inst/doc/intro-diversity-estimation.R

In breakaway: Species Richness Estimation and Modeling

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# install.packages("remotes")
# remotes::install_github("adw96/breakaway")
library(breakaway)

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# install.packages("magrittr")
library(magrittr)

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# install.packages("openxlsx")
# pasolli_et_al <- openxlsx::read.xlsx("https://ars.els-cdn.com/content/image/1-s2.0-S0092867419300017-mmc4.xlsx", sheet = 2)
data("pasolli_et_al")

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ft <- pasolli_et_al$`#.Samples` %>% make_frequency_count_table
ft %>% head(10)

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ft %>% tail(10)

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ft %>% sample_richness

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estimated_richness <- breakaway(ft)
estimated_richness

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estimated_richness$model

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plot(estimated_richness)

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estimated_richness_10 <- breakaway(ft, cutoff = 10)
estimated_richness_10

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estimated_richness_10 %$% model

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estimated_richness_kemp_10 <- kemp(ft, cutoff = 10)
estimated_richness_kemp_10

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estimated_richness_kemp_10 %$% plot