[Swift-commit] r3250 - SwiftApps
noreply at svn.ci.uchicago.edu
noreply at svn.ci.uchicago.edu
Mon Feb 22 20:55:25 CST 2010
Author: wilde
Date: 2010-02-22 20:55:25 -0600 (Mon, 22 Feb 2010)
New Revision: 3250
Removed:
SwiftApps/RunR.sh
SwiftApps/RunSwiftScript.sh
SwiftApps/TestSwift.R
SwiftApps/bootstrapdemo.R
SwiftApps/pboot.R
SwiftApps/swiftapply.swift
Log:
Added to wrong dir.
Deleted: SwiftApps/RunR.sh
===================================================================
--- SwiftApps/RunR.sh 2010-02-23 02:49:50 UTC (rev 3249)
+++ SwiftApps/RunR.sh 2010-02-23 02:55:25 UTC (rev 3250)
@@ -1,13 +0,0 @@
-#! /usr/bin/env Rscript
-
-argv = commandArgs(TRUE)
-
-load(argv[1]);
-
-result=list()
-for(c in 1:length(rcall$arglistbatch)) {
- # FIXME: run this under try/catch and save error status in results object (need to make it a list: rval + error status)
- result[[c]] = do.call( rcall$func, rcall$arglistbatch[[c]] )
-}
-
-save(result,file=argv[2])
Deleted: SwiftApps/RunSwiftScript.sh
===================================================================
--- SwiftApps/RunSwiftScript.sh 2010-02-23 02:49:50 UTC (rev 3249)
+++ SwiftApps/RunSwiftScript.sh 2010-02-23 02:55:25 UTC (rev 3250)
@@ -1,32 +0,0 @@
-rundir=$1
-site=$2
-
-cd $rundir
-
-cat >tc <<EOF
-$site RunR /home/wilde/SwiftR/RunR.sh null null null
-EOF
-
-cat >sites.xml <<EOF
-<config>
- <pool handle="local">
- <execution provider="local" url="none" />
- <profile namespace="karajan" key="initialScore">10000</profile>
- <profile namespace="karajan" key="jobThrottle">.03</profile>
- <filesystem provider="local"/>
- <workdirectory>$(pwd)</workdirectory>
- </pool>
- <pool handle="pbs">
- <profile namespace="globus" key="maxwalltime">00:00:10</profile>
- <profile namespace="globus" key="maxtime">1800</profile>
- <execution provider="coaster" url="none" jobManager="local:pbs"/>
- <profile namespace="globus" key="workersPerNode">8</profile>
- <profile namespace="karajan" key="initialScore">10000</profile>
- <profile namespace="karajan" key="jobThrottle">.00</profile>
- <filesystem provider="local"/>
- <workdirectory>$(pwd)</workdirectory>
- </pool>
-</config>
-EOF
-
-swift -tc.file tc -sites.file sites.xml ../swiftapply.swift
Deleted: SwiftApps/TestSwift.R
===================================================================
--- SwiftApps/TestSwift.R 2010-02-23 02:49:50 UTC (rev 3249)
+++ SwiftApps/TestSwift.R 2010-02-23 02:55:25 UTC (rev 3250)
@@ -1,31 +0,0 @@
-require(boot)
-source("Swift.R")
-
-args=list(ducks,dogs)
-sumcrits <- function(duckdata,dogdata) { sum( duckdata$plumage, dogdata$mvo ) }
-res = do.call(sumcrits,args)
-cat("Test of do.call(sumcrits)\n")
-print(res)
-
-arglist = rep(list(args),9)
-
-cat("\nTest of swiftapply(sumcrits,arglist)\n")
-res = swiftapply(sumcrits,arglist)
-print(res)
-
-cat("\nTest of swiftapply(sumcrits,arglist,callsperbatch=10)\n")
-res = swiftapply(sumcrits,arglist,callsperbatch=10)
-print(res)
-
-cat("\nTest of swiftapply(sumcrits,arglist,callsperbatch=2)\n")
-res = swiftapply(sumcrits,arglist,callsperbatch=2)
-print(res)
-
-cat("\nTest of swiftapply(sumcrits,arglist,callsperbatch=3)\n")
