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Questions tagged [inext]

An R package providing simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation of species diversity (Hill numbers) for individual-based (abundance) data or sampling-unit- based (incidence) data.

23 questions
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Using iNEXT with a list object as in ciliates dataset, but with abundance data

In the exemplary work flow of the iNEXT vignette, the ciliates dataset is analyzed to show the diversity estimation based on raw species incidence data. Ciliates is a List of 3 object, made up of 3 habitats with multiple samples each. The dataset I…
NaurasD
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Need to fix this issue with inext package

I'm learning to use the iNEXT package and when I run the code, I get this error: Error in if (t > sum(y)) { : missing value where TRUE/FALSE needed Here is a little fragment of my datase: Localidad n MorfoSp1 MorfoSp2 MorfoSp3 MorfoSp4…
Juan Diego Tovar Garcia
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Incidence Raw data structure for iNext package / error: Error in yi[i]:(nT - 1) : NA/NaN argument

I have a presence/absence data matrix: 24 species as rows and 6 Locations as columns. If a species is present at a location it has the value 1, if it is absent it has the value 0. Now i want to do diversity analyses with the iNext function and…
Drips
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Error for large list (arguments imply differing number of rows) using EstimateD function (iNext package) (R)

I have difficulties to apply the estimateD function in the iNEXT package to my own data. I am working on bees and I have a very large dataset of count of records in grid cells covering a particular region. I want to compute Hill diversities for each…
Nicolas Leclercq
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Best way to calculate how many additional individuals would be needed to sample 100% of asymptotic species richness of a sample/region - iNEXT?

I am starting to use SPADE and iNEXT R packages. I think I have finally got my head around most of what I need so far but... Chao et al, (2009) present an Excel calculator to calculate how many additional individuals would be needed to sample 100%…
Amber Cobley
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1 answer

Trouble adding elements to legend (iNEXT / ggplot2)

I have made a rarefaction curves using the iNEXT package in R and added two horizontal lines for the asymptotes of both curves manually (the package does not do that, so I tried to utilize ggplot functions and it seemed to work), furthermore I…
Ben
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iNEXT se not found

I am using iNEXT to make a rarefaction curve from abundance data. The ggiNEXT function returns the error "object 'se' not found" even when I put se=FALSE into the function. Help? >out<-iNEXT(Sum3) >ggiNEXT(out) Error in fortify.iNEXT(x, type = type)…
Bianca
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Change dataframe in sample by sampling unit format to incidence-frequency format (Prep dataframe for iNext incidence dataframe)

I have a dataframe like so: df<- data.frame(region = c("1","1","1","1","1","2","3","3","3"), loc = c("104","104","104","105","105","106","107", "108", "109"), interact = c("A_B","A_B", "B_C", "C_D", "A_B", "E_F",…
Danielle
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Converting data into the correct format for INEXT analysis

I plan to use the iNEXT function (from the iNEXT package) to analyse potential differences between two pond types. These data are presence/absence and in a sites by species matrix e.g. Pond.type <- c("A", "A", "A", "B", "B", "B") Sample.no <-…
AlanL
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Labeling reference sample size for iNEXT and ggiNEXT type 1 plots

I want to label the reference sample size for each of my assemblages when creating a sample size based sampling curve with ggiNEXT. This information is stored in: iNEXT_Obj$DataInfo$n. I am looking for a way to include these labels within the…
Rlbrubak
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How do I determine the default color palette used by function ggiNEXT in the package iNEXT?

I am trying to match the aesthetics of ggiNEXT objects in a series of manually generated ggplot2 figures. Sample figure is below, where colors of lines and 95% confidence intervals are those chosen by default by function ggiNEXT (code taken directly…
overcup
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How do I generate a sample completeness~diversity order plot in iNext?

I am trying to create a plot in the style of the sample completeness~diversity order plot shown below, but referencing a different dataset. The plot shown above is Fig. 3a in Chao et al. 2020. I want to create a plot in this style for the ciliate…
overcup
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Converting matrix data frame to a list but I can't the same entry data to iNEXT

I am trying to convert a matrix data frame like this (lowland): species DT1 DT3 DT6 DT7 DT12 DT13 DT14 DT15 DT28 DT29 1 M_vaccinifolia 0 0 0 0 0 0 1 0 0 1 2 M_vaccinifolia 0 0 0 0 0 0 0 0 0 …
Romulo Cenci
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Show shared and unique characteristics in a data

I have a dataset of OTUs (observations) and plant species. I want to visualize the shared and unique OTUs among the plant species. Here is the a part of the data .OTU.ID T..kraussiana R..venulosa T..africanum T..repens I..evansiana Z..capensis…
ngwoke chukwubuikem
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Override aesthetics of custom plot

I am not sure exactly how to override aesthetic properties of a custom plot made with ggplot. The only way I could think of right now was using the functionality of the grid package, though is really hackish. Maybe there is a easier way, like using…
Valentin_Ștefan
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