<!--
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Custom Units}
-->

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

The goal of this vignette is to explain how to estimate asymptotic
complexity for custom units (other than the defaults, seconds and
kilobytes).

## Simple regex example

Let us consider a simple adaptation of the regex example from the
README.  The code below defines a function which replaces all
occurrences of the character `a` with some other string `replace`, in
`subject`.

```{r}
gsub_replace <- function(replace,subject){
  string <- gsub("a",replace,subject)
  data.frame(string, nchar=nchar(string))
}
gsub_replace("-","foobar")
gsub_replace("--","foobar")
```

The output above shows that we can replace the `a` in `foobar` with
either one or two dashes, and the output is a data frame with one row
and two columns, including the numeric `nchar` column which we may
want to visualize as a function of `N`. To do that in the code below,
we use that function inside a call to `atime` with `result=TRUE`
(required in order to save the resulting 1 row data frames).

```{r}
atime.gsub.list <- atime::atime(
  setup={
    subject <- paste(rep("a", N), collapse="")
    pattern <- paste(rep(c("a?", "a"), each=N), collapse="")
  },
  constant.replacement=gsub_replace("constant size replacement",subject),
  linear.replacement=gsub_replace(subject,subject),
  result=TRUE)
plot(atime.gsub.list)
```

The output above shows that atime computes and plots nchar, in
addition to the usual kilobytes and seconds. In this case, it is
useful to see the different asymptotic slopes of linear and constant
replacement, for both `nchar` and `seconds`. To estimate their
asymptotic complexity classes, we use the code below,

```{r}
ref.gsub.list <- atime::references_best(atime.gsub.list)
plot(ref.gsub.list)
```

The plot above clearly shows the linear complexity of constant
replacement, and the quadratic complexity of linear replacement.

## Dynamic programming algorithms for change-point detection

The time complexity of the Dynamic Programming algorithm implemented
in the PeakSegDisk package depends on the number of intervals
(candidate changepoints stored), so we may want to look at how the
number of intervals changes with the data size `N`. Also we must input a
non-negative penalty parameter, and then the algorithm outputs a
certain number of segments, again which may be interesting to look at
as a function of data size `N`. Here we compute the mean number of
intervals for real Mono27ac data, and synthetic count data which are
always increasing.

First, in the code below, we define the data sets, as a function of
data size `N`,

```{r}
library(data.table)
data(Mono27ac, package="PeakSegDisk", envir=environment())
setup <- quote({
  data.list <- list(real=Mono27ac$coverage[1:N])
  data.list$synthetic <- data.table(data.list$real)[, count := 1:.N]
})
```

Next, we define a list of expressions to run for each data size:

```{r}
penalty <- 1e6
(expr.list <- c(
  if(requireNamespace("PeakSegDisk"))atime::atime_grid(
    list(Data=c("real","synthetic")),
    FPOP={
      fit <- PeakSegDisk::PeakSegFPOP_df(data.list[[Data]], penalty)
      fit$loss[, .(intervals=mean.intervals, segments)]
    }),
  atime::atime_grid(mean={
    mean(data.list$real$count)
    data.frame(intervals=NA, segments=1)
  })
))
```

The output above shows the expressions which will be run for each data
size. Note that each expression returns a data frame with one row and
two numeric columns, `intervals` and `segments`, which will be
used as additional units in asymptotic complexity analysis.

Next, we use `substitute` to use the `setup` we defined above as
an argument to `atime`, along with the other required arguments:

```{r}
(atime.DP.lang <- substitute(atime::atime(
  N=as.integer(10^seq(1, 3, by=0.5)),
  setup=SETUP,
  expr.list=expr.list,
  seconds.limit=Inf,
  result=TRUE),
  list(SETUP=setup)))
```

Next we run the timings:

```{r}
atime.DP.list <- eval(atime.DP.lang)
plot(atime.DP.list)
```

The plot above shows the timings in both kinds of data (real and
synthetic). Clearly the algorithm has much fewer intervals, in real
data than in synthetic increasing data. The code below computes and
plots the best asymptotic references:

```{r}
ref.DP.list <- atime::references_best(atime.DP.list)
plot(ref.DP.list)
```

The plot above
shows one panel/facet from top to bottom, for each unit. It is clear
that there is a substantial difference in the number of intervals
stored by the algorithm, between real and synthetic increasing
data. From the plot above, it should be clear that 

* the number of intervals grows slowly (log) for real data, and much
  faster (linear) for synthetic increasing data,
* the memory usage (kilobytes) is grows slowly (log or constant), 
* the computation time grows slowly for real data (expected
  log-linear), and much faster for synthetic increasing data (expected quadratic).

Exercise for the reader: to see the expected asymptotic time
complexity in the last plot, re-do the previous analyses, increasing
the penalty as well as the max data size N. (which were kept small in
the code above in order to reduce computation time on CRAN)


