I understand what set.seed() does and when I might use it, but I still have many questions about the function. Here are a few:
Is it possible to "reset" set.seed() to something "more random" if you have called set.seed() earlier in your session? Is that even necessary?
Is it possible to view the seed that R is currently using?
Is there a way to make set.seed() allow alphanumeric seeds, the way one can enter them at random.org (be sure you are in the advanced mode, and see "Part 3" of the form to see what I mean)?
Just for fun:
set.seed.alpha <- function(x) {
require("digest")
hexval <- paste0("0x",digest(x,"crc32"))
intval <- type.convert(hexval) %% .Machine$integer.max
set.seed(intval)
}
So you can do:
set.seed.alpha("hello world")
(in fact x can be any R object, not just an alphanumeric string)
It's possible, if you set the seed to something like the final digits of your time epoch, but it's really not necessary. The intended use of PRNGs is that you set the seed once at the start of a session, and use successive generated variates from this. Do things differently, and you don't get to enjoy the various good theoretical and empirical properties the R RNGs have.
But I'm not sure you really understand the purpose of set.seed. It's not really there for you to get 'more random' numbers. If you are doing some kind of application for which the R PRNG is insufficient (for instance, if you require cryptographic randomness), you might as well generate all your random numbers by some alternate method and use them directly. The real purpose of set.seed is to produce reproducibility in results using RNGs. If you start the same analysis using the same sequence of random number generations, and set the seed to the same value, you will always get the same result. This is helpful in debugging, and for others reviewing your results.
To use the epoch time, do something like
t <- as.numeric(Sys.time())
seed <- 1e8 * (t - floor(t))
set.seed(seed); print(seed)
For your question 3 there is the char2seed function in the TeachingDemos package which will take a character string (alhpa numeric) and convert it to an integer and by default use that to set a new seed. The idea was that students could use their name (or some combination/subset of names) as a seed so each student gets a different dataset, but the teacher can reproduce each student's dataset.
For an answer to 2, first see the help page ?RNGkind.
To find the kind of RNG in use:
RNGkind()
# [1] "Mersenne-Twister" "Inversion"
The Mersenne Twister is the default.
From the help page:
‘"Mersenne-Twister":’ From Matsumoto and Nishimura (1998). A
twisted GFSR with period 2^19937 - 1 and equidistribution in
623 consecutive dimensions (over the whole period). The
‘seed’ is a 624-dimensional set of 32-bit integers plus a
current position in that set.
To find the current seed in use, you need to first call the random number generator.
runif(1, 0, 1)
# [1] 0.9834062
.Random.seed
# [Gives a 626 length vector]
Calling set.seed(some_integer) followed by .Random.seed,
will always give the same 626 length vector if you use the same some_integer. To put it differently, the 626-length vector is determined solely by some_integer, given one is using the Mersenne Twister, of course.
Also, of course, running set.seed to some fixed value will give you the same values for calls to random number routines following it. That's the main use for it in practice, to give reproducibility. E.g.
set.seed(1)
runif(5, 0, 1)
# [1] 0.2655087 0.3721239 0.5728534 0.9082078 0.2016819
rnorm(1, 0, 1)
# [1] 1.272429
set.seed(1)
runif(5, 0, 1)
# [1] 0.2655087 0.3721239 0.5728534 0.9082078 0.2016819
rnorm(1, 0, 1)
# [1] 1.272429
All the basic number generator code in R is in the file src/main/RNG.c in the source code.
It is in C, but fairly easy to follow.
I have the same issue as in question 1. I then figure I can simply reset seed in the loop by:
set.seed(123)
x<- rnorm(10,1,1)
set.seed(null)
This way at the end of each loop the seed just got deleted. It worked for me.
Related
I'm trying to perform multiple imputation on a dataset in R where I have two variables, one of which needs to be the same or greater than the other one. I have set up the method and the predictive matrix, but I am having trouble understanding how to configure the post-processing. The manual (or main paper - van Buuren and Groothuis-Oudshoorn, 2011) states (section 3.5): "The mice() function has an argument post that takes a vector of strings of R commands. These commands are parsed and evaluated just after the univariate imputation function returns, and thus provide a way to post-process the imputed values." There are a couple of examples, of which the second one seems most useful:
R> post["gen"] <- "imp[[j]][p$data$age[!r[,j]]<5,i] <- levels(boys$gen)[1]"
this suggests to me that I could do:
R> ini <- mice(cbind(boys), max = 0, print = FALSE)
R> post["A"] <- "imp[[j]][p$data$B[!r[,j]]>p$data$A[!r[,j]],i] <- levels(boys$A)[boys$B]"
However, this doesn't work (when I plot A v B, I get random scatter rather than the points being confined to one half of the graph where A >= B).
