/
README.Rmd
300 lines (242 loc) · 11.1 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
```{r setup,include=FALSE}
# set the knitr options ... for everyone!
# if you unset this, then vignette build bonks. oh, joy.
#opts_knit$set(progress=TRUE)
opts_knit$set(eval.after='fig.cap')
# for a package vignette, you do want to echo.
# opts_chunk$set(echo=FALSE,warning=FALSE,message=FALSE)
opts_chunk$set(warning=FALSE,message=FALSE)
#opts_chunk$set(results="asis")
opts_chunk$set(cache=TRUE,cache.path="nodist/cache/")
#opts_chunk$set(fig.path="github_extra/figure/",dev=c("pdf","cairo_ps"))
#opts_chunk$set(fig.path="github_extra/figure/",dev=c("png","pdf"))
opts_chunk$set(fig.path="tools/figure/",dev=c("png"))
opts_chunk$set(fig.width=5,fig.height=4,dpi=64)
# doing this means that png files are made of figures;
# the savings is small, and it looks like shit:
#opts_chunk$set(fig.path="figure/",dev=c("png","pdf","cairo_ps"))
#opts_chunk$set(fig.width=4,fig.height=4)
# for figures? this is sweave-specific?
#opts_knit$set(eps=TRUE)
# this would be for figures:
#opts_chunk$set(out.width='.8\\textwidth')
# for text wrapping:
options(width=64,digits=2)
opts_chunk$set(size="small")
opts_chunk$set(tidy=TRUE,tidy.opts=list(width.cutoff=50,blank=TRUE))
#PDQutils.meta <- packageDescription('PDQutils')
```
# PDQutils
[![Build Status](https://github.com/shabbychef/PDQutils/workflows/R-CMD-check/badge.svg)](https://github.com/shabbychef/PDQutils/actions)
[![codecov.io](http://codecov.io/github/shabbychef/PDQutils/coverage.svg?branch=master)](http://codecov.io/github/shabbychef/PDQutils?branch=master)
[![CRAN](http://www.r-pkg.org/badges/version/PDQutils)](https://cran.r-project.org/package=PDQutils)
[![Downloads](http://cranlogs.r-pkg.org/badges/PDQutils?color=green)](http://www.r-pkg.org/pkg/PDQutils)
[![Total](http://cranlogs.r-pkg.org/badges/grand-total/PDQutils?color=green)](http://www.r-pkg.org/pkg/PDQutils)
PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher Approximations
-- Steven E. Pav, shabbychef@gmail.com
## Installation
This package may be installed from CRAN; the latest development version may be
installed via [drat](https://github.com/eddelbuettel/drat "drat"), or built from
[github](https://www.github.com/shabbychef/PDQutils "PDQutils"):
```{r install,eval=FALSE,echo=TRUE}
# install via CRAN:
install.packages('PDQutils')
# get latest dev release via drat:
if (require(drat)) {
drat:::add('shabbychef')
install.packages('PDQutils')
}
# get snapshot from github (may be buggy)
if (require(devtools)) {
install_github('shabbychef/PDQutils')
}
```
# Basic Usage
Approximating the distribution of a random variable via the Gram Charlier, Edgeworth, or Cornish Fisher
expansions is most convenient when the random variable can be decomposed as the sum of a
small number of independent random variables whose cumulants can be computed. For example,
suppose $Y = \sum_{1 \le i \le k} \sqrt{X_i / \nu_i}$ where the $X_i$ are independent central
chi-square random variables with degrees of freedom $\nu_1,\nu_2,...,\nu_k$. I will call this
a 'snak' distribution, for 'sum of Nakagami', since each summand follows a
[Nakagami distribution](https://en.wikipedia.org/wiki/Nakagami_distribution "Nakagami distribution").
We can easily write code that generates variates from this distribution given a vector
of the degrees of freedom:
```{r rsnak,eval=TRUE,echo=TRUE}
rsnak <- function(n,dfs) {
samples <- Reduce('+',lapply(dfs,function(k) { sqrt(rchisq(n,df=k)/k) }))
}
```
Let's take one hundred thousand draws from this distribution and see whether it is approximately normal,
by performing a q-q plot against a normal distribution.
```{r testit,eval=TRUE,echo=TRUE,cache=TRUE,dpi=200,out.width='600px',out.height='500px'}
n.samp <- 1e5
dfs <- c(8,15,4000,10000)
set.seed(18181)
# now draw from the distribution
rvs <- rsnak(n.samp,dfs)
data <- data.frame(draws=rvs)
mu <- mean(rvs)
sigma <- sd(rvs)
library(ggplot2)
ph <- ggplot(data, aes(sample = draws)) + stat_qq(distribution=function(p) { qnorm(p,mean=mu,sd=sigma) }) +
geom_abline(slope=1,intercept=0,colour='red') +
theme(text=element_text(size=8)) +
labs(title="Q-Q plot (against normality)")
print(ph)
```
While this is very nearly normal, we can get a better approximation.
