---
title: "rdiversity examples"
date: '`r format(Sys.Date(), "%B %d %Y")`'
author: "Sonia Mitchell"
output:
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  toc: true
  toc_depth: 2
  vignette: >
    %\VignetteIndexEntry{rdiversity-examples}
    %\VignetteEngine{knitr::knitr}
    %\VignetteEncoding{UTF-8}
---

## Generating a metacommunity 

Before calculating diversity a `metacommunity` object must be created. This object contains all the information needed to calculate diversity. In the following example, we generate a metacommunity (`partition`) comprising two species ("cows" and "sheep"), and partitioned across three subcommunities (a, b, and c).

```{r}
# Load the package into R
library(rdiversity)

# Initialise data
partition <- data.frame(a=c(1,1),b=c(2,0),c=c(3,1))
row.names(partition) <- c("cows", "sheep")
```
The `metacommunity()` function takes two arguments, `partition` and `similarity`. When species are considered completely distinct, an identity matrix is required, which is generated automatically if the `similarity` argument is missing, as below:

```{r}
# Generate metacommunity object
meta <- metacommunity(partition = partition)
```

Note that a warning is displayed when abundances (rather than relative abundances) are entered into the `partition` argument. Both are acceptable inputs.

When species share some similarity and a similarity matrix is available, then a similarity object (and the metacommunity object) is generated in the following way:

```{r}
# Initialise similarity matrix
s <- matrix(c(1, 0.5, 0.5, 1), nrow = 2)
row.names(s) <- c("cows", "sheep")
colnames(s) <- c("cows", "sheep")

# Generate similarity object 
s <- similarity(similarity = s, dat_id = "my_taxonomic")

# Generate metacommunity object
meta <- metacommunity(partition = partition, similarity = s)
```

Alternatively, if a distance matrix is available, then a distance object is generated in the following way: 

```{r}
# Initialise distance matrix
d <- matrix(c(0, 0.7, 0.7, 0), nrow = 2)
row.names(d) <- c("cows", "sheep")
colnames(d) <- c("cows", "sheep")

# Generate distance object
d <- distance(distance = d, dat_id = "my_taxonomic")

# Convert the distance object to similarity object (by means of a linear or exponential transform)
s <- dist2sim(dist = d, transform = "linear")

# Generate metacommunity object
meta <- metacommunity(partition = partition, similarity = s)
```

Each `metacommunity` object contains the following slots:

* `@type_abundance` : the abundance of types within a metacommunity,  
* `@similarity` : the pair-wise similarity of types within a metacommunity,  
* `@ordinariness` : the ordinariness of types within a metacommunity,  
* `@subcommunity_weights` :  the relative weights of subcommunities within a metacommunity, and
* `@type_weights` : the relative weights of types within a metacommunity.

## Calculating diversity
### Method 1
This method uses a wrapper function to simplify the pipeline and is recommended if only a few measures are being calculated.

A complete list of these functions is shown below:

* `raw_sub_alpha()` : estimate of naive-community metacommunity diversity  
* `norm_sub_alpha()` : similarity-sensitive diversity of subcommunity *j* in isolation  
* `raw_sub_rho()` : redundancy of subcommunity *j*  
* `norm_sub_rho()` : representativeness of subcommunity *j*  
* `raw_sub_beta()` : distinctiveness of subcommunity *j*  
* `norm_sub_beta()` : estimate of effective number of distinct subcommunities  
* `sub_gamma()` : contribution per individual toward metacommunity diversity  
* `raw_meta_alpha()` : naive-community metacommunity diversity  
* `norm_meta_alpha()` : average similarity-sensitive diversity of subcommunities  
* `raw_meta_rho()` : average redundancy of subcommunities  
* `norm_meta_rho()` : average representativeness of subcommunities  
* `raw_meta_beta()` : average distinctiveness of subcommunities  
* `norm_meta_beta()` : effective number of distinct subcommunities  
* `meta_gamma()` : metacommunity similarity-sensitive diversity  

Each of these functions take two arguments, `meta` (a `metacommunity` object) and `qs` (a vector of q values), and output results as a `rdiv` object. For example, to calculate normalised subcommunity alpha diversity for *q=0*, *q=1*, and *q=2*:

```{r}
# Initialise data
partition <- data.frame(a=c(1,1),b=c(2,0),c=c(3,1))
row.names(partition) <- c("cows", "sheep")

# Generate a metacommunity object
meta <- metacommunity(partition)

# Calculate diversity
norm_sub_alpha(meta, 0:2)
```

However, if multiple measures are required and computational efficiency is an issue, then the following method is recommended (the same results are obtained).

