I want to use the bootMer() feature of the lme4 package using linear mixed model and also using boot.ci to get 95% CIs by parametric bootstrapping, and have been getting the warnings of the type "In bootMer(object, bootFun, nsim = nsim, ...) : some bootstrap runs failed (30/100)”.
My code is:
> lmer(LLA ~ 1 +(1|PopID/FamID), data=fp1) -> LLA
> LLA.boot <- bootMer(LLA, qst, nsim=999, use.u=F, type="parametric")
Warning message:
In bootMer(LLA, qst, nsim = 999, use.u = F, type = "parametric") :
some bootstrap runs failed (3/999)
> boot.ci(LLA.boot, type=c("norm", "basic", "perc"))
BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
Based on 996 bootstrap replicates
CALL :
boot.ci(boot.out = LLA.boot, type = c("norm", "basic", "perc"))
Intervals :
Level Normal Basic Percentile
95% (-0.2424, 1.0637 ) (-0.1861, 0.8139 ) ( 0.0000, 1.0000 )
Calculations and Intervals on Original Scale
my problem is why Bootstrap fails for a few values ? and Confidence interval estimated using boot.ci at 95% show negative value, though there are no negative values in the array of values generated by bootstrap.'
The result of plot(LLA.boot):
It's not surprising, for a slightly difficult or unstable model, that a few parametric bootstrap runs might fail to converge for numerical reasons. You should be able to retrieve the specific error messages via attr(LLA.boot,"boot.fail.msgs") (this really should be documented, but isn't ...) In general I wouldn't worry about it too much if the failure fraction is very small (which it is in this case); if were large (say >5-10%) I would revisit my data and model and try to see if there was something else wrong that was manifesting itself in this way.
As for the confidence intervals: the "basic" and "norm" methods use Normal and bias-corrected Normal approximations, respectively, so it's not surprising that intervals should go beyond the range of the computed values. Since your function is
Qst <- function(x){
uu <- unlist(VarCorr(x))
uu[2]/(uu[3]+uu[2])}
}
its possible range is from 0 to 1, and your percentile bootstrap CI shows this range is attained. If your model were perfectly uninformative, the distribution of Qst would be uniform (mean=0.5, sd=sqrt(1/12)=0.288) and the Normal approximation to the CI would be
> 0.5+c(-1,1)*1.96*sqrt(1/12)
[1] -0.06580326 1.06580326
The upper end is about in the same place as your Normal CI, but your lower limit is even smaller, suggesting that there may even be some bimodality in the sampling distribution of your estimate (this is confirmed by the distribution plot you posted). In any case, I suspect that the bottom line is that your confidence intervals (however computed) are so wide that they're telling you that your data provide almost no practical information about the value of Qst ... In particular, it looks like the majority of your bootstrap replicates are finding singular fits, in which one or the other of the variances are estimated as zero. I'm guessing your data set is just not large enough to estimate these variances very precisely.
For more information on how the Normal and bias-corrected Normal approximations are computed, see boot:::basic.ci and boot:::norm.ci or chapter 5 of Davison and Hinkley as cited in ?boot.ci.
Related
I'm wondering how to use replication weights and the confint implementation of the survey package to construct bootstrap confidence intervals/standard errors.
Looking at the survey package's implementation of confint, it seems as though it's simply taking the standard error of the theta list generated after replication, and multiplying it by the statistic corresponding to a given alpha range.
But that doesn't really correspond with any bootstrap implementation I'm aware of. Typically, you'd instead be using a percentile of the distribution of theta to get the sample mean's distribution's confidence interval. The T and BCa intervals are another matter.
Here is my R Code. I have not used the provided weights, instead letting repweights weights be generated as "sample with replacement" weights with equal probability.
data(api)
d <- apiclus1 %>% select(fpc, dnum,api99)
dclus1<-svydesign(id=~dnum, data=d, fpc=~fpc)
rclus1<-as.svrepdesign(dclus1,type="bootstrap", replicates=100)
To test the confidence intervals, we can use:
test_mean <- svymean(~api99, rclus1)
confint(test_mean, df=degf(rclus1))
confint(test_mean, df=degf(rclus1)) - mean(d$api99)
Which results:
2.5 % 97.5 %
api99 554.2971 659.6592
2.5 % 97.5 %
api99 -52.68107 52.68107
So clearly the interval is symmetric, which defeats some of the purpose of using the bootstrap.
So let's try this:
test_bs <- withReplicates(rclus1, function(w, data) weighted.mean(data$api99, w), return.replicates=T)
This will bootstrap the replicates, where the weights are the repweights (which I assume are with replacement weights). Here are the intervals using BCa intervals on the replications:
bca(test$replicates) - mean(d$api99)
-43.2878 49.1148
Clearly not symmetric.
Using percentile intervals:
c(quantile(test$replicates, 0.025),quantile(test$replicates, 0.975)) - mean(d$api99)
2.5% 97.5%
-45.50944 48.06085
Valliant implements percentile intervals this way, which should be equivalent to my percentile intervals:
smho.boot.a <- as.svrepdesign(design = smho.dsgn,
type = "subbootstrap",
replicates = 500)
# total & CI for EOYCNT based on RW bootstrap
a1 <- svytotal( ̃EOYCNT, design = smho.boot.a,
na.rm=TRUE,
return.replicates = TRUE)
# Compute CI based on bootstrap percentile method.
ta1 <- quantile(a1$replicates, c(0.025, 0.975))
I'm looking for clarifications on
a. How to construct bootstrap CIs with survey package for statistics of interest
b. If my withReplication implementation of the bootstrap is correct
The percentile stuff doesn't actually work with multistage survey data (or, at least, it isn't known to work (or, at least, it isn't known to me to work)). Survey bootstraps just estimate the variance. You don't get the higher order accuracy for smooth functions that way, but you do get asymptotically the right variance. To get asymmetric intervals you need to bootstrap some suitable function of the parameter, as svyciprop and svyquantile (and in a sense svyglm) do.
If you assume simple random sampling with replacement of clusters then you could make the percentile bootstrap and extensions work, but that's not a common structure for real-world surveys (and it doesn't really need the survey package)
I'm sure the maintainer of the package would be happy to implement a bootstrap that gave better asymmetric intervals and worked for multistage samples, if someone pointed out suitable references to him.
I am trying to understand bootstrapping in R using the Boot package. I am trying to do a simple spearman rank correlation. I have some code based on a tutorial I found online but am having some issues interpreting the output. The code is below:
*Note: these data are just random numbers I used to help me learn how to run the boot function. They do not represent anything.
test_a=data.frame(v1 = c(1,5,8,3,2,9,5,10,3,5), v2 = c(3,4,7,2,1,10,3,8,8,2))
attach(test_a)
cor.test(v1, v2, method = "spearman")
function_2 = function(test_a, i) {
d2 = test_a[i,]
return(cor(d2$v1, d2$v2, method="spearman"))
}
set.seed(1)
test_boot = boot(test_a, function_2, R=1000)
test_boot
I get the following output:
boot(data = test_a, statistic = function_2, R = 1000)
Bootstrap Statistics :
original bias std. error
t1* 0.6397639 -0.04253283 0.2547429
Which all makes sense to me. But I guess my confusion is with the boot.ci function
ci = boot.ci(test_boot, conf=0.95)
I get the following output:
> ci
BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
Based on 1000 bootstrap replicates
CALL :
boot.ci(boot.out = test_boot, conf = 0.95)
Intervals :
Level Normal Basic
95% ( 0.1830, 1.1816 ) ( 0.3173, 1.2987 )
Level Percentile BCa
95% (-0.0192, 0.9622 ) (-0.1440, 0.9497 )
Calculations and Intervals on Original Scale
And this is where I am a bit lost. I can't really find a source that explains in layman's terms in the context of a correlation coefficient, because obviously you cannot have a correlation > 1.0, yet this spits out a confidence interval (at least with two methods) that goes above 1. The sources that discuss these different confidence intervals frankly have been a bit confusing. Is there any one of these that is better for certain parameters than others? It is also possible I am completely misinterpreting what I am doing as well.
I also include the results of plot(test_boot) for your reference.
The eventual goal (with actual data) once I am more confident in running and interpreting results of bootstrapping would be to run tests for trends with time (Mann-Kendall test for trends and Thiel-Sen Slope Estimator, I cannot use parametric statistics with my data :/) and compare my observed dataset with bootstrapped samples.
Any help would really be appreciated. Thank you in advance!
The two top intervals are normal theory intervals. They use the bootstrap to calculate the standard error and then make symmetric intervals that may or may not respect the bounds of the statistic. The bottom two intervals are percentile intervals (the first is a raw percentile interval and the second is a bias-corrected, accelerated interval). These identify particular values of the bootstrap statistics that define the CI. As such, they will always respect the theoretical bounds of the statistic being bootstrapped.
I am trying to fit t-distributions to my data but am unable to do so. My first try was
fitdistr(myData, "t")
There are 41 warnings, all saying that NaNs are produced. I don't know how, logarithms seem to be involved. So I adjusted my data somewhat so that all data is >0, but I still have the same problem (9 fewer warnings though...). Same problem with sstdFit(), produces NaNs.
So instead I try with fitdist which I've seen on stackoverflow and CrossValidated:
fitdist(myData, "t")
I then get
Error in mledist(data, distname, start, fix.arg, ...) :
'start' must be defined as a named list for this distribution
What does this mean? I tried looking into the documentation but that told me nothing. I just want to possibly fit a t-distribution, this is so frustrating :P
Thanks!
Start is the initial guess for the parameters of your distribution. There are logs involved because it is using maximum likelihood and hence log-likelihoods.
library(fitdistrplus)
dat <- rt(100, df=10)
fit <- fitdist(dat, "t", start=list(df=2))
I think it's worth adding that in most cases, using the fitdistrplus package to fit a t-distribution to real data will lead to a very bad fit, which is actually quite misleading. This is because the default t-distribution functions in R are used, and they don't support shifting or scaling. That is, if your data has a mean other than 0, or is scaled in some way, then the fitdist function will simply lead to a bad fit.
In real life, if data fits a t-distribution, it is usually shifted (i.e. has a mean other than 0) and / or scaled. Let's generate some data like that:
data = 1.5*rt(10000,df=5) + 0.5
Given this data has been sampled from the t-distribution with 5 degrees of freedom, you'd think that trying to fit a t-distribution to this should work quite nicely. But actually, here is the result. It estimates a df of 2, and provides a bad fit as shown in the qq plot.
> fit_bad <- fitdist(data,"t",start=list(df=3))
> fit_bad
Fitting of the distribution ' t ' by maximum likelihood
Parameters:
estimate Std. Error
df 2.050967 0.04301357
> qqcomp(list(fit_bad)) # generates plot to show fit
When you fit to a t-distribution you want to not only estimate the degrees of freedom, but also a mean and scaling parameter.
The metRology package provides a version of the t-distribution called t.scaled that has a mean and sd parameter in addition to the df parameter [metRology]. Now let's fit it again:
> library("metRology")
> fit_good <- fitdist(data,"t.scaled",
start=list(df=3,mean=mean(data),sd=sd(data)))
> fit_good
Fitting of the distribution ' t.scaled ' by maximum likelihood
Parameters:
estimate Std. Error
df 4.9732159 0.24849246
mean 0.4945922 0.01716461
sd 1.4860637 0.01828821
> qqcomp(list(fit_good)) # generates plot to show fit
Much better :-) The parameters are very close to how we generated the data in the first place! And the QQ plot shows a much nicer fit.
I would like to get the bootstrapped t-value and the bootstrapped p-value of a lm.
I have the following code (basically copied from a paper) which works.
# First of all you need the following packages
install.packages("car")
install.packages("MASS")
install.packages("boot")
library("car")
library("MASS")
library("boot")
boot.function <- function(data, indices){
data <- data[indices,]
mod <- lm(prestige ~ income + education, data=data) # the liear model
# the first element of the following vector contains the t-value
# and the second element is the p-value
c(summary(mod)[["coefficients"]][2,3], summary(mod)[["coefficients"]][2,4])
}
Now, I compute the bootstrapping model, which gives me the following:
duncan.boot <- boot(Duncan, boot.function, 1999)
duncan.boot
ORDINARY NONPARAMETRIC BOOTSTRAP
Call:
boot(data = Duncan, statistic = boot.function, R = 1999)
Bootstrap Statistics :
original bias std. error
t1* 5.003310e+00 0.288746545 1.71684664
t2* 1.053184e-05 0.002701685 0.01642399
I have two questions:
My understanding is that the bootsrapped value is the original plus the bias, which means that both bootstrapped values (the bootstrapped t-value as well as the bootstrapped p-value) are greater than the original values. This in turn is not possible, because if the t-value rises (which means more significance) the p-values MUST be lower, right? Therefore I think that I have not yet really understood the output of the boot function (here: duncan.boot). How do I compute the bootstrapped values?
I do not understand how the boot() works. If you look at duncan.boot <- boot(Duncan, boot.function, 1999) you see that I have not passed any arguments for the function "boot.function". I suppose that R sets data <- Duncan. But since I have not passed anything for the argument "indices", I do not understand how the following line in the function "boot.function" works data <- data[indices,]
I hope the questions make sense!??
The boot function is "expecting" to get a function that has two arguments: the first being a data.frame and the second being an "indices" vector (possibly with duplicate entries and probably not using all the indices) to use in selecting rows and probably having some duplicate or triplicates.) It then samples with replacement determined by the pattern of duplicates and triplicates from the original dataframe (multiple times determined by "R" with different "choice sets"), passes those to the indices argument in the boot.function, and then collects the results of the R number of function applications.
Regarding what is reported by the print method for boot objects, take a look at this (done after examining the returned object with str()
> duncan.boot$t0
[1] 5.003310e+00 1.053184e-05
> apply(duncan.boot$t, 2, mean)
[1] 5.342895220 0.002607943
> apply(duncan.boot$t, 2, mean) - duncan.boot$t0
[1] 0.339585441 0.002597411
It becomes more obvious that the T0 value is from the original data while the bias is the difference between the mean of the boot()-ed values and the T0 values. I don't think it makes a lot of sense to be asking why p-values based on parametric considerations are increasing in association with an increase in estimated t-statistics. You are really in two disparate regions of statistical thought when you do that. I would have interpreted the increase in p-values as an effect of the sampling process, which does not take into account the Normal distribution assumptions. It is simply saying something about the sampling distribution of the p-value (which is really just another sample statistic).
(Comment: The sourcebook used at the time of R development was Davison and Hinkley's "Bootstrap Methods and their Applications". I'm no claiming any support for my answer above, but I thought to put it in as a reference after Hagen Brenner asked about sampling with two indices in the comments below. There are many unexpected aspects of bootstrapping that arise after one goes beyond the simple parametric estimation and I would first turn to that reference if I were tackling more complex sampling situations.)
I am attempting to use boot.ci from R's boot package to calculate bias- and skew-corrected bootstrap confidence intervals from a parametric bootstrap. From my reading of the man pages and experimentation, I've concluded that I have to compute the jackknife estimates myself and feed them into boot.ci, but this isn't stated explicitly anywhere. I haven't been able to find other documentation, although to be fair I haven't looked at the original Davison and Hinkley book on which the code is based ...
If I naively run b1 <- boot(...,sim="parametric") and then boot.ci(b1), I get the error influence values cannot be found from a parametric bootstrap. This error occurs if and only if I specify type="all" or type="bca"; boot.ci(b1,type="bca") gives the same error. So does empinf(b1). The only way I can get things to work is to explicitly compute jackknife estimates (using empinf() with the data argument) and feed these into boot.ci.
Construct data:
set.seed(101)
d <- data.frame(x=1:20,y=runif(20))
m1 <- lm(y~x,data=d)
Bootstrap:
b1 <- boot(d$y,
statistic=function(yb,...) {
coef(update(m1,data=transform(d,y=yb)))
},
R=1000,
ran.gen=function(d,m) {
unlist(simulate(m))
},
mle=m1,
sim="parametric")
Fine so far.
boot.ci(b1)
boot.ci(b1,type="bca")
empinf(b1)
all give the error described above.
This works:
L <- empinf(data=d$y,type="jack",
stype="i",
statistic=function(y,f) {
coef(update(m1,data=d[f,]))
})
boot.ci(b1,type="bca",L=L)
Does anyone know if this is the way I'm supposed to be doing it?
update: The original author of the boot package responded to an e-mail:
... you are correct that the issue is that you are doing a
parametric bootstrap. The bca intervals implemented in boot are
non-parametric intervals and this should have been stated
explicitely somewhere. The formulae for parametric bca intervals
are not the same and depend on derivatives of the least favourable
family likelihood when there are nuisance parameters as in your
case. (See pp 206-207 in Davison & Hinkley) empinf assumes that the
statistic is in one of forms used for non-parametric bootstrapping
(which you did in your example call to empinf) but your original
call to boot (correctly) had the statistic in a different form
appropriate for parametric resampling.
You can certainly do what you're doing but I am not sure of the
theoretical properties of mixing parametric resampling with
non-parametric interval estimation.
After looking at the boot.ci page I decided to use a boot-object constructed along the lines of an example in Ch 6 of Davison and Hinkley and see whether it generated the errors you observed. I do get a warning but no errors.:
require(boot)
lmcoef <- function(data, i){
d <- data[i, ]
d.reg <- lm(y~x, d)
c(coef(d.reg)) }
lmboot <- boot(d, lmcoef, R=999)
m1
boot.ci(lmboot, index=2) # I am presuming that the interest is in the x-coefficient
#----------------------------------
BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
Based on 999 bootstrap replicates
CALL :
boot.ci(boot.out = lmboot, index = 2)
Intervals :
Level Normal Basic
95% (-0.0210, 0.0261 ) (-0.0236, 0.0245 )
Level Percentile BCa
95% (-0.0171, 0.0309 ) (-0.0189, 0.0278 )
Calculations and Intervals on Original Scale
Warning message:
In boot.ci(lmboot, index = 2) :
bootstrap variances needed for studentized intervals