Assigning values to environments - merging them?
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Helen Zhou ▴ 140
@helen-zhou-2654
Last seen 6.4 years ago
United States
Dear Sir/Madam I have two questions. 1) I am currently trying to add a lot of values to an environment. A simplistic example is: names <- as.character(1:100000) values <- data.frame(a=rep("a", 4), b=(rep("b", 4))) environment <- new.env(parent=emptyenv()) for (i in 1:100000) { assign(names[i], values, envir=environment) } I find that as I gets bigger this runs increasingly slow. Is this caused by the increasing size of the enviroment? Or by something else? And is there a way for me to avoid this? 2) Assume that I have two different environments that I would like to merge into one so all the values are shared, how can I accomplish this? For example with: e1 <- new.env(parent = emptyenv()) e2 <- new.env(parent = emptyenv()) assign("a", 3, envir=e1) assign("b", 4, envir=e2) how can I join e1 and e2 so I have for example e3 containing all the values. This seems to happen if I have: e1 <- e2 <- new.env(parent = emptyenv()) assign("a", 3, envir=e1) assign("b", 4, envir=e2) but is there a way to do it for enviroments that are already existing. Thanks you for any help you can give me. I am sorry if my questions are very simple, but I am a bit confused by the concept of environemnts and how to work with them. Yours truly. Mrs Helen Zhou
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@james-w-macdonald-5106
Last seen 8 days ago
United States
Hi Helen, Helen Zhou wrote: > Dear Sir/Madam > > I have two questions. > > 1) I am currently trying to add a lot of values to an > environment. A simplistic example is: > > names <- as.character(1:100000) > values <- data.frame(a=rep("a", 4), b=(rep("b", 4))) > environment <- new.env(parent=emptyenv()) > for (i in 1:100000) { > assign(names[i], values, envir=environment) > } Ouch! You don't want to do that. See multiassign() in the Biobase package. > > I find that as I gets bigger this runs increasingly > slow. Is this caused by the increasing size of the > enviroment? Or by something else? And is there a way > for me to avoid this? > > 2) Assume that I have two different environments that > I would like to merge into one so all the values are > shared, how can I accomplish this? For example with: > > e1 <- new.env(parent = emptyenv()) > e2 <- new.env(parent = emptyenv()) > assign("a", 3, envir=e1) > assign("b", 4, envir=e2) > > how can I join e1 and e2 so I have for example e3 > containing all the values. This seems to happen if I > have: > > e1 <- e2 <- new.env(parent = emptyenv()) > assign("a", 3, envir=e1) > assign("b", 4, envir=e2) > > but is there a way to do it for enviroments that are > already existing. I don't know of a way to merge environments directly. However, you could just pull things out of each env into two lists, concatenate, and stuff into a new env. l1 <- as.list(e1) l2 <- as.list(e2) e3 <- l2e(c(l1, l2)) Best, Jim > > Thanks you for any help you can give me. I am sorry if > my questions are very simple, but I am a bit confused > by the concept of environemnts and how to work with > them. > > Yours truly. > Mrs Helen Zhou > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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There is a slightly simpler way for merging two environments using l2e's second argument: e3 <- l2e(as.list(e1), e2) -Christos > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > James W. MacDonald > Sent: Tuesday, June 10, 2008 1:45 PM > To: Helen Zhou > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Assigning values to environments - merging them? > > Hi Helen, > > Helen Zhou wrote: > > Dear Sir/Madam > > > > I have two questions. > > > > 1) I am currently trying to add a lot of values to an > environment. A > > simplistic example is: > > > > names <- as.character(1:100000) > > values <- data.frame(a=rep("a", 4), b=(rep("b", 4))) > > environment <- new.env(parent=emptyenv()) > > for (i in 1:100000) { > > assign(names[i], values, envir=environment) > > } > > Ouch! You don't want to do that. See multiassign() in the > Biobase package. > > > > > I find that as I gets bigger this runs increasingly slow. Is this > > caused by the increasing size of the enviroment? Or by > something else? > > And is there a way for me to avoid this? > > > > 2) Assume that I have two different environments that I > would like to > > merge into one so all the values are shared, how can I accomplish > > this? For example with: > > > > e1 <- new.env(parent = emptyenv()) > > e2 <- new.env(parent = emptyenv()) > > assign("a", 3, envir=e1) > > assign("b", 4, envir=e2) > > > > how can I join e1 and e2 so I have for example e3 > containing all the > > values. This seems to happen if I > > have: > > > > e1 <- e2 <- new.env(parent = emptyenv()) assign("a", 3, envir=e1) > > assign("b", 4, envir=e2) > > > > but is there a way to do it for enviroments that are > already existing. > > I don't know of a way to merge environments directly. > However, you could just pull things out of each env into two > lists, concatenate, and stuff into a new env. > > l1 <- as.list(e1) > l2 <- as.list(e2) > e3 <- l2e(c(l1, l2)) > > Best, > > Jim > > > > > > > Thanks you for any help you can give me. I am sorry if my questions > > are very simple, but I am a bit confused by the concept of > > environemnts and how to work with them. > > > > Yours truly. > > Mrs Helen Zhou > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Dear Christos, James and Wolfgang Thanks you for your kind help. That was just what I needed! Yours truly Helen --- Christos Hatzis <christos.hatzis at="" nuverabio.com=""> wrote: > There is a slightly simpler way for merging