I have also tried using the ifdo() function, as suggested in another sx post:
post["A"] <- "ifdo(A < B), B"
However, it seems the ifdo() function is not yet implemented. I tried running the code suggested for inspiration but afraid my R programming skills are not that brilliant.
So, in summary, has anyone any advice about how to implement post-processing in mice such that value A >= value B in the final imputed datasets?
Ok, so I've found an answer to my own question - but maybe this isn't the best way to do it.
In FIMD, there is a suggestion to do this kind of thing outside the imputation process, which thus gives:
R> long <- mice::complete(imp, "long", include = TRUE)
R> long$A <- with(long, ifelse(B < A, B, A))
This seems to work, so I'm happy.
I would like to perform pathway enrichment analyses.
I have 21 list of significant genes, and mutiple types of pathways I would like to check (ie. check for enrichment in KEGG pathways, GOterms, complexes etc.).
I found this example of code, on an old BioC post. However, I am having trouble adapting it for myself.
Firstly,
1- what does this mean? I don't know this multiple colon syntax.
hyperg <- Category:::.doHyperGInternal
2 - I don't understand how this line works. hyperg.test is a function that needs 3 variables passed to it, correct? Is this line somehow passing "genes.by.pathways, significant.genes, and all.geneIDs to thr hyperg.test?
pVals.by.pathway<-t(sapply(genes.by.pathway, hyperg.test, significant.genes, all.geneIDs))
Code that I would like to adapt
library(KEGGREST)
library(org.Hs.eg.db)
# created named list, length 449, eg:
# path:hsa00010: "Glycolysis / Gluconeogenesis"
pathways <- keggList("pathway", "hsa")
# make them into KEGG-style human pathway identifiers
human.pathways <- sub("path:", "", names(pathways))
# for demonstration, just use the first ten pathways
demo.pathway.ids <- head(human.pathways, 10)
demo.pathways <- setNames(keggGet(demo.pathway.ids), demo.pathway.ids)
genes.by.pathway <- lapply(demo.pathways, function(demo.pathway) {
demo.pathway$GENE[c(TRUE, FALSE)]
})
all.geneIDs <- keys(org.Hs.eg.db)
# chose one of these for demonstration. the first (a whole genome random
# set of 100 genes) has very little enrichment, the second, a random set
# from the pathways themselves, has very good enrichment in some pathways
set.seed(123)
significant.genes <- sample(all.geneIDs, size=100)
#significant.genes <- sample(unique(unlist(genes.by.pathway)), size=10)
# the hypergeometric distribution is traditionally explained in terms of
# drawing a sample of balls from an urn containing black and white balls.
# to keep the arguments straight (in my mind at least), I use these terms
# here also
hyperg <- Category:::.doHyperGInternal
hyperg.test <-
function(pathway.genes, significant.genes, all.genes, over=TRUE)
{
white.balls.drawn <- length(intersect(significant.genes, pathway.genes))
white.balls.in.urn <- length(pathway.genes)
total.balls.in.urn <- length(all.genes)
black.balls.in.urn <- total.balls.in.urn - white.balls.in.urn
balls.pulled.from.urn <- length(significant.genes)
hyperg(white.balls.in.urn, black.balls.in.urn,
balls.pulled.from.urn, white.balls.drawn, over)
}
pVals.by.pathway <-
t(sapply(genes.by.pathway, hyperg.test, significant.genes, all.geneIDs))
print(pVals.by.pathway)
The reason you are getting your error is because it appears you don't have the Category package installed from bioconductor. I suspect this because of the triple colon operator :::. This operator is very similar to the double colon operator ::. Whereas with :: you can access exported objects from a package without loading it, the ::: allows access to non-exported objects (in this case the hyperg function from Category). If you install the Category package the code runs without error.
With regard to the sapply statement:
pVals.by.pathway<-t(sapply(genes.by.pathway, hyperg.test, significant.genes, all.geneIDs))
You can break this down into the separate parts to understand it. Firstly, the sapply is iterating over the elements of gene.by.pathway and passing them to the first argument of hyperg.test. The following arguments are the two addition parameters. It is a little unclear and I personally recommend that people explicitly identify the parameters to avoid unexpected surprises and avoids the need for the exact same order. This is a little repetitive in this case but a good way to avoid a silly bug (e.g. putting significant.genes after all.geneIds)
Rewritten:
pVals.by.pathway <-
t(sapply(genes.by.pathway, hyperg.test, significant.genes=significant.genes, all.genes=all.geneIDs))
Once this loop completes, the sapply function simplifies the output in to a matrix. However, the output is much more user-friendly by taking the transpose t.
