Nothing
cat(cli::col_yellow("test reftable:\n"))
myrnorm <- function(mu,s2,sample.size) {
s <- rnorm(n=sample.size,mean=mu,sd=sqrt(s2))
return(c(mean=mean(s),var=var(s)))
} # simulate means and variances of normal samples of size 'sample.size'
set.seed(123)
# simulated data with stands for the actual data to be analyzed:
ssize <- 40L
(Sobs <- myrnorm(mu=4,s2=1,sample.size=ssize) )
## Construct initial reference table:
# Uniform sampling in parameter space:
parsp <- init_reftable(lower=c(mu=2.8, s2=0.4, sample.size=ssize),
upper=c(mu=5.2, s2=2.4, sample.size=ssize))
# Build simulation table:
# set.seed(456)
simuls <- add_reftable(Simulate="myrnorm", parsTable=parsp)
## trivial projections which should produce an y=x regression:
#mufit <- project("mu",stats=c("mean","var"),data=simuls, method="randomForest")
#s2fit <- project("s2",stats=c("mean","var"),data=simuls, method="randomForest")
mufit <- project("mu",stats=c("mean","var"),data=simuls)
s2fit <- project("s2",stats=c("mean","var"),data=simuls)
## apply projections on simulated statistics
projectors <- list("MEAN"=mufit,"VAR"=s2fit)
projectors <- list2env(projectors)
corrSobs <- project(Sobs,projectors=projectors)
corrSimuls <- project(simuls,projectors=projectors)
# Infer surface:
densv <- infer_SLik_joint(corrSimuls,stat.obs=corrSobs)
# Usual workflow using inferred surface:
slik_1 <- MSL(densv) ## find the maximum of the log-likelihood surface
#slik_j <- refine(slik_j,maxit=5, update_projectors=TRUE)
# Convenience function for plotting projections...
plot_importance(slik_1, parm="mu")
slik_j <- refine(slik_1)
# slik_j <- refine(slik_j)
plot(slik_j)
testthat::test_that(
'Warning expected for plot_proj(slik_1, parm="mu") as projectors were updated in the input slik_1 object.',
{
warn <- ""
withCallingHandlers(
plot_proj(slik_1, parm="mu"), warning=function(w) {
warn <<- conditionMessage(w)
invokeRestart("muffleWarning")
})
testthat::expect_true(substr(warn,1,23)=="Projectors were updated")
}
)
# No warning expected on this one:
plot_proj(slik_j)
# etc:
profile(slik_j,c(mu=4)) ## profile summary logL for given parameter value
confint(slik_j,"mu") ## compute 1D confidence interval for given parameter
plot1Dprof(slik_j,pars="s2",gridSteps=40) ## 1D profile
# goftest(slik_j, nsim = 300L) # goodness of fit test
if (requireNamespace("xLLiM", quietly=TRUE)) { # workflow with xLLiM::gllim
densvx <- infer_SLik_joint(corrSimuls,stat.obs=corrSobs, using="xLLiM")
# Usual workflow using inferred surface:
slik_jx <- MSL(densvx,
eval_RMSEs = FALSE # had to add this bc of hard to fix issue in RMSE computation.
# I need to allow browsing from errors in bootstrap replicates to debug this. (___F I X M E___)
) ## find the maximum of the log-likelihood surface
#slik_j <- refine(slik_j,maxit=5, update_projectors=TRUE)
slik_jx <- refine(slik_jx)
SLRT(slik_jx, h0=slik_jx$MSL$MSLE+0.1, nsim = 100L) # LRT
goftest(slik_jx, nsim = 300L) # goodness of fit test
} else warning("package 'xLLiM' not available for testing.")
if (FALSE) { # example of distinct trainsample
trainsample <- sample(nrow(.get_reft_raw(slik_j)),1000)
mufit <- project("mu",stats=c("mean","var"),data=.get_reft_raw(slik_j)[trainsample,])
s2fit <- project("s2",stats=c("mean","var"),data=.get_reft_raw(slik_j)[trainsample,])
## apply projections on simulated statistics
projectors <- list("MEAN"=mufit,"VAR"=s2fit)
projectors <- list2env(projectors)
corrSobs <- project(Sobs,projectors=projectors)
corrSimuls <- project(.get_reft_raw(slik_j)[-trainsample,],projectors=projectors)
# Infer surface:
densv <- infer_SLik_joint(corrSimuls,stat.obs=corrSobs)
# Usual workflow using inferred surface:
slik_j <- MSL(densv)
plot(slik_j)
}
if (FALSE) { # example of reprojecting accumulated simulations
remufit <- project("mu",stats=c("mean","var"),data=.get_reft_raw(slik_j), method="REML", train_cP_size=400, trainingsize=1000)
res2fit <- project("s2",stats=c("mean","var"),data=.get_reft_raw(slik_j), method="REML", train_cP_size=400, trainingsize=1000)
reprojectors <- list("MEAN"=remufit,"VAR"=res2fit)
reprojectors <- list2env(reprojectors)
recorrSobs <- project(Sobs,projectors=reprojectors)
recorrSimuls <- project(.get_reft_raw(slik_j),projectors=reprojectors)
# Infer surface:
redensv <- infer_SLik_joint(recorrSimuls,stat.obs=recorrSobs)
# Usual workflow using inferred suface:
reslik_j <- MSL(redensv) ## find the maximum of the log-likelihood surface
plot(reslik_j)
}
if (FALSE) { # 1-parameter example
parsp1 <- data.frame(mu=4,
s2=runif(npoints,min=0.4,max=2.4),sample.size=ssize)
# Build simulation table:
simuls1 <- add_reftable(Simulate="myrnorm", parsTable=parsp1)
s2fit1 <- project("s2",stats=c("mean","var"),data=simuls1)
## apply projections on simulated statistics
projectors1 <- list("VAR"=s2fit1)
projectors1 <- list2env(projectors1)
corrSobs1 <- project(Sobs,projectors=projectors1)
corrSimuls1 <- project(simuls1,projectors=projectors1)
# Infer surface:
densv1 <- infer_SLik_joint(corrSimuls1,stat.obs=corrSobs1)
# Usual workflow using inferred surface:
slik_j1 <- MSL(densv1) ## find the maximum of the log-likelihood surface
slik_j1 <- refine(slik_j1,maxit=5, update_projectors=TRUE)
plot(slik_j1)
# etc:
confint(slik_j1,"s2") ## compute 1D confidence interval for given parameter
plot1Dprof(slik_j1,pars="s2",gridSteps=40) ## 1D profile
}
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