Title:	Biodiversity Index Calculation and Bootstrap Confidence Interval Estimation
Version:	1.0.4
Description:	Provides tools for the calculation of common biodiversity indices from count data. Additionally, it incorporates bootstrapping techniques to generate multiple samples, facilitating the estimation of confidence intervals around these indices. Furthermore, the package allows for the exploration of how variation in these indices changes with differing numbers of sites, making it a useful tool with which to begin an ecological analysis. Methods are based on the following references: Chao et al. (2014) <doi:10.1890/13-0133.1>, Chao and Colwell (2022) <doi:10.1002/9781119902911.ch2>, Hsieh, Ma,' and Chao (2016) <doi:10.1111/2041-210X.12613>.
License:	MIT + file LICENSE
Encoding:	UTF-8
RoxygenNote:	7.2.3
Imports:	ggplot2, stats
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0), vegan
Depends:	R (≥ 2.10)
LazyData:	true
Config/testthat/edition:	3
VignetteBuilder:	knitr
URL:	https://github.com/csim063/biosampleR
BugReports:	https://github.com/csim063/biosampleR/issues
NeedsCompilation:	no
Packaged:	2023-09-13 03:36:49 UTC; simpk
Author:	Craig Eric Simpkins [aut, cre]
Maintainer:	Craig Eric Simpkins <simpkinscraig063@gmail.com>
Repository:	CRAN
Date/Publication:	2023-09-13 18:30:02 UTC

Barro-Colorado Island Tree Counts

Description

This dataset contains tree counts from Barro-Colorado Island. It has 50 rows each representing the counts taken from a separate one hectare plot for each of the 225 species (columns)

Usage

BCI

Format

A data frame with 50 rows and 225 columns:

Abarema.macradenia

Count for Abarema.macradenia

Vachellia.melanoceras

Count for Vachellia.melanoceras

Acalypha.diversifolia

Count for Acalypha.diversifolia

Acalypha.macrostachya

Count for Acalypha.macrostachya

Adelia.triloba

Count for Adelia.triloba

Aegiphila.panamensis

Count for Aegiphila.panamensis

Alchornea.costaricensis

Count for Alchornea.costaricensis

Alchornea.latifolia

Count for Alchornea.latifolia

Alibertia.edulis

Count for Alibertia.edulis

Allophylus.psilospermus

Count for Allophylus.psilospermus

Alseis.blackiana

Count for Alseis.blackiana

Amaioua.corymbosa

Count for Amaioua.corymbosa

Anacardium.excelsum

Count for Anacardium.excelsum

Andira.inermis

Count for Andira.inermis

Annona.spraguei

Count for Annona.spraguei

Apeiba.glabra

Count for Apeiba.glabra

Apeiba.tibourbou

Count for Apeiba.tibourbou

Aspidosperma.desmanthum

Count for Aspidosperma.desmanthum

Astrocaryum.standleyanum

Count for Astrocaryum.standleyanum

Astronium.graveolens

Count for Astronium.graveolens

Attalea.butyracea

Count for Attalea.butyracea

Banara.guianensis

Count for Banara.guianensis

Beilschmiedia.pendula

Count for Beilschmiedia.pendula

Brosimum.alicastrum

Count for Brosimum.alicastrum

Brosimum.guianense

Count for Brosimum.guianense

Calophyllum.longifolium

Count for Calophyllum.longifolium

Casearia.aculeata

Count for Casearia.aculeata

Casearia.arborea

Count for Casearia.arborea

Casearia.commersoniana

Count for Casearia.commersoniana

Casearia.guianensis

Count for Casearia.guianensis

Casearia.sylvestris

Count for Casearia.sylvestris

Cassipourea.guianensis

Count for Cassipourea.guianensis

Cavanillesia.platanifolia

Count for Cavanillesia.platanifolia

Cecropia.insignis

Count for Cecropia.insignis

Cecropia.obtusifolia

Count for Cecropia.obtusifolia

Cedrela.odorata

Count for Cedrela.odorata

Ceiba.pentandra

Count for Ceiba.pentandra

Celtis.schippii

Count for Celtis.schippii

Cespedesia.spathulata

Count for Cespedesia.spathulata

Chamguava.schippii

Count for Chamguava.schippii

Chimarrhis.parviflora

Count for Chimarrhis.parviflora

Maclura.tinctoria

Count for Maclura.tinctoria

Chrysochlamys.eclipes

Count for Chrysochlamys.eclipes

Chrysophyllum.argenteum

Count for Chrysophyllum.argenteum

Chrysophyllum.cainito

Count for Chrysophyllum.cainito

Coccoloba.coronata

Count for Coccoloba.coronata

Coccoloba.manzinellensis

Count for Coccoloba.manzinellensis

Colubrina.glandulosa

Count for Colubrina.glandulosa

Cordia.alliodora

Count for Cordia.alliodora

Cordia.bicolor

Count for Cordia.bicolor

Cordia.lasiocalyx

Count for Cordia.lasiocalyx

Coussarea.curvigemma

Count for Coussarea.curvigemma

Croton.billbergianus

Count for Croton.billbergianus

Cupania.cinerea

Count for Cupania.cinerea

Cupania.latifolia

Count for Cupania.latifolia

Cupania.rufescens

Count for Cupania.rufescens

Cupania.seemannii

Count for Cupania.seemannii

Dendropanax.arboreus

Count for Dendropanax.arboreus

Desmopsis.panamensis

Count for Desmopsis.panamensis

Diospyros.artanthifolia

Count for Diospyros.artanthifolia

Dipteryx.oleifera

Count for Dipteryx.oleifera

Drypetes.standleyi

Count for Drypetes.standleyi

Elaeis.oleifera

Count for Elaeis.oleifera

Enterolobium.schomburgkii

Count for Enterolobium.schomburgkii

Erythrina.costaricensis

Count for Erythrina.costaricensis

Erythroxylum.macrophyllum

Count for Erythroxylum.macrophyllum

Eugenia.florida

Count for Eugenia.florida

Eugenia.galalonensis

Count for Eugenia.galalonensis

Eugenia.nesiotica

Count for Eugenia.nesiotica

Eugenia.oerstediana

Count for Eugenia.oerstediana

Faramea.occidentalis

Count for Faramea.occidentalis

Ficus.colubrinae

Count for Ficus.colubrinae

Ficus.costaricana

Count for Ficus.costaricana

Ficus.insipida

Count for Ficus.insipida

Ficus.maxima

Count for Ficus.maxima

Ficus.obtusifolia

Count for Ficus.obtusifolia

Ficus.popenoei

Count for Ficus.popenoei