Generally speaking, when trying to understand complex apply statements I find it best to break them apart in to smaller parts and see what the objects themselves look like.
I need to generate a vector of "random" numbers, except that they need to be fully deterministic. The distribution from which the numbers come is not so important. What is a simple way to do this in R?
The reason for not using something like runif is that it returns a different sequence every time it is called.
The reason for not generating one sequence (with runif) and reusing it is that the calls are made on different machines. I could hardcode the sequence into a script, but the length of the sequence needed is unknown at design-time, so a pseudorandom sequence based on some hardcoded seed is preferable.
Are you aware of the set.seed() command?
R> set.seed(42); runif(3)
[1] 0.914806 0.937075 0.286140
R> set.seed(42); runif(3) # same seed, same numbers
[1] 0.914806 0.937075 0.286140
R> set.seed(12345); runif(3) # different seed, different numbers
[1] 0.720904 0.875773 0.760982
R>
There is also the SoDa package (and manual [PDF]) which allows you to wrap other operations and recover the starting and ending seed. It's just a wrapper around set.seed() but you can check for yourself (e.g. in unit tests) more easily.
I would like to find all combinations of vector elements that matches a specific condition. The function expand.grid returns all possible combinations without checking for a specific condition. It is possible to test for a specific condition after using the expand.grid function, but in some situations the number of possible combinations is too large to generate them with expand.grid. Therefore is there a function that allows me to check for a condition while generating all possible combinations.
This is a simplified version of the problem:
A <- seq.int(12, from=0, by=1)*15
B <- seq.int(27, from=0, by=1)*23
C <- seq.int(18, from=0, by=1)*18
D <- seq.int(33, from=0, by=1)*10
out<-expand.grid(A,B,C,D) #out is a dataframe with 235144 x 4 as dimensions
idx<-which(rowSums(out)<=400 & rowSums(out)>=300) #Only a small fraction of 'out' is needed
results <- out(idx,)
In a word, no. After all, if you knew a priori which combinations were desirable/undesirable, you could exclude them from the expansion, e.g. expand.grid(A[A<20],B[B<15],...) . In the general case, which I'm assuming is your real question, you have no simple way to exclude portions of the input vectors.
You might just want to write a multilevel loop which tests each combination in turn and saves or rejects it. This will be slow (again, unless you come up with some clever algorithm to predict regions which are all TRUE or FALSE). So, in the long run, you may be better off using some of the R-packages which partition large calculations (and datasets) so as to avoid exceeding your memory limits.
Now that I've said all that, someone's going to post a link to a package which does exactly that :-(
I am trying to understand how set.seed works in R. I understand it, can reproduce random samples, but I don't know what is the difference between set.seed(1) and set.seed(123) ?
What do the argument in the bracket mean ?
The seed argument in set.seed is a single value, interpreted as an integer (as defined in help(set.seed()). The seed in set.seed produces random values which are unique to that seed (and will be same irrespective of the computer you run and hence ensures reproducibility). So the random values generated by set.seed(1) and set.seed(123) will not be the same but the random values generated by R in your computer using set.seed(1) and by R in my computer using the same seed are the same.
set.seed(1)
x<-rnorm(10,2,1)
> x
[1] 1.373546 2.183643 1.164371 3.595281 2.329508 1.179532 2.487429 2.738325 2.575781 1.694612
set.seed(123)
y<-rnorm(10,2,1)
> y
[1] 1.4395244 1.7698225 3.5587083 2.0705084 2.1292877 3.7150650 2.4609162 0.7349388 1.3131471 1.5543380
> identical(x,y)
[1] FALSE
The majority of computer programs uses deterministic algorithms to generate random numbers (which is the reason why the numbers they generate are not truly random, but pseudorandom, which is good enough for most purposes). R is no different, and you can think of the random numbers it generates as being part of a very long string of "random" numbers that, when summoned, just starts at some point and spits out pseudorandom numbers for you. By using set.seed() you are basically giving the program a starting point instead of letting it choose its own. That's why any user running the same seed number will get the same results.
You can run ?RNGkind for more information on the subject.