+1), f=logistic_ll, gr=TRUE, he=TRUE, y=dat$y, x=dat$X, hessian = TRUE, iterlim=5000, check.analyticals=TRUE))$estimate
Assume A follows Exponential distribution; B follows Gamma distribution
How to plot the PDF of 0.5*(A+B)
This is fairly straight forward using the "distr" package:
library(distr)
A <- Exp(rate=3)
B <- Gammad(shape=2, scale=3)
conv <- 0.5*(A+B)
plot(conv)
plot(conv, to.draw.arg=1)
Edit by JD Long
Resulting plot looks like this:
If you're just looking for fast graph I usually do the quick and dirty simulation approach. I do some draws, slam a Gaussian density on the draws and plot that bad boy:
numDraws <- 1e6
gammaDraws <- rgamma(numDraws, 2)
expDraws <- rexp(numDraws)
combined <- .5 * (gammaDraws + expDraws)
plot(density(combined))
output should look a little like this:
Here is an attempt at doing the convolution (which #Jim Lewis refers to) in R. Note that there are probably much more efficient ways of doing this.
lower <- 0
upper <- 20
t <- seq(lower,upper,0.01)
fA <- dexp(t, rate = 0.4)
fB <- dgamma(t,shape = 8, rate = 2)
## C has the same distribution as (A + B)/2
dC <- function(x, lower, upper, exp.rate, gamma.rate, gamma.shape){
integrand <- function(Y, X, exp.rate, gamma.rate, gamma.shape){
dexp(Y, rate = exp.rate)*dgamma(2*X-Y, rate = gamma.rate, shape = gamma.shape)*2
}
out <- NULL
for(ix in seq_along(x)){
out[ix] <-
integrate(integrand, lower = lower, upper = upper,
X = x[ix], exp.rate = exp.rate,
gamma.rate = gamma.rate, gamma.shape = gamma.shape)$value
}
return(out)
}
fC <- dC(t, lower=lower, upper=upper, exp.rate=0.4, gamma.rate=2, gamma.shape=8)
## plot the resulting distribution
plot(t,fA,
ylim = range(fA,fB,na.rm=TRUE,finite = TRUE),
xlab = 'x',ylab = 'f(x)',type = 'l')
lines(t,fB,lty = 2)
lines(t,fC,lty = 3)
legend('topright', c('A ~ exp(0.4)','B ~ gamma(8,2)', 'C ~ (A+B)/2'),lty = 1:3)
I'm not an R programmer, but it might be helpful to know that for independent random variables with PDFs f1(x) and f2(x), the PDF
of the sum of the two variables is given by the convolution f1 * f2 (x) of the two input PDFs.