`maxnodf`

calculates the maximum NODF value that can be
achieved in a bipartite network with a given number of rows, columns and
links.

You can install `maxnodf`

from github with:

```
install.packages("devtools") # install devtools if needed
::install_github("christophhoeppke/maxnodf") devtools
```

`maxnodf`

has three functions:

`maxnodf()`

For a given network, `maxnodf`

calculates the maximum
nestedness that can be achieved in a network with a given number of
rows, columns and links, subject to the constraint that all rows and
columns must have at least one link (i.e. row and column totals must
always be >= 1). As input, `maxnodf()`

takes either a
numeric matrix describing a bipartite network (a bipartite incidence
matrix where elements are positive numbers if nodes interact, and 0
otherwise) or a numeric vector of length three of the form
`c(#Rows, #Columns, #Links)`

.

This allows nestedness values to be normalised as NODF/max(NODF) following Song et al (2017), where NODF is the raw NODF of the network and max(NODF) is the maximum nestedness that can be achieved in a network with the same number of rows, columns and links as web, subject to the constraint that all rows and columns must have at least one link (as calculated by maxnodf())

`maxnodf`

has three algorithms for finding the maximum
nestedness of a bipartite network. These can be set using the
`quality`

argument. Lower quality settings are faster, but
find worse optima. Higher quality settings are slower, but find better
optima.

`quality = 0`

, uses a greedy algorithm.`quality = 1`

, uses a greedy algorithm plus hillclimbing.`quality = 2`

, uses a simulated annealing algorithm, with the greedy algorithm output as the start point. Best results, but requires the most computation time.

`NODFc()`

To control for maximum nestedness, connectance and network size, Song
et al. (2017) propose the NODF_c metric: (NODF/max(NODF))/(C * log(S))
where C is the network connectance, S is the geometric mean of the
number of plants and pollinators in the network, NODF is the raw NODF of
the network and max(NODF) is the maximum nestedness that can be achieved
in a network with the same number of rows, columns and links as web,
subject to the constraint that all rows and columns must have at least
one link (as calculated by `maxnodf()`

). `NODFc`

calculates this NODF_c metric. As input, `NODFc`

takes a
numeric matrix describing a bipartite network, as well as the same
`quality`

argument values described above.

`nodf_cpp()`

A simple function that takes a bipartite matrix as input, and returns
the raw NODF value of the matrix. Used internally by
`maxnodf`

. Calculation is quick, because it is implemented in
C++.

```
<- matrix(0,10,10) # initialise an empty network
m 1,] <- 1 # ensure all row species have at least one link
m[1] <- 1 # ensure all column species have at least one link
m[,2:10,2:10] <- sample(0:1, 9 * 9, replace = TRUE) # randomise the rest of the matrix
m[maxnodf(web = m, quality = 2) # calculate the maximum nestedness
```

The code is released under the MIT license (see `LICENSE`

file).

Song, C., Rohr, R.P. and Saavedra, S., 2017. Why are some plant–pollinator networks more nested than others? Journal of Animal Ecology, 86(6), pp.1417-1424.