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#
# Copyright 2007-2021 by the individuals mentioned in the source code history
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
library(OpenMx)
library(testthat)
context("mxSave")
dir <- tempdir() # safe place to create files
mxOption(key="Checkpoint Directory", value=dir)
# Simulate some data
sampleSize <- 250
x=rnorm(sampleSize, mean=0, sd=1)
y= 0.5*x + rnorm(sampleSize, mean=0, sd=1)
tmpFrame <- data.frame(x, y)
tmpNames <- names(tmpFrame)
# Create a model that includes an expected covariance matrix,
# an expectation function, a fit function, and an observed covariance matrix
data <- mxData(cov(tmpFrame), type="cov", numObs = sampleSize)
expCov <- mxMatrix(type="Symm", nrow=2, ncol=2, values=c(.2,.1,.2), free=TRUE, name="expCov")
plan <- omxDefaultComputePlan()
plan$steps <- c(plan$steps,
CK=mxComputeCheckpoint(path=file.path(dir,"backendChkpt.omx"),
standardErrors = TRUE, gradient = TRUE, vcov=TRUE,
toReturn=TRUE, sampleSize = TRUE))
testModel <- mxModel(model="testFish", expCov, data,
mxExpectationNormal(covariance="expCov", dimnames=tmpNames),
mxFitFunctionML(),
plan)
#Use mxRun to optimize the free parameters in the expected covariance matrix
modelOut <- mxRun(testModel, checkpoint = TRUE)
modelRestored <- mxRestore(testModel, strict = TRUE) # old checkpoint output
omxCheckCloseEnough(coef(modelRestored), coef(modelOut), 1e-5)
bckpt <- read.table(file.path(dir,"backendChkpt.omx"),
header=TRUE, sep="\t", stringsAsFactors=FALSE, check.names=FALSE)
bckpt2 <- modelOut$compute$steps$CK$log
omxCheckEquals(colnames(bckpt), colnames(bckpt2))
for (cx in colnames(bckpt)) {
if (cx == 'timestamp') next
omxCheckEquals(substr(as.character(bckpt[1,cx]), 1,10),
substr(as.character(bckpt2[1,cx]), 1,10))
}
modelRestored <- mxRestoreFromDataFrame(testModel, bckpt)
omxCheckCloseEnough(coef(modelRestored), coef(modelOut), 1e-5)
omxCheckCloseEnough(modelRestored$output$standardErrors, modelOut$output$standardErrors, 1e-5)
omxCheckCloseEnough(modelRestored$output$gradient, modelOut$output$gradient, 1e-5)
omxCheckCloseEnough(modelRestored$output$vcov, modelOut$output$vcov, 1e-5)
summary(modelRestored)
# Save the ending state of modelOut in a checkpoint file
mxSave(modelOut, chkpt.prefix="z")
modelRestored <- mxRestore(testModel, chkpt.prefix="z", strict=TRUE)
omxCheckCloseEnough(coef(modelRestored), coef(modelOut), 1e-5)
# ---------
testModel$compute$steps$CK$vcovFilter <-
c("testFish.expCov[1,1]", "testFish.expCov[1,2]")
testModel$compute$steps$CK$useVcovFilter <- TRUE
modelOut <- mxRun(testModel, checkpoint = TRUE)
bckpt <- read.table(file.path(dir,"backendChkpt.omx"),
header=TRUE, sep="\t", stringsAsFactors=FALSE, check.names=FALSE)
bckpt2 <- modelOut$compute$steps$CK$log
expect_equal(length(grep('^V', colnames(bckpt))), 4)
expect_true(all(!is.na(match(c("VtestFish.expCov[1,1]:testFish.expCov[1,1]",
"VtestFish.expCov[2,2]:testFish.expCov[2,2]"),
colnames(bckpt)))))
expect_equal(colnames(bckpt), colnames(bckpt2))
# ---------
m1 <- mxModel("case")
m1 <- mxOption(m1, "checkPoint Directory", "./tmp")
expect_equal(mxOption(m1, "Checkpoint directory"), "./tmp")
expect_equal(names(m1$options), "Checkpoint Directory")
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