I was trying to maximize my Likelihood with the R package 'optimx'. Here is my code. With the initial value (5,5) and (1,1), I got different Maximized likelihood. I also have tried different method like 'Nelder=Mead', but the estimated log likelihood are different under different methods...
library('optimx')
n=225
X = matrix(runif(225),ncol=1)
e2 = matrix(runif(225,0,2),ncol=1)
set.seed(123)
This is the function to generate some data I will use
get_mls_basis<- function(p){
depth <- ceiling(runif(1)*p)
knot <- matrix(rep(0,depth+1),ncol=1)
lr <- runif(1) > 0.5
x <- matrix(rep(0,n),ncol=1)
not_finished <- 1
while (not_finished == 1) {
data_indx = ceiling(runif(1)*n)
var = matrix(rep(0,depth),ncol=1)
for (j in 1:depth) {
not_ok <- 1
while (not_ok == 1) {
ind <- ceiling(runif(1)*p)
if (!is.element (ind,var[1:j]))
{
var[j] <- ind
not_ok <- 0
}
}
}
x_v <- as.matrix(X[data_indx, var])
knot[1:depth] <- rgamma(depth,1,1)
knot[1:depth] <- knot[1:depth] / sqrt(sum(knot^2))
knot[depth+1] <- -x_v %*% knot[1:depth]
ones <- matrix(rep(1,n),ncol=1)
temp <- as.matrix(cbind(X[,var], ones)) %*% knot
if (lr == 0) {
for (i in 1:n)
{
temp[i] <- max(0,temp[i])
}
}
else {
for (i in 1:n)
{
temp[i] <- min(0,temp[i])
}
}
x <- temp
not_finished <- all(x==0)
}
mx <- mean(x)
stx <- sd(x)
x <- (x-mx)/stx
x
}
This is my log likelihood
Lik1<-function(theta, basis){
theta0=theta[1]
theta1=theta[2]
L=-n/2*log(theta0)-sum(basis/2)*log(theta1)-0.5/theta0*sum(e2/theta1^basis)
return(L)
}
basis1=get_mls_basis(1)
Here I used 5 as initial value
optimx(par=c(5,5), Lik1,
basis=basis1,method='bobyqa',control = list(maximize=TRUE))
I'm trying to cache the inverse of matrix:
makeCacheMatrix <- function(x = matrix()) {
m <- NULL
set <- function(y) {
x <<- y
m <<- NULL
}
get <- function() x
setinverse <- function(inverse) m <<- inverse
getinverse <- function() m
list(set = set, get = get, setinvervse = setinverse, getinverse = getinverse)
}
cacheSolve <- function(x, ...) {
m <- x$getinverse()
if (! is.null(m)) {
message("getting cached data")
return(m)
}
data <- x$get()
m <- solve(data, ...)
x$setinverse(m)
m
}
But got the following errors:
**Error in x$setinverse(m) : attempt to apply non-function**
How to fix this? Thanks!
the following code worked for me
rm(list = ls())
makeCacheMatrix <- function(ma = matrix()) {
im <- NULL
setMatrix <- function(y) {
ma <<- y
im <<- NULL
}
getMatrix <- function() ma
setinverse <- function(inv) im <<- inv
getinverse <- function() im
list(setMatrix = setMatrix,
getMatrix = getMatrix,
setinverse = setinverse,
getinverse = getinverse)
}
cacheSolve <- function(x, ...) {
im <- x$getinverse()
if (!is.null(im)) {
message("getting cached inverse matrix")
return(im)
}
data <- x$getMatrix()
i <- solve(data, ...)
x$setinverse(i)
i
}
##testing the functions
B <- matrix(c(1,2,3,4),2,2)
B1 <- makeCacheMatrix(B)
cacheSolve(B1) #inverse returned after computation, no message
cacheSolve(B1) #inverse returned from cache and message is printed here
B2 <- makeCacheMatrix(-B)
cacheSolve(B1)
cacheSolve(B2)
I am trying to add a progress bar to a bootstrap function in R.
I tried to make the example function as simple as possible (hence i'm using mean in this example).
library(boot)
v1 <- rnorm(1000)
rep_count = 1
m.boot <- function(data, indices) {
d <- data[indices]
setWinProgressBar(pb, rep_count)
rep_count <- rep_count + 1
Sys.sleep(0.01)
mean(d, na.rm = T)
}
tot_rep <- 200
pb <- winProgressBar(title = "Bootstrap in progress", label = "",
min = 0, max = tot_rep, initial = 0, width = 300)
b <- boot(v1, m.boot, R = tot_rep)
close(pb)
The bootstrap functions properly, but the problem is that the value of rep_count does not increase in the loop and the progress bar stays frozen during the process.
If I check the value of rep_count after the bootstrap is complete, it is still 1.
What am i doing wrong? maybe the boot function does not simply insert the m.boot function in a loop and so the variables in it are not increased?
Thank you.
You could use the package progress as below:
library(boot)
library(progress)
v1 <- rnorm(1000)
#add progress bar as parameter to function
m.boot <- function(data, indices, prog) {
#display progress with each run of the function
prog$tick()
d <- data[indices]
Sys.sleep(0.01)
mean(d, na.rm = T)
}
tot_rep <- 200
#initialize progress bar object
pb <- progress_bar$new(total = tot_rep + 1)
#perform bootstrap
boot(data = v1, statistic = m.boot, R = tot_rep, prog = pb)
I haven't quite figured out yet why it's necessary to set the number of iterations for progress_bar to be +1 the total bootstrap replicates (parameter R), but this is what was necessary in my own code, otherwise it throws an error. It seems like the bootstrap function is run one more time than you specify in parameter R, so if the progress bar is set to only run R times, it thinks the job is finished before it really is.
The pbapply package was designed to work with vectorized functions. There are 2 ways to achieve that in the context of this question: (1) write a wrapper as was suggested, which will not produce the same object of class 'boot'; (2) alternatively, the line lapply(seq_len(RR), fn) can be written as pblapply(seq_len(RR), fn). Option 2 can happen either by locally copying/updating the boot function as shown in the example below, or asking the package maintainer, Brian Ripley, if he would consider adding a progress bar directly or through pbapply as dependency.
My solution (changes indicated by comments):
library(boot)
library(pbapply)
boot2 <- function (data, statistic, R, sim = "ordinary", stype = c("i",
"f", "w"), strata = rep(1, n), L = NULL, m = 0, weights = NULL,
ran.gen = function(d, p) d, mle = NULL, simple = FALSE, ...,
parallel = c("no", "multicore", "snow"), ncpus = getOption("boot.ncpus",
1L), cl = NULL)
{
call <- match.call()
stype <- match.arg(stype)
if (missing(parallel))
parallel <- getOption("boot.parallel", "no")
parallel <- match.arg(parallel)
have_mc <- have_snow <- FALSE
if (parallel != "no" && ncpus > 1L) {
if (parallel == "multicore")
have_mc <- .Platform$OS.type != "windows"
else if (parallel == "snow")
have_snow <- TRUE
if (!have_mc && !have_snow)
ncpus <- 1L
loadNamespace("parallel")
}
if (simple && (sim != "ordinary" || stype != "i" || sum(m))) {
warning("'simple=TRUE' is only valid for 'sim=\"ordinary\", stype=\"i\", n=0', so ignored")
simple <- FALSE
}
if (!exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE))
runif(1)
seed <- get(".Random.seed", envir = .GlobalEnv, inherits = FALSE)
n <- NROW(data)
if ((n == 0) || is.null(n))
stop("no data in call to 'boot'")
temp.str <- strata
strata <- tapply(seq_len(n), as.numeric(strata))
t0 <- if (sim != "parametric") {
if ((sim == "antithetic") && is.null(L))
L <- empinf(data = data, statistic = statistic, stype = stype,
strata = strata, ...)
if (sim != "ordinary")
m <- 0
else if (any(m < 0))
stop("negative value of 'm' supplied")
if ((length(m) != 1L) && (length(m) != length(table(strata))))
stop("length of 'm' incompatible with 'strata'")
if ((sim == "ordinary") || (sim == "balanced")) {
if (isMatrix(weights) && (nrow(weights) != length(R)))
stop("dimensions of 'R' and 'weights' do not match")
}
else weights <- NULL
if (!is.null(weights))
weights <- t(apply(matrix(weights, n, length(R),
byrow = TRUE), 2L, normalize, strata))
if (!simple)
i <- index.array(n, R, sim, strata, m, L, weights)
original <- if (stype == "f")
rep(1, n)
else if (stype == "w") {
ns <- tabulate(strata)[strata]
1/ns
}
else seq_len(n)
t0 <- if (sum(m) > 0L)
statistic(data, original, rep(1, sum(m)), ...)
else statistic(data, original, ...)
rm(original)
t0
}
else statistic(data, ...)
pred.i <- NULL
fn <- if (sim == "parametric") {
ran.gen
data
mle
function(r) {
dd <- ran.gen(data, mle)
statistic(dd, ...)