-res = swiftapply(sumcrits,arglist,callsperbatch=3)
-print(res)
-
-cat("\nTest of swiftapply(sumcrits,arglist,callsperbatch=20)\n")
-res = swiftapply(sumcrits,arglist,callsperbatch=20)
-print(res)
-
Deleted: SwiftApps/bootstrapdemo.R
===================================================================
--- SwiftApps/bootstrapdemo.R 2010-02-23 02:49:50 UTC (rev 3249)
+++ SwiftApps/bootstrapdemo.R 2010-02-23 02:55:25 UTC (rev 3250)
@@ -1,71 +0,0 @@
-#
-# OpenMx Script to demonstrate use of R's boot package for bootstrapping
-#
-# Author: M.C. Neale 1 September 2009
-#
-
-# Load required libraries
-require(OpenMx)
-require(boot)
-
-# Define a function called mles which will return maximum likelihood estimates
-# It uses the demoOneFactor dataset and one factor model on the OpenMx homepage
-# http://openmx.psyc.virginia.edu
-
-
-mles<-function(dataset,wt){
-cat("in mles=");
-require(OpenMx)
- manifests <- names(dataset)
- latents <- c("G")
- covwt <- cov.wt(dataset,wt)
- mlevals <- mxRun(mxModel("One Factor", type="RAM",
- manifestVars = manifests,
- latentVars = latents,
- mxPath(from=latents, to=manifests),
- mxPath(from=manifests, arrows=2),
- mxPath(from=latents, arrows=2,
- free=F, values=1.0),
- mxData(covwt$cov, type="cov",
- numObs=500)))
- return(as.vector(mlevals at output$estimate))}
-
-# Run 100 bootstraps (a smallish number)
-
-boot.out=list()
-
-boot.out[[1]] = pboot(demoOneFactor,mles,R=100)
-#boot.out[[2]] = boot(demoOneFactor,mles,R=8)
-#boot.out[[3]] = boot(demoOneFactor,mles,R=9)
-
-print("done booting - boot.out is:")
-print(boot.out)
-print("end of boot.out")
-
-# For comparison, take a look at the SE output from running the homepage job once
-data(demoOneFactor)
-manifests <- names(demoOneFactor)
-latents <- c("G")
-factorModel <- mxModel("One Factor", type="RAM",
- manifestVars = manifests,
- latentVars = latents,
- mxPath(from=latents, to=manifests),
- mxPath(from=manifests, arrows=2),
- mxPath(from=latents, arrows=2,
- free=F, values=1.0),
- mxData(cov(demoOneFactor), type="cov",
- numObs=500))
-facrun<-mxRun(factorModel)
-summary(facrun)
-
-# the estimates and standard errors should match up pretty well, though the number of replicates R above might be increased
-# therefore, only the factorModel estimates are compared:
-
-loadings<-facrun at matrices$A at values[1:5,6]
-errors<-diag(facrun at matrices$S at values[1:5,1:5])
-estimates<-as.vector(c(loadings,errors))
-omxCheckCloseEnough(as.vector(c(0.3971525,0.5036615,0.5772418,0.7027743,0.7962506,0.04081422,0.03802001,0.04082720,0.03938708,0.03628711)),estimates,.001)
-
-# The above should indicate that the results are close enough.
-
-
Deleted: SwiftApps/pboot.R
===================================================================
--- SwiftApps/pboot.R 2010-02-23 02:49:50 UTC (rev 3249)
+++ SwiftApps/pboot.R 2010-02-23 02:55:25 UTC (rev 3250)
@@ -1,118 +0,0 @@
-pboot =
-function (data, statistic, R, sim = "ordinary", stype = "i",
- strata = rep(1, n), L = NULL, m = 0, weights = NULL,
- ran.gen = function(d, p) d, mle = NULL, simple = FALSE, ...)