### Method 2
This method requires that we first calculate the species-level components, by passing a `metacommunity` object to the appropriate function; `raw_alpha()`, `norm_alpha()`, `raw_beta()`, `norm_beta()`, `raw_rho()`, `norm_rho()`, or `raw_gamma()`. Subcommunity- and metacommunity-level diversities are calculated using the functions `subdiv()` and `metadiv()`. Since both subcommunity and metacommunity diversity measures are transformations of the same species-level component, this method is computationally more efficient.

```{r}
# Initialise data
partition <- data.frame(a=c(1,1),b=c(2,0),c=c(3,1))
row.names(partition) <- c("cows", "sheep")

# Generate a metacommunity object
meta <- metacommunity(partition)

# Calculate the species-level component for normalised alpha
component <- norm_alpha(meta)

# Calculate normalised alpha at the subcommunity-level 
subdiv(component, 0:2)

# Likewise, calculate normalised alpha at the metacommunity-level 
metadiv(component, 0:2)
```

In some instances, it may be useful to calculate **all** subcommunity (or metacommunity) measures. In which case, a `metacommunity` object may be passed directly to `subdiv()` or `metadiv()`:

```{r}
# Calculate all subcommunity diversity measures
subdiv(meta, 0:2)

# Calculate all metacommunity diversity measures
metadiv(meta, 0:2)
```

## Taxonomic diversity
1. Initialise data:
```{r}
# Taxonomic lookup table
Species <- c("tenuifolium", "asterolepis", "simplex var.grandiflora", "simplex var.ochnacea")
Genus <- c("Protium", "Quararibea", "Swartzia", "Swartzia")
Family <- c("Burseraceae", "Bombacaceae", "Fabaceae", "Fabaceae")
Subclass <- c("Sapindales", "Malvales", "Fabales", "Fabales")
lookup <- cbind.data.frame(Species, Genus, Family, Subclass)

# Partition matrix
partition <- matrix(rep(1, 8), nrow = 4)
colnames(partition) <- LETTERS[1:2]
rownames(partition) <- lookup$Species

```
and assign values for each taxonomic level:
```{r}
values <- c(Species = 0, Genus = 1, Family = 2, Subclass = 3, Other = 4)
```

2. Generate a distance object from a lookup table using the `tax2dist()` 
function:
```{r}
d <- tax2dist(lookup, values)
```
By default the `tax2dist()` argument `precompute_dist` is TRUE, such that a pairwise distance matrix is calculated automatically and is stored in `d@distance`. If the taxonomy is too large, `precompute_dist` can be set to FALSE, which enables pairwise taxonomic similarity to be calculated on the fly, in step 4. 

3. Convert the distance object to similarity object (by means of a linear or exponential transform) using the `dist2sim()` function:
```{r}
s <- dist2sim(d, "linear")
```

4. Generate a metacommunity object using the `metacommunity()` function:
```{r}
meta <- metacommunity(partition, s)
```

5. Calculate diversity:
```{r}
meta_gamma(meta, 0:2)
```

## Phylogenetic diversity
Phylogenetic diversity measures can be broadly split into two categories – those that look at the phylogeny as a whole, such as Faith’s (1992) phylogenetic diversity (Faith’s PD), and those that look at pairwise tip distances, such as mean pairwise distance (MPD; Webb, 2000). The framework of measures presented in this package is able to quantify phylogenetic diversity using both of these methods.

### Distance-based phylogenetic diversity

1. Initialise data:
```{r}
# Example data
tree <- ape::rtree(4)
partition <- matrix(1:12, ncol=3)
partition <- partition/sum(partition)
```

2. Generate a distance matrix using the `phy2dist()` function: 
```{r}
d <- phy2dist(tree)
```
By default the `phy2dist()` argument `precompute_dist` is TRUE, such that a pairwise distance matrix is calculated automatically and is stored in `d@distance`. If the taxonomy is too large, `precompute_dist` can be set to FALSE, which enables pairwise taxonomic similarity to be calculated on the fly, in step 4. 

