I am working with a dataset that includes bat species captured in two different land uses (degraded and forest) using mist nets. The dataset is structured with species abundance data, and I have calculated the mist net meter per hour as a measure of trapping effort (calculated as mist net length x duration of time the net was deployed). I am not sure if the data arranged appropriately to produce species rarefaction curve using iNEXT package.
- Dataset columns include land use type, individual species counts, mist net meter per hour (effort) for each mist net deployed. N.B: net.hour was calculated by multiplying the mist.net length with time.deployed (time was converted into decimal to perform the calculation).
| Land_use | Cysp | Heti | Maso | total.indvl.captured| mist.net length |time.deployed| net.hour(L*T)|
| -------- | -----|------|------|---------------------|-----------------|-------------|--------------|
| Degraded | 22 | 0 | 3 | 25 | 18 | 5:30 | 99 |
| Degraded | 1 | 1 | 0 | 2 | 12 | 8:30 | 102 |
| Forest | 0 | 0 | 4 | 4 | 6 | 9:00 | 54 |
| Forest | 3 | 2 | 0 | 5 | 24 | 6:15 | 150 |
| Degraded | 0 | 0 | 1 | 1 | 12 | 7:15 | 87 |
| Degraded | 1 | 0 | 0 | 1 | 6 | 6:15 | 37.5 |
| Forest | 0 | 0 | 2 | 2 | 6 | 4:30 | 27 |
| Forest | 4 | 1 | 0 | 5 | 12 | 8:30 | 102 |
I tried using iNEXT package, but I could not even make a graph where I can present 2 rarefaction curve in one graph - one for the degraded land-use and another for the forest land-use, and Y axis will depict the Estimated number of species, and X axis will depict the Number of individual or trapping hour. I am aiming to perform Mao Tau rarefaction curves for the captured species, where species richness is rarefied based on mist net meter per hour and then rescaled to the number of individuals (or trapping hour). This analysis needs to be done using the iNEXT package in R. The requirement is to have both interpolated and extrapolated lines on the curves, with the extrapolated lines serving as estimates for double the reference sample size. Additionally, I need to include shaded areas representing the 95% confidence intervals for each curve.
The graph should be something like that:
