the question I am trying to ask is how to I change one of the values of my variables (noted as LO$M in my list) after I pass a certain time.
The thing I am trying to achieve is that after 20,000 seconds passing I would like to change my value of Lac to the value of Lac at time 20,0000 +10,000
So at t = 20,000, Lac = Lac + 10,000
The issue I am having with my code is that within my if command I have if tt>= 20000, but this leads to the issue that every value of Lac after 20,000 being increased by 10,000 when what i want is that the FIRST value after 20,000 be increased by 10,000.
Basically, after 20,000 of my experiment passing I am trying to inject 10,000 more Lac into the experiment.
My code is given below:
LO = list()
LO$M = c(i = 1, ri = 0, I = 50, Lac = 20, ILac = 0, o = 1, Io = 0, RNAP = 100, RNAPo = 0, r = 0, z = 0)
LO$Pre = matrix(c(1,0,0,0,0,0,0,0,0,0,0,
0,1,0,0,0,0,0,0,0,0,0,
0,0,1,1,0,0,0,0,0,0,0,
0,0,0,0,1,0,0,0,0,0,0,
0,0,1,0,0,1,0,0,0,0,0,
0,0,0,0,0,0,1,0,0,0,0,
0,0,0,0,0,1,0,1,0,0,0,
0,0,0,0,0,0,0,0,1,0,0,
0,0,0,0,0,0,0,0,1,0,0,
0,0,0,0,0,0,0,0,0,1,0,
0,0,0,1,0,0,0,0,0,0,1,
0,1,0,0,0,0,0,0,0,0,0,
0,0,1,0,0,0,0,0,0,0,0,
0,0,0,0,1,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,1,0,
0,0,0,0,0,0,0,0,0,0,1), ncol=11, byrow=TRUE)
LO$Post = matrix(c(1,1,0,0,0,0,0,0,0,0,0,
0,1,1,0,0,0,0,0,0,0,0,
0,0,0,0,1,0,0,0,0,0,0,
0,0,1,1,0,0,0,0,0,0,0,
0,0,0,0,0,0,1,0,0,0,0,
0,0,1,0,0,1,0,0,0,0,0,
0,0,0,0,0,0,0,0,1,0,0,
0,0,0,0,0,1,0,1,0,0,0,
0,0,0,0,0,1,0,1,0,1,0,
0,0,0,0,0,0,0,0,0,1,1,
0,0,0,0,0,0,0,0,0,0,1,
0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,
0,0,0,1,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0), ncol=11, byrow=TRUE)
LO$h = function(x,t,th=c(0.02,0.1,0.005,0.1,1,0.01,0.1,0.01,0.03,0.1,1e-05,0.01,0.002,0.01,0.001))
{
with(as.list(c(x, th)), {
return(c(th[1]*i, th[2]*ri, th[3]*I*Lac, th[4]*ILac, th[5]*I*o, th[6]*Io, th[7]*o*RNAP,
th[8]*RNAPo, th[9]*RNAPo, th[10]*r, th[11]*Lac*z, th[12]*ri, th[13]*I,
th[13]*ILac, th[14]*r, th[15]*z))
})
}
gillespie1 = function (N, n, ...)
{
tt = 0
x = N$M
S = t(N$Post - N$Pre)
u = nrow(S)
v = ncol(S)
tvec = vector("numeric", n)
xmat = matrix(ncol = u, nrow = n + 1)
xmat[1, ] = x
for (i in 1:n) {
h = N$h(x, tt, ...)
tt = tt + rexp(1, sum(h))
j = sample(v, 1, prob = h)
x = x + S[, j]
tvec[i] = tt
xmat[i + 1, ] = x
if( tt >=20000){
x[4] = x[4] +10000
}
}
return(list(t = tvec, x = xmat))
}
newout = gillespie1(LO,200000)
matplot(newout$x[,4], type="l", lwd=0.25, col="grey")
I don't have a high enough reputation to attach images, but it should look something like this:
https://gyazo.com/0ffd940a22df23b2ccfdf4a17e85dca8
Sorry if this isn't clear. Thanks
In this example, you have the function myTask(). When you call execMyTask(), you will execute myTask()once, and after that, you will execute it at random intervals between 1 to max_wait milliseconds. When you get tired, you can kill the task with tclTaskDelete().
