Description Usage Arguments Details Value Author(s) Examples

View source: R/CommunityProfile.R

Calculates the diversity or entropy profile of a community, applying a community function to a vector of orders.

1 2 3 4 5 6 7 8 9 10 | ```
CommunityProfile(FUN, NorP, q.seq = seq(0, 2, 0.1),
NumberOfSimulations = 0, Alpha = 0.05, BootstrapMethod = "Chao2015",
size = 1, ..., CheckArguments = TRUE)
as.CommunityProfile(x, y, low = NULL, high = NULL)
is.CommunityProfile(x)
## S3 method for class 'CommunityProfile'
plot(x, ..., main = NULL,
xlab = "Order of Diversity", ylab = "Diversity", ylim = NULL,
LineWidth = 2, ShadeColor = "grey75", BorderColor = "red")
CEnvelope(Profile, LineWidth = 2, ShadeColor = "grey75", BorderColor = "red", ...)
``` |

`FUN` |
The function to be applied to each value of |

`NorP` |
A numeric vector. Contains either abundances or probabilities. |

`q.seq` |
A numeric vector: the sequence of diversity orders to address. Default is from 0 to 2. |

`NumberOfSimulations` |
The number of simulations to run, 0 by default. |

`Alpha` |
The risk level, 5% by default. |

`BootstrapMethod` |
The method used to obtain the probabilities to generate bootstrapped communities from observed abundances. See |

`size` |
The size of simulated communities used to compute the bootstrap confidence envelope. 1 (default) means that the actual size must be used. |

`x` |
An object to be tested or plotted or the vector of orders of community profiles in |

`y` |
Entropy or diversity values of each order, corresponding to |

`low` |
Entropy or diversity lower bound of the confidence envelope, corresponding to |

`high` |
Entropy or diversity higher bound of the confidence envelope, corresponding to |

`Profile` |
An |

`...` |
Additional arguments to be passed to |

`main` |
The main title of the plot. |

`xlab` |
The x axis label of the plots. |

`ylab` |
The y axis label of the plot. |

`ylim` |
The interval of y values plotted. |

`LineWidth` |
The width of the line that represents the actual profile. |

`ShadeColor` |
The color of the shaded confidence envelope. |

`BorderColor` |
The color of the bounds of the confidence envelope. |

`CheckArguments` |
Logical; if |

The function `CommunityProfile`

is used to calculate diversity or entropy profiles based on community functions such as `Tsallis`

or `ChaoPD`

. The first two arguments of the function must be a probability or abundance vector and a number (*q*).
Additional arguments cannot be checked. Unexpected results may be returned if `FUN`

is not used properly.

If `NumberOfSimulations`

is greater than 0, a bootstrap confidence interval is produced by simulating communities with `rCommunity`

and calculating their profiles. The size of those communities may be that of the actual community or specified by `size`

.

`CommunityProfile`

objects can be plotted. They can also be added to the current plot by `CEnvelope`

.

A `CommunityProfile`

, which is a list:

`x` |
The order |

`y` |
The entropy or diversity values returned by |

`low` |
The lower bound of the confidence interval |

`high` |
The upper bound of the confidence interval |

Eric Marcon <[email protected]>, Bruno Herault <[email protected]>

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ```
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Plot diversity estimated without bias correction
plot(CommunityProfile(Diversity, Paracou618.MC$Ps, seq(0, 2, 0.2)),
lty=3, ylim=c(50, 350))
# Estimate diversity, with a condidence envelope
# (only 10 simulations to save time, should be 1000)
Profile <- CommunityProfile(Diversity, as.AbdVector(Paracou618.MC$Ns),
seq(0, 2, 0.2), Correction="UnveilJ", NumberOfSimulations=10)
# Complete the plot, and add the legend
CEnvelope(Profile, main="Paracou Plots Diversity")
legend("topright", c("Bias Corrected", "Biased"), lty=c(1,3), inset=0.01)
# Advanced use with beta-diversity functions :
# Profile of the beta entropy of the first community of Paracou618.
# Observed and expected probabilities are bound into a 2-column matrix
# An intermediate function is necessary to separate them before calling TsallisBeta
# The CheckArguments is mandatory but does not need to be set: CommunityProfile() sets it to FALSE
CommunityProfile(function(PandPexp, q, CheckArguments)
{TsallisBeta(PandPexp[, 1], PandPexp[, 2], q)},
NorP=cbind(Paracou618.MC$Psi[, 1], Paracou618.MC$Ps), q.seq=seq(0, 2, 0.2))
``` |

entropart documentation built on Feb. 6, 2018, 1:04 a.m.

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