The package iNEXT offers function DataInfo for that:ĭataInfo (hp.
Rarify data code#
To fix this, please upload the following quick fix solution (this will source a code from GitHub which will provide temporary plot.iNEXT function which works in R 4.0.x version).īefore the analysis, let's oversee the data in each of the data frames first. This bug means that the plot.iNEXT function (plot function applied on the object of iNEXT class) is returning a bug. PLEASE NOTE: currently under the R version 4, iNEXT suffers from a bug, given that it was not modified to the fourth generation of R. # install.packages ('iNEXT') library (iNEXT )
Rarify data install#
You may need to install the package from CRAN first if you haven't used it before:
Anne Chao (Tsing-Hua University, Hsinchu, Taiwan). In case of hp.incid, the first row additionally contains the information about the number of subplots for which incidences were recorded (25 in case of all localities) this is necessary for the calculation of incidence-based rarefaction (see further).įor all calculations in this exercise, we will use the library iNEXT, developed by the team of prof. Let's see the result of all three options.īoth hp.abund and hp.incid are data frames, with species in rows and localities (1-ha plots) in columns the cells are filled either by numbers of individuals of given species ( hp.abund) or the number of incidences (out of 25) of each species ( hp.incid). Another option is to standardize data to the same number of individuals (this is possible in case of abundance-based data) or the same coverage (this is possible for both abundance- and incidence-based data). The original data are standardized to the area (at each locality, the total of 0.25 ha was surveyed), which is a common approach for vegetation ecologists.
For this, we need to standardize data to a common base. Our aim will be to compare diversities of forest vegetation in different elevation. Dataset is prepared in two forms: abundance data ( hp.abund) contains numbers of individuals for each species at each locality incidence-based data ( hp.incid) contains incidences of each species at each locality (incidence is the presence of species in a subplot made within each locality each species at the locality can incidence number up to 25, i.e. At each locality, a 1-ha plot has been established, and within the plot, 25 10×10-m subplots have been sampled on an even grid (since there are gaps between the subplots, in total 25×0.01-ha = 0.25-ha area was surveyed within each locality see data description for details). We will use vegetation data from One-hectar plots in different forest types across Taiwan, containing the survey of woody species at seven localities sampled in different elevations in Taiwan.
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