}
}
else {
if (!simple && ncol(i) > n) {
pred.i <- as.matrix(i[, (n + 1L):ncol(i)])
i <- i[, seq_len(n)]
}
if (stype %in% c("f", "w")) {
f <- freq.array(i)
rm(i)
if (stype == "w")
f <- f/ns
if (sum(m) == 0L)
function(r) statistic(data, f[r, ], ...)
else function(r) statistic(data, f[r, ], pred.i[r,
], ...)
}
else if (sum(m) > 0L)
function(r) statistic(data, i[r, ], pred.i[r, ],
...)
else if (simple)
function(r) statistic(data, index.array(n, 1, sim,
strata, m, L, weights), ...)
else function(r) statistic(data, i[r, ], ...)
}
RR <- sum(R)
res <- if (ncpus > 1L && (have_mc || have_snow)) {
if (have_mc) {
parallel::mclapply(seq_len(RR), fn, mc.cores = ncpus)
}
else if (have_snow) {
list(...)
if (is.null(cl)) {
cl <- parallel::makePSOCKcluster(rep("localhost",
ncpus))
if (RNGkind()[1L] == "L'Ecuyer-CMRG")
parallel::clusterSetRNGStream(cl)
res <- parallel::parLapply(cl, seq_len(RR), fn)
parallel::stopCluster(cl)
res
}
else parallel::parLapply(cl, seq_len(RR), fn)
}
}
else pblapply(seq_len(RR), fn) #### changed !!!
t.star <- matrix(, RR, length(t0))
for (r in seq_len(RR)) t.star[r, ] <- res[[r]]
if (is.null(weights))
weights <- 1/tabulate(strata)[strata]
boot.return(sim, t0, t.star, temp.str, R, data, statistic,
stype, call, seed, L, m, pred.i, weights, ran.gen, mle)
}
## Functions not exported by boot
isMatrix <- boot:::isMatrix
index.array <- boot:::index.array
boot.return <- boot:::boot.return
## Now the example
m.boot <- function(data, indices) {
d <- data[indices]
mean(d, na.rm = T)
}
tot_rep <- 200
v1 <- rnorm(1000)
b <- boot2(v1, m.boot, R = tot_rep)
The increased rep_count is a local variable and lost after each function call. In the next iteration the function gets rep_count from the global environment again, i.e., its value is 1.
You can use <<-:
rep_count <<- rep_count + 1
This assigns to the rep_count first found on the search path outside the function. Of course, using <<- is usually not recommended because side effects of functions should be avoided, but here you have a legitimate use case. However, you should probably wrap the whole thing in a function to avoid a side effect on the global environment.
There might be better solutions ...
I think i found a possible solution. This merges the answer of #Roland with the convenience of the pbapply package, using its functions startpb(), closepb(), etc..
library(boot)
library(pbapply)
v1 <- rnorm(1000)
rep_count = 1
tot_rep = 200
m.boot <- function(data, indices) {
d <- data[indices]
setpb(pb, rep_count)
rep_count <<- rep_count + 1
Sys.sleep(0.01) #Just to slow down the process
mean(d, na.rm = T)
}
pb <- startpb(min = 0, max = tot_rep)
b <- boot(v1, m.boot, R = tot_rep)
closepb(pb)
rep_count = 1
As previously suggested, wrapping everything in a function avoids messing with the rep_count variable.
The progress bar from the package dplyr works well:
library(dplyr)
library(boot)
v1 <- rnorm(1000)
m.boot <- function(data, indices) {
d <- data[indices]
p$tick()$print() # update progress bar
Sys.sleep(0.01)
mean(d, na.rm = T)
}
tot_rep <- 200
p <- progress_estimated(tot_rep+1) # init progress bar
b <- boot(v1, m.boot, R = tot_rep)
You can use the package pbapply
library(boot)
library(pbapply)
v1 <- rnorm(1000)
rep_count = 1
# your m.boot function ....
m.boot <- function(data, indices) {
d <- data[indices]
mean(d, na.rm = T)
}
# ... wraped in `bootfunc`
bootfunc <- function(x) { boot(x, m.boot, R = 200) }
# apply function to v1 , returning progress bar
pblapply(v1, bootfunc)
# > b <- pblapply(v1, bootfunc)
# > |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% Elapsed time: 02s