Ficus.tonduzii

Count for Ficus.tonduzii

Ficus.trigonata

Count for Ficus.trigonata

Ficus.yoponensis

Count for Ficus.yoponensis

Garcinia.intermedia

Count for Garcinia.intermedia

Garcinia.madruno

Count for Garcinia.madruno

Genipa.americana

Count for Genipa.americana

Guapira.myrtiflora

Count for Guapira.myrtiflora

Guarea.fuzzy

Count for Guarea.fuzzy

Guarea.grandifolia

Count for Guarea.grandifolia

Guarea.guidonia

Count for Guarea.guidonia

Guatteria.dumetorum

Count for Guatteria.dumetorum

Guazuma.ulmifolia

Count for Guazuma.ulmifolia

Guettarda.foliacea

Count for Guettarda.foliacea

Gustavia.superba

Count for Gustavia.superba

Hampea.appendiculata

Count for Hampea.appendiculata

Hasseltia.floribunda

Count for Hasseltia.floribunda

Heisteria.acuminata

Count for Heisteria.acuminata

Heisteria.concinna

Count for Heisteria.concinna

Hirtella.americana

Count for Hirtella.americana

Hirtella.triandra

Count for Hirtella.triandra

Hura.crepitans

Count for Hura.crepitans

Hieronyma.alchorneoides

Count for Hieronyma.alchorneoides

Inga.acuminata

Count for Inga.acuminata

Inga.cocleensis

Count for Inga.cocleensis

Inga.goldmanii

Count for Inga.goldmanii

Inga.laurina

Count for Inga.laurina

Inga.semialata

Count for Inga.semialata

Inga.nobilis

Count for Inga.nobilis

Inga.oerstediana

Count for Inga.oerstediana

Inga.pezizifera

Count for Inga.pezizifera

Inga.punctata

Count for Inga.punctata

Inga.ruiziana

Count for Inga.ruiziana

Inga.sapindoides

Count for Inga.sapindoides

Inga.spectabilis

Count for Inga.spectabilis

Inga.umbellifera

Count for Inga.umbellifera

Jacaranda.copaia

Count for Jacaranda.copaia

Lacistema.aggregatum

Count for Lacistema.aggregatum

Lacmellea.panamensis

Count for Lacmellea.panamensis

Laetia.procera

Count for Laetia.procera

Laetia.thamnia

Count for Laetia.thamnia

Lafoensia.punicifolia

Count for Lafoensia.punicifolia

Licania.hypoleuca

Count for Licania.hypoleuca

Licania.platypus

Count for Licania.platypus

Lindackeria.laurina

Count for Lindackeria.laurina

Lonchocarpus.heptaphyllus

Count for Lonchocarpus.heptaphyllus

Luehea.seemannii

Count for Luehea.seemannii

Macrocnemum.roseum

Count for Macrocnemum.roseum

Maquira.guianensis.costaricana

Count for Maquira.guianensis.costaricana

Margaritaria.nobilis

Count for Margaritaria.nobilis

Marila.laxiflora

Count for Marila.laxiflora

Maytenus.schippii

Count for Maytenus.schippii

Miconia.affinis

Count for Miconia.affinis

Miconia.argentea

Count for Miconia.argentea

Miconia.elata

Count for Miconia.elata

Miconia.hondurensis

Count for Miconia.hondurensis

Mosannona.garwoodii

Count for Mosannona.garwoodii

Myrcia.gatunensis

Count for Myrcia.gatunensis

Myrospermum.frutescens

Count for Myrospermum.frutescens

Nectandra.cissiflora

Count for Nectandra.cissiflora

Nectandra.lineata

Count for Nectandra.lineata

Nectandra.purpurea

Count for Nectandra.purpurea

Ochroma.pyramidale

Count for Ochroma.pyramidale

Ocotea.cernua

Count for Ocotea.cernua

Ocotea.oblonga

Count for Ocotea.oblonga

Ocotea.puberula

Count for Ocotea.puberula

Ocotea.whitei

Count for Ocotea.whitei

Oenocarpus.mapora

Count for Oenocarpus.mapora

Ormosia.amazonica

Count for Ormosia.amazonica

Ormosia.coccinea

Count for Ormosia.coccinea

Ormosia.macrocalyx

Count for Ormosia.macrocalyx

Pachira.quinata

Count for Pachira.quinata

Pachira.sessilis

Count for Pachira.sessilis

Perebea.xanthochyma

Count for Perebea.xanthochyma

Cinnamomum.triplinerve

Count for Cinnamomum.triplinerve

Picramnia.latifolia

Count for Picramnia.latifolia

Piper.reticulatum

Count for Piper.reticulatum

Platymiscium.pinnatum

Count for Platymiscium.pinnatum

Platypodium.elegans

Count for Platypodium.elegans

Posoqueria.latifolia

Count for Posoqueria.latifolia

Poulsenia.armata

Count for Poulsenia.armata

Pourouma.bicolor

Count for Pourouma.bicolor

Pouteria.fossicola

Count for Pouteria.fossicola

Pouteria.reticulata

Count for Pouteria.reticulata

Pouteria.stipitata

Count for Pouteria.stipitata

Prioria.copaifera

Count for Prioria.copaifera

Protium.costaricense

Count for Protium.costaricense

Protium.panamense

Count for Protium.panamense

Protium.tenuifolium

Count for Protium.tenuifolium

Pseudobombax.septenatum

Count for Pseudobombax.septenatum

Psidium.friedrichsthalianum

Count for Psidium.friedrichsthalianum

Psychotria.grandis

Count for Psychotria.grandis

Pterocarpus.rohrii

Count for Pterocarpus.rohrii

Quararibea.asterolepis

Count for Quararibea.asterolepis

Quassia.amara

Count for Quassia.amara

Randia.armata

Count for Randia.armata

Sapium.broadleaf

Count for Sapium.broadleaf

Sapium.glandulosum

Count for Sapium.glandulosum

Schizolobium.parahyba

Count for Schizolobium.parahyba

Senna.dariensis

Count for Senna.dariensis

Simarouba.amara

Count for Simarouba.amara

Siparuna.guianensis

Count for Siparuna.guianensis

Siparuna.pauciflora

Count for Siparuna.pauciflora

Sloanea.terniflora

Count for Sloanea.terniflora

Socratea.exorrhiza

Count for Socratea.exorrhiza

Solanum.hayesii

Count for Solanum.hayesii

Sorocea.affinis

Count for Sorocea.affinis

Spachea.membranacea

Count for Spachea.membranacea

Spondias.mombin

Count for Spondias.mombin

Spondias.radlkoferi

Count for Spondias.radlkoferi

Sterculia.apetala

Count for Sterculia.apetala

Swartzia.simplex.var.grandiflora

Count for Swartzia.simplex.var.grandiflora

Swartzia.simplex.continentalis

Count for Swartzia.simplex.continentalis

Symphonia.globulifera

Count for Symphonia.globulifera

Handroanthus.guayacan

Count for Handroanthus.guayacan

Tabebuia.rosea

Count for Tabebuia.rosea

Tabernaemontana.arborea

Count for Tabernaemontana.arborea

Tachigali.versicolor

Count for Tachigali.versicolor

Talisia.nervosa

Count for Talisia.nervosa

Talisia.princeps

Count for Talisia.princeps

Terminalia.amazonia

Count for Terminalia.amazonia

Terminalia.oblonga

Count for Terminalia.oblonga

Tetragastris.panamensis

Count for Tetragastris.panamensis

Tetrathylacium.johansenii

Count for Tetrathylacium.johansenii

Theobroma.cacao

Count for Theobroma.cacao

Thevetia.ahouai

Count for Thevetia.ahouai

Tocoyena.pittieri

Count for Tocoyena.pittieri

Trattinnickia.aspera

Count for Trattinnickia.aspera

Trema.micrantha

Count for Trema.micrantha

Trichanthera.gigantea

Count for Trichanthera.gigantea

Trichilia.pallida

Count for Trichilia.pallida

Trichilia.tuberculata

Count for Trichilia.tuberculata

Trichospermum.galeottii

Count for Trichospermum.galeottii

Triplaris.cumingiana

Count for Triplaris.cumingiana

Trophis.caucana

Count for Trophis.caucana

Trophis.racemosa

Count for Trophis.racemosa

Turpinia.occidentalis

Count for Turpinia.occidentalis

Unonopsis.pittieri

Count for Unonopsis.pittieri

Virola.multiflora

Count for Virola.multiflora

Virola.sebifera

Count for Virola.sebifera

Virola.surinamensis

Count for Virola.surinamensis

Vismia.baccifera

Count for Vismia.baccifera

Vochysia.ferruginea

Count for Vochysia.ferruginea

Xylopia.macrantha

Count for Xylopia.macrantha

Zanthoxylum.ekmanii

Count for Zanthoxylum.ekmanii

Zanthoxylum.juniperinum

Count for Zanthoxylum.juniperinum

Zanthoxylum.panamense

Count for Zanthoxylum.panamense

Zanthoxylum.setulosum

Count for Zanthoxylum.setulosum

Zuelania.guidonia

Count for Zuelania.guidonia

Source

https://www.science.org/doi/10.1126/science.1066854

Calculate the change in variance with increasing number of sites

Description

Calculate the change in variance with increasing number of sites

Usage

calc_delta_var(
  data,
  col_name,
  site_name = "num_sites",
  rep_name = "rep",
  visualize = FALSE
)

Arguments

Value

A data frame with the number of sites and the variance and standard deviation of the mean of the biodiversity index for each number of sites.

Examples

ss <- generate_subsamples(BCI,
                         min_sