CommunityProfile: Diversity or Entropy Profile of a community
In entropart: Entropy Partitioning to Measure Diversity

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.

CommunityProfile(FUN, NorP, q.seq = seq(0, 2, 0.1), 
    NumberOfSimulations = 0, Alpha = 0.05, BootstrapMethod = "Chao2015", 
    ..., 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 q.
`NorP`	A numeric vector or a two-column matrix. Contains either abundances or probabilities. Two-column matrices should contain the observed abundances (or probabilities) in the first column and the expected ones in the second column, to allow using beta diversity functions.
`q.seq`	A numeric vector: the sequence of divrsity 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 `rCommunity`.
`x`	An object to be tested or plotted or the vector of orders of community profiles in `as.CommunityProfile`.
`y`	Entropy or diversity values of each order, corresponding to `x` values.
`low`	Entropy or diversity lower bound of the confidence envelope, corresponding to `x` values.
`high`	Entropy or diversity higher bound of the confidence envelope, corresponding to `x` values.
`Profile`	An `CommunityProfile` to be plotted.
`...`	Additional arguments to be passed to `FUN` in `CommunityProfile`, to `plot` in `plot.CommunityProfile` or to `lines` in `CEnvelope`.
`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 `TRUE`, the function arguments are verified. Should be set to `FALSE` to save time when the arguments have been checked elsewhere.

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 or a two-column matrix (for beta diversity functions) 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.

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 q values
`y`	The entropy or diversity values returned by `FUN`
`low`	The lower bound of the confidence interval
`high`	The upper bound of the confidence interval

Eric Marcon <Eric.Marcon@ecofog.gf>, Bruno Herault <Bruno.Herault@ecofog.gf>

  # 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)