View source: R/Sample_quadrats.R

sample_quadrats | R Documentation |

This function allows to sample quadratic subplots from a spatially-explicit
community. The output format are a sites x species abundance table and a
sites x xy-coordinates table. The sites x species abundance is
a classical data format used in community ecology. The table generated
can be for instance be further analysed with the package `vegan`

.

```
sample_quadrats(
comm,
n_quadrats = 20,
quadrat_area = 0.01,
plot = TRUE,
method = "random",
avoid_overlap = TRUE,
x0 = 0,
y0 = 0,
delta_x = 0.1,
delta_y = 0.1,
seed = NULL
)
```

`comm` |
Community object from which the samples are generated |

`n_quadrats` |
(integer) Number of sampling quadrats |

`quadrat_area` |
(numeric) Area of the sampling quadrats |

`plot` |
(logical) Should the sampling design be plotted? default to TRUE. |

`method` |
(character) Available methods are |

`avoid_overlap` |
(logical) For the random sampling try to generate a design without overlap of quadrats . Default is TRUE. |

`x0` , `y0` |
(numeric value) Lower left corner of the first quadrat in transect and grid sampling |

`delta_x` |
(numeric value) Distance between consecutive quadrats in transect and grid sampling in x-direction (the distance between the left sides is measured) |

`delta_y` |
(numeric value) Distance between consecutive quadrats in transect and grid sampling in y-direction (the distance between the lower sides is measured) |

`seed` |
(integer) Any integer passed to |

A list with two items, `spec_dat`

and `xy_dat`

.
`spec_dat`

is a data.frame with sampling quadrats in rows and species abundances
in columns, and `xy_dat`

is a data.frame with sampling quadrats in rows
and the xy-coordinates of the quadrats (lower left corner) in columns.

```
library(vegan)
sim_com1 <- sim_poisson_community(100, 10000)
comm_mat1 <- sample_quadrats(sim_com1, n_quadrats = 100,
quadrat_area = 0.002, method = "grid")
specnumber(comm_mat1$spec_dat)
diversity(comm_mat1$spec_dat, index = "shannon")
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.