two > environments using l2e's > second argument: > > e3 <- l2e(as.list(e1), e2) > > -Christos > > > -----Original Message----- > > From: bioconductor-bounces at stat.math.ethz.ch > > [mailto:bioconductor-bounces at stat.math.ethz.ch] On > Behalf Of > > James W. MacDonald > > Sent: Tuesday, June 10, 2008 1:45 PM > > To: Helen Zhou > > Cc: bioconductor at stat.math.ethz.ch > > Subject: Re: [BioC] Assigning values to > environments - merging them? > > > > Hi Helen, > > > > Helen Zhou wrote: > > > Dear Sir/Madam > > > > > > I have two questions. > > > > > > 1) I am currently trying to add a lot of values > to an > > environment. A > > > simplistic example is: > > > > > > names <- as.character(1:100000) > > > values <- data.frame(a=rep("a", 4), b=(rep("b", > 4))) > > > environment <- new.env(parent=emptyenv()) > > > for (i in 1:100000) { > > > assign(names[i], values, envir=environment) > > > } > > > > Ouch! You don't want to do that. See multiassign() > in the > > Biobase package. > > > > > > > > I find that as I gets bigger this runs > increasingly slow. Is this > > > caused by the increasing size of the enviroment? > Or by > > something else? > > > And is there a way for me to avoid this? > > > > > > 2) Assume that I have two different environments > that I > > would like to > > > merge into one so all the values are shared, how > can I accomplish > > > this? For example with: > > > > > > e1 <- new.env(parent = emptyenv()) > > > e2 <- new.env(parent = emptyenv()) > > > assign("a", 3, envir=e1) > > > assign("b", 4, envir=e2) > > > > > > how can I join e1 and e2 so I have for example > e3 > > containing all the > > > values. This seems to happen if I > > > have: > > > > > > e1 <- e2 <- new.env(parent = emptyenv()) > assign("a", 3, envir=e1) > > > assign("b", 4, envir=e2) > > > > > > but is there a way to do it for enviroments that > are > > already existing. > > > > I don't know of a way to merge environments > directly. > > However, you could just pull things out of each > env into two > > lists, concatenate, and stuff into a new env. > > > > l1 <- as.list(e1) > > l2 <- as.list(e2) > > e3 <- l2e(c(l1, l2)) > > > > Best, > > > > Jim > > > > > > > > > > > > Thanks you for any help you can give me. I am > sorry if my questions > > > are very simple, but I am a bit confused by the > concept of > > > environemnts and how to work with them. > > > > > > Yours truly. > > > Mrs Helen Zhou > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > Affymetrix and cDNA Microarray Core > > University of Michigan Cancer Center > > 1500 E. Medical Center Drive > > 7410 CCGC > > Ann Arbor MI 48109 > > 734-647-5623 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > >
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@wolfgang-huber-3550
Last seen 5 weeks ago
EMBL European Molecular Biology Laborat…
Dear Helen, for your first question, try with setting "hash=TRUE" in your call to "new.env". See below (absolute timings are of course machine dependent). e1=new.env() e2=new.env(hash=TRUE) nm=paste(1:25000) print( system.time( for(v in nm) assign(v, pi, envir=e1) ) ) user system elapsed 3.004 0.008 3.025 print( system.time( for(v in nm) assign(v, pi, envir=e2) ) ) user system elapsed 0.152 0.000 0.151 ---------------------------------- Re your second question: a) you could have a look at the function "mget", and at "multiassign" in Biobase. The first is written in C and promises to be fast, the second contains a loop written in R, but may still be fast enough. b) you could set the parent environment of one of your environments to be the other; when you look up a name in the former, and it is not found there, the value found in the parent is returned. a=new.env() b=new.env() parent.env(b) = a assign("q", 1, env=a) get("q", a) [1] 1 get("q", b) [1] 1 c) Note that your example code probably does not do what you expect: e1 <- e2 <- new.env(parent = emptyenv()) > e1 <environment: 0x27813e0=""> > e2 <environment: 0x27813e0=""> They point to the *same* workspace in memory. If you want to learn more about environments (and many other useful things), I recommend this book http://www.amazon.co.uk/Programming-Bioinformatics-Chapman-Computer- Analysis/dp/1420063677 Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Helen Zhou a ?crit 10/06/2008 17:36: > Dear Sir/Madam > > I have two questions. > > 1) I am currently trying to add a lot of values to an > environment. A simplistic example is: > > names <- as.character(1:100000) > values <- data.frame(a=rep("a", 4), b=(rep("b", 4))) > environment <- new.env(parent=emptyenv()) > for (i in 1:100000) { > assign(names[i], values, envir=environment) > } > > I find that as I gets bigger this runs increasingly > slow. Is this caused by the increasing size of the > enviroment? Or by something else? And is there a way > for me to avoid this? > > 2) Assume that I have two different environments that > I would like to merge into one so all the values are > shared, how can I accomplish this? For example with: > > e1 <- new.env(parent = emptyenv()) > e2 <- new.env(parent = emptyenv()) > assign("a", 3, envir=e1) > assign("b", 4, envir=e2) > > how can I join e1 and e2 so I have for example e3 > containing all the values. This seems to happen if I > have: > > e1 <- e2 <- new.env(parent = emptyenv()) > assign("a", 3, envir=e1) > assign("b", 4, envir=e2) > > but is there a way to do it for enviroments that are > already existing. > > Thanks you for any help you can give me. I am sorry if > my questions are very simple, but I am a bit confused > by the concept of environemnts and how to work with > them. > > Yours truly. > Mrs Helen Zhou > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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