Using the additivity
property of cumulants, we can compute the cumulants of $Y$ easily if we have the cumulants of
the $X_i$. These in turn can be computed from the raw moments. See
[wikipedia](https://en.wikipedia.org/wiki/Chi_distribution "chi distribution") for the raw moments
of the Chi distribution. The following function computes the cumulants:
```{r snakcu,eval=TRUE,echo=TRUE}
# for the moment2cumulant function:
library(PDQutils)
# compute the first ord.max raw cumulants of the sum of Nakagami variates
snak_cumulants <- function(dfs,ord.max=10) {
# first compute the raw moments
moms <- lapply(dfs,function(k) {
ords <- 1:ord.max
moms <- 2 ^ (ords/2.0) * exp(lgamma((k+ords)/2) - lgamma(k/2))
# we are dividing the chi by sqrt the d.f.
moms <- moms / (k ^ (ords/2.0))
moms
})
# turn moments into cumulants
cumuls <- lapply(moms,moment2cumulant)
# sum the cumulants
tot.cumul <- Reduce('+',cumuls)
return(tot.cumul)
}
```
We can now implement the 'dpq' functions trivially using the Edgeworth and Cornish Fisher
approximations, as follows:
```{r dpqsnak,eval=TRUE,echo=TRUE}
library(PDQutils)
dsnak <- function(x,dfs,ord.max=6,...) {
raw.cumul <- snak_cumulants(dfs,ord.max)
retval <- dapx_edgeworth(x,raw.cumul,support=c(0,Inf),...)
return(retval)
}
psnak <- function(q,dfs,ord.max=6,...) {
raw.cumul <- snak_cumulants(dfs,ord.max)
retval <- papx_edgeworth(q,raw.cumul,support=c(0,Inf),...)
return(retval)
}
qsnak <- function(p,dfs,ord.max=10,...) {
raw.cumul <- snak_cumulants(dfs,ord.max)
retval <- qapx_cf(p,raw.cumul,support=c(0,Inf),...)
return(retval)
}
```
The density and distribution functions could also have been implemented via the
Gram Charlier expansion, although there seems to be little justification for so doing,
as the Edgeworth expansion is
[often a better approximation](http://arxiv.org/abs/astro-ph/9711239 "Blinnikov and Moessner").
```{r dpqsnak_gca,eval=TRUE,echo=TRUE}
dsnak_2 <- function(x,dfs,ord.max=10,...) {
raw.moment <- cumulant2moment(snak_cumulants(dfs,ord.max))
retval <- dapx_gca(x,raw.moment,support=c(0,Inf),...)
return(retval)
}
psnak_2 <- function(q,dfs,ord.max=10,...) {
raw.moment <- cumulant2moment(snak_cumulants(dfs,ord.max))
retval <- papx_gca(q,raw.moment,support=c(0,Inf),...)
return(retval)
}
```
The q-q plot looks better now:
```{r improvedqq,eval=TRUE,echo=TRUE,cache=TRUE,dpi=450,out.width='600px',out.height='500px'}
data <- data.frame(draws=rvs)
library(ggplot2)
ph <- ggplot(data, aes(sample = draws)) + stat_qq(distribution=function(p) { qsnak(p,dfs=dfs) }) +
geom_abline(slope=1,intercept=0,colour='red') +
theme(text=element_text(size=8)) +
labs(title="Q-Q against qsnak (C-F appx.)")
print(ph)
```
Note that the q-q plot uses the approximate quantile function, qsnak. If we compute the
approximate CDF of the random draws, we hope it will be nearly uniform, and indeed
it is:
```{r snakuni,eval=TRUE,echo=TRUE,cache=TRUE,dpi=450,out.width='600px',out.height='500px'}
apx.p <- psnak(rvs,dfs=dfs)
if (require(ggplot2)) {
#qplot(apx.p, stat="ecdf", geom="step")
ggplot(data.frame(pv=apx.p),aes(x=pv)) + stat_ecdf(geom='step')
}
```
# Edgeworth versus Gram Charlier
[Blinnikov and Moessner](http://arxiv.org/abs/astro-ph/9711239 "Blinnikov and Moessner") note that
the Gram Charlier expansion will actually _diverge_ for some distributions when more terms in
the expansion are considered, behaviour which is not seen for the Edgeworth expansion. We will consider
the case of a chi-square distribution with 5 degrees of freedom. The 2 and 6 term Gram Charlier expansions
are shown, along with the true value of the PDF, replicating figure 1 of Blinnikov and Moessner:
```{r chisetup,eval=TRUE,echo=TRUE,dpi=200,out.width='600px',out.height='500px'}
# compute moments and cumulants:
df <- 5
max.ord <- 20
subords <- 0:(max.ord - 1)
raw.cumulants <- df * (2^subords) * factorial(subords)
raw.moments <- cumulant2moment(raw.cumulants)
# compute the PDF of the rescaled variable:
xvals <- seq(-sqrt(df/2) * 0.99,6,length.out=1001)
chivals <- sqrt(2*df) * xvals + df
pdf.true <- sqrt(2*df) * dchisq(chivals,df=df)
pdf.gca2 <- sqrt(2*df) * dapx_gca(chivals,raw.moments=raw.moments[1:2],support=c(0,Inf))
pdf.gca6 <- sqrt(2*df) * dapx_gca(chivals,raw.moments=raw.moments[1:6],support=c(0,Inf))
all.pdf <- data.frame(x=xvals,true=pdf.true,gca2=pdf.gca2,gca6=pdf.gca6)
# plot it by reshaping and ggplot'ing
require(reshape2)
arr.data <- melt(all.pdf,id.vars='x',variable.name='pdf',value.name='density')
require(ggplot2)
ph <- ggplot(arr.data,aes(x=x,y=density,group=pdf,colour=pdf)) + geom_line()
print(ph)
```
Compare this with the 2 and 4 term Edgeworth expansions, replicating figure 6 of Blinnikov and Moessner:
```{r chitwo,eval=TRUE,echo=TRUE,dpi=200,out.width='600px',out.height='500px'}
# compute the PDF of the rescaled variable:
xvals <- seq(-sqrt(df/2) * 0.99,6,length.out=1001)
chivals <- sqrt(2*df) * xvals + df
pdf.true <- sqrt(2*df) * dchisq(chivals,df=df)
pdf.edgeworth2 <- sqrt(2*df) * dapx_edgeworth(chivals,raw.cumulants=raw.cumulants[1:4],support=c(0,Inf))
pdf.edgeworth4 <- sqrt(2*df) * dapx_edgeworth(chivals,raw.cumulants=raw.cumulants[1:6],support=c(0,Inf))
all.pdf <- data.frame(x=xvals,true=pdf.true,edgeworth2=pdf.edgeworth2,edgeworth4=pdf.edgeworth4)
# plot it by reshaping and ggplot'ing
require(reshape2)
arr.data <- melt(all.pdf,id.vars='x',variable.name='pdf',value.name='density')
require(ggplot2)
ph <- ggplot(arr.data,aes(x=x,y=density,group=pdf,colour=pdf)) + geom_line()
print(ph)
```
# Rearranging for monotonicity
In one of a series of papers, [Chernozhukov et. al.](http://arxiv.org/abs/0708.1627 "Chernozhukov et. al.")
demonstrate the use of monotonic rearrangements in Edgeworth and Cornish-Fisher expansions of the CDF
and quantile functions, which are, by definition, non-decreasing. It is shown that monotone rearrangement
reduces the error of an initial approximation. This is easy enough to code with tools readily available
in R. First, let us compute the 8 term Gram Charlier approximation to the CDF of the Chi-square with
5 degrees of freedom. This should display non-monotonicity. Then we compute the monotonic rearrangement:
```{r chithree,eval=TRUE,echo=TRUE,dpi=200,out.width='600px',out.height='500px'}
df <- 5
max.ord <- 20
subords <- 0:(max.ord - 1)
raw.cumulants <- df * (2^subords) * factorial(subords)
raw.moments <- cumulant2moment(raw.cumulants)
# compute the CDF of the rescaled variable:
xvals <- seq(-sqrt(df/2) * 0.99,6,length.out=1001)
chivals <- sqrt(2*df) * xvals + df
cdf.true <- pchisq(chivals,df=df)
cdf.gca8 <- papx_gca(chivals,raw.moments=raw.moments[1:8],support=c(0,Inf))
# it is this simple:
require(quantreg)
in.fn <- stepfun(xvals,c(0,cdf.gca8))
out.fn <- rearrange(in.fn)
cdf.rearranged <- out.fn(xvals)
all.cdf <- data.frame(x=xvals,true=cdf.true,gca8=cdf.gca8,rearranged=cdf.rearranged)
# plot it by reshaping and ggplot'ing
require(reshape2)
arr.data <- melt(all.cdf,id.vars='x',variable.name='cdf',value.name='density')
require(ggplot2)
ph <- ggplot(arr.data,aes(x=x,y=density,group=cdf,colour=cdf)) + geom_line()
print(ph)
```