-{
- call <- match.call()
- 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)
- if (isMatrix(data))
- n <- nrow(data)
- else n <- length(data)
- temp.str <- strata
- strata <- tapply(1L:n, as.numeric(strata))
- if ((n == 0) || is.null(n))
- stop("no data in call to boot")
- 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), 2, normalize, strata))
- if (!simple)
- i <- index.array(n, R, sim, strata, m, L, weights)
- if (stype == "f")
- original <- rep(1, n)
- else if (stype == "w") {
- ns <- tabulate(strata)[strata]
- original <- 1/ns
- }
- else original <- 1L:n
- if (sum(m) > 0) {
- t0 <- statistic(data, original, rep(1, sum(m)), ...)
- lt0 <- length(t0)
- }
- else {
- t0 <- statistic(data, original, ...)
- lt0 <- length(t0)
- }
- }
- else {
- t0 <- statistic(data, ...)
- lt0 <- length(t0)
- }
- t.star <- matrix(NA, sum(R), lt0)
- pred.i <- NULL
- if (sim == "parametric") {
- for (r in 1L:R) {
- t.star[r, ] <- statistic(ran.gen(data, mle), ...)
- }
- }
- else {
- if (!simple && ncol(i) > n) {
- pred.i <- as.matrix(i[, (n + 1L):ncol(i)])
- i <- i[, 1L:n]
- }
- if (stype == "f") {
-print("CASE 1")
- f <- freq.array(i)
- if (sum(m) == 0)
- for (r in 1L:sum(R)) t.star[r, ] <- statistic(data,
- f[r, ], ...)
- else for (r in 1L:sum(R)) t.star[r, ] <- statistic(data,
- f[r, ], pred.i[r, ], ...)
- }
- else if (stype == "w") {
-print("CASE 2")
- f <- freq.array(i)
- if (sum(m) == 0)
- for (r in 1L:sum(R)) t.star[r, ] <- statistic(data,
- f[r, ]/ns, ...)
- else for (r in 1L:sum(R)) t.star[r, ] <- statistic(data,
- f[r, ]/ns, pred.i[r, ], ...)
- }
- else if (sum(m) > 0) {
-print("CASE 3")
- for (r in 1L:sum(R)) t.star[r, ] <- statistic(data,
- i[r, ], pred.i[r, ], ...)
- }
- else if (simple) {
-print("CASE 4")
- for (r in 1L:sum(R)) {
- inds <- index.array(n, 1, sim, strata, m, L,
- weights)
- t.star[r, ] <- statistic(data, inds, ...)
- }
- }
- else {
-cat("CASE 5 - sum(R)=",sum(R))
- # for (r in 1L:sum(R)) t.star[r, ] <- statistic(data, i[r, ], ...)
- alists = list()
- for (r in 1L:sum(R)) alists[[r]] <- list(data,i[r,],...)
- reslist = swiftapplyb(statistic,alists,callsperbatch=25)
- for (r in 1L:sum(R)) t.star[r, ] <- reslist[[r]]
- }
- }
- dimnames(t.star) <- NULL
- 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)
-}
Deleted: SwiftApps/swiftapply.swift
===================================================================
--- SwiftApps/swiftapply.swift 2010-02-23 02:49:50 UTC (rev 3249)
+++ SwiftApps/swiftapply.swift 2010-02-23 02:55:25 UTC (rev 3250)
@@ -1,13 +0,0 @@
-type RFile;
-
-app (RFile result) RunR (RFile rcall)
-{
- RunR @rcall @result;
-}
-
-RFile rcalls[] <simple_mapper; prefix="cbatch.", suffix=".Rdata", padding=0>;
-RFile results[] <simple_mapper; prefix="rbatch.", suffix=".Rdata", padding=0>;
-
-foreach c, i in rcalls {
- results[i] = RunR(c);
-}
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