library(tcltk2)
myTask <- function() cat("some task!\n")
id = "execMyTask"
execMyTask <- function(max_wait = 3000) {
id <- toString(match.call()[[1]])
myTask()
wait = sample(1:max_wait, 1)
cat("Waiting", wait, "miliseconds\n") # replace with your function
if (is.null(tclTaskGet(id))) {
tclTaskSchedule(wait=wait, execMyTask(), id=id, redo = TRUE)
} else {
tclTaskChange(wait=wait, execMyTask(), id=id, redo = TRUE)
}
}
execMyTask()
tclTaskDelete(id)
So far, there is a little problem with this approach, because we can not supply arguments to the function fun in tclTaskChange().
Hi I want to convert a matrix of genotypes, encoded as triples to a matrix encoded as 0, 1, 2, i.e.
c(0,0,1) <-> 0; c(0,1,0) <-> 1; c(0,0,1) <-> 2
First here is some code to generate the matrix that needs to be reduced.
# generate genotypes
expand.G = function(n,p){
probs = runif(n = p)
G012.rows = matrix(rbinom(2,prob = probs,n=n*p),nrow = p)
colnames(G012.rows) = paste('s',1:n,sep = '')
rownames(G012.rows) = paste('g',1:p, sep = '')
G012.cols = t(G012.rows)
expand.geno = function(g){
if(g == 0){return(c(1,0,0))}
if(g == 1){return(c(0,1,0))}
if(g == 2){return(c(0,0,1))}
}
gtype = c()
for(i in 1:length(c(G012.cols))){
gtype = c(
gtype,
expand.geno(c(G012.cols)[i])
)
}
length(gtype)
G = matrix(gtype,byrow = T, nrow = p)
colnames(G) = paste('s',rep(1:n,each = 3),c('1','2','3'),sep = '')
rownames(G) = paste('g',1:p, sep = '')
print(G[1:10,1:15])
print(G012.rows[1:10,1:5])
return(G)
}
The output has 3n columns and p rows, where n is sample size and p is number of genotypes. Now we can reduce the matrix back to 0,1,2 coding with the following functions
reduce012 = function(x){
if(identical(x, c(1,0,0))){
return(0)
} else if(identical(x, c(0,1,0))){
return(1)
} else if(identical(x, c(0,0,1))){
return(2)
} else {
return(NA)
}
}
reduce.G = function(G.gen){
G.vec =
mapply(function(i,j) reduce012(as.numeric(G.gen[i,(3*j-2):(3*j)])),
i=expand.grid(1:(ncol(G.gen)/3),1:nrow(G.gen))[,2],
j=expand.grid(1:(ncol(G.gen)/3),1:nrow(G.gen))[,1]
)
G = matrix(G.vec, nrow = ncol(G.gen)/3, ncol = nrow(G.gen))
colnames(G) = rownames(G.gen)
return(G)
}
reduce.G.loop = function(G.gen){
G = matrix(NA,nrow = ncol(G.gen)/3, ncol = nrow(G.gen))
for(i in 1:nrow(G.gen)){
for(j in 1:(ncol(G.gen)/3)){
G[j,i] = reduce012(as.numeric(G.gen[i,(3*j-2):(3*j)]))
}
}
colnames(G) = rownames(G.gen)
return(G)
}
The output is n rows by p columns. It is incidental, but intentional, that the matrix encoded as 0,1,2 is the transpose of the matrix encoded as triples.
The code is not particularly fast. What is bothering me is that the the timing goes with n^2. Can you explain or supply more efficient code?
G = expand.G(1000,20)
system.time(reduce.G(G))
system.time(reduce.G.loop(G))
G = expand.G(2000,20)
system.time(reduce.G(G))
system.time(reduce.G.loop(G))
G = expand.G(4000,20)
system.time(reduce.G(G))
system.time(reduce.G.loop(G))
You can simply make an accessor lookup table:
decode <- array(dim = c(3, 3, 3))
decode[cbind(1, 0, 0) + 1] <- 0
decode[cbind(0, 1, 0) + 1] <- 1
decode[cbind(0, 0, 1) + 1] <- 2
And then, just do:
matrix(decode[matrix(t(G + 1), ncol = 3, byrow = TRUE)], ncol = nrow(G))
This full vectorized R version will give you the same matrix, without dimnames and super fast.
Yet, if you have much larger matrices, you should really use Rcpp for both memory and timing issues.
This seems to be a about three times faster than your version (renamed reduce.G.orig):
reduce.G <- function(G) {
varmap = c("100"=0, "010"=1, "001"=2)
result <- do.call(rbind, lapply(1:(ncol(G)/3)-1, function(val)
varmap[paste(G[,3*val+1], G[,3*val+2], G[,3*val+3], sep="")]))
colnames(result) <- rownames(G)
result
}
system.time(reduce.G(G))
# user system elapsed
# 0.156 0.000 0.155
system.time(reduce.G.orig(G))
# user system elapsed
# 0.444 0.000 0.441
identical(reduce.G(G), reduce.G.orig(G))
# [1] TRUE
I am applying spectral clustering to a dataset with 4200 rows and 2 columns.
spec <- specClust(df1, centers=7, nn = 7, method = "symmetric")
I have the below error.
n .Call("R_igraph_arpack", func, extra, options, env, sym, PACKAGE = "igraph") :
At arpack.c:944 : ARPACK error, Maximum number of iterations reached
In addition: Warning message:
In .Call("R_igraph_arpack", func, extra, options, env, sym, PACKAGE = "igraph") :
At arpack.c:776 :ARPACK solver failed to converge (1001 iterations, 0/7 eigenvectors converged)
How do i increase the iterations of arpack because this doesnt work:
spec <- specClust(df1, centers=7, nn = 7, method = "symmetric",iter.max=301000)
Digging into the specClust, the ... does not pass anything to the arpack call.
The simplest thing to do I think is to copy the specClust code add maxiter=10000 and source the function in your script.
specCLust2 <- function (data, centers = NULL, nn = 7, method = "symmetric",
gmax = NULL, max.iter = 10000, ...)
{
call = match.call()
if (is.data.frame(data))
data = as.matrix(data)
da = apply(data, 1, paste, collapse = "#")
indUnique = which(!duplicated(da))
indAll = match(da, da[indUnique])
data2 = data
data = data[indUnique, ]
n <- nrow(data)
data = scale(data, FALSE, TRUE)
if (is.null(gmax)) {
if (!is.null(centers))
gmax = centers - 1L
else gmax = 1L
}
test = TRUE
while (test) {
DC = mydist(data, nn)
sif <- rbind(1:n, as.vector(DC[[2]]))
g <- graph(sif, directed = FALSE)
g <- decompose(g, min.vertices = 4)
if (length(g) > 1) {
if (length(g) >= gmax)
nn = nn + 2
else test = FALSE
}
else test = FALSE
}
W <- DC[[1]]
n <- nrow(data)
wi <- W[, nn]
SC <- matrix(1, nrow(W), nn)
SC[] <- wi[DC[[2]]] * wi
W = W^2/SC
alpha = 1/(2 * (nn + 1))
qua = abs(qnorm(alpha))
W = W * qua
W = dnorm(W, sd = 1)
DC[[1]] = W
L = Laplacian(DC, nn, method)
f <- function(x, extra) as.vector(extra %*% x)
if (is.null(centers))
kmax = 25
else kmax = max(centers)
###
#add the maxiter parameter to the arpack call, below
###
U <- arpack(f, extra = L, options = list(n = n, which = "SM",
nev = kmax, ncv = 2 * kmax, mode = 1, maxiter=max.iter), sym = TRUE)
ind <- order(U[[1]])
U[[2]] = U[[2]][indAll, ind]
U[[1]] = U[[1]][ind]
if (is.null(centers)) {
tmp = which.max(diff(U[[1]])) + 1
centers = which.min(AUC(U[[1]][1:tmp]))
}
if (method == "symmetric") {
rs = sqrt(rowSums(U[[2]]^2))
U[[2]] = U[[2]]/rs
}
result = kmeans(U[[2]], centers = centers, nstart = 20, ...)
archeType = getClosest(U[[2]][indAll, ], result$centers)
result$eigenvalue = U[[1]]
result$eigenvector = U[[2]]
result$data = data2
result$indAll = indAll
result$indUnique = indUnique
result$L = L
result$archetype = archeType
result$call = call
class(result) = c("specClust", "kmeans")
result
}