3. Convert the distance object to similarity object (by means of a linear or exponential transform) using the `dist2sim()` function:
```{r}
s <- dist2sim(d, "linear")
```

4. Generate a metacommunity object using the `metacommunity()` function
```{r}
meta <- metacommunity(partition, s)
```

5. Calculate diversity
```{r}
meta_gamma(meta, 0:2)
```

### Branch-based phylogenetic diversity
1. Initialise data:
```{r}
tree <- ape::rtree(4)
partition <- matrix(1:12, ncol=3)
partition <- partition/sum(partition)
colnames(partition) <- letters[1:3]
row.names(partition) <- paste0("sp",1:4)
tree$tip.label <- row.names(partition)
```

2. Generate a similarity object using the `phy2branch()` function
```{r}
s <- phy2branch(tree, partition)
```

3. Generate a metacommunity object using the `metacommunity()` function
```{r}
meta <- metacommunity(partition, s)
```

4. Calculate diversity
```{r}
meta_gamma(meta, 0:2)
```


**Note that**: a metacommunity that was generated using this approach will contain three additional slots:

* `@raw_abundance` : the relative abundance of terminal species (where types are then considered to be historical species),
* `@raw_structure` : the length of evolutionary history of each historical species
* `@parameters` : parameters associated with historical species

## Genetic diversity
1. Initialise data:
Note: the package `pinfsc50` must be installed for this example to work.
```{r, eval = FALSE}
library(rdiversity)
vcf_file <- system.file("extdata", "pinf_sc50.vcf.gz", package = "pinfsc50")
#read in twice: first for the column names then for the data
tmp_vcf <- readLines(vcf_file)
vcf_data <- read.table(vcf_file, stringsAsFactors = FALSE)
# filter for the columns names
vcf_names <- unlist(strsplit(tmp_vcf[grep("#CHROM",tmp_vcf)],"\t"))
names(vcf_data) <- vcf_names
partition <- cbind.data.frame(A = c(rep(1, 9), rep(0, 9)), B = c(rep(0, 9), rep(1, 9)))
partition <- partition/sum(partition)
```

2. Generate a distance matrix using the `gen2dist()` function:
```{r, eval = FALSE}
d <- gen2dist(vcf)
```

3. Convert the distance object to a similarity object (by means of a linear or exponential transform) using the `dist2sim()` function:
```{r, eval = FALSE}
s <- dist2sim(d, transform = 'l')
```
Note: the `dist2sim()` function contains an optional argument, `max_d`, which defines the distance at which pairs of individuals have similarity zero. If not supplied this is set to the maximum distance observed in the distance matrix. If comparing different windows on a genome, for example, it is necessary to ensure `max_d` is the same for each analysis.

4. Generate a metacommunity object using the `metacommunity()` function:
```{r, eval = FALSE}
rownames(partition) <- rownames(s@similarity)
meta <- metacommunity(partition, s)
```

5. Calculate diversity, for example beta diversity measures are used to identify trends such as differentiation:
```{r, eval = FALSE}
norm_meta_beta(meta, 0:2)
```

### User defined distance
```{r}
partition <- matrix(sample(6), nrow = 3)
rownames(partition) <- paste0("sp", 1:3)
partition <- partition / sum(partition)

d <- matrix(c(0,.75,1,.75,0,.3,1,.3,0), nrow = 3)
rownames(d) <- paste0("sp", 1:3)
colnames(d) <- paste0("sp", 1:3)
d <- distance(d, "my_taxonomy")
s <- dist2sim(d, "linear")

meta <- metacommunity(partition, s)
```

### User defined similarity
```{r}
partition <- matrix(sample(6), nrow = 3)
rownames(partition) <- paste0("sp", 1:3)
partition <- partition / sum(partition)

s <- matrix(c(1,.8,0,.8,1,.1,0,.1,1), nrow = 3)
rownames(s) <- paste0("sp", 1:3)
colnames(s) <- paste0("sp", 1:3)
s <- similarity(s, "my_functional")

meta <- metacommunity(partition, s)
```

## Additional tools

### `repartition()`

```{r}
tree <- ape::rtree(5)
tree$tip.label <- paste0("sp", 1:5)

partition <- matrix(rep(1,10), nrow = 5)
row.names(partition) <- paste0("sp", 1:5)
partition <- partition / sum(partition)
s <- phy2branch(tree, partition)
meta <- metacommunity(partition, s)

new_partition <- matrix(sample(10), nrow = 5)
row.names(new_partition) <- paste0("sp", 1:5)
new_partition <- new_partition / sum(new_partition)

new_meta <- repartition(meta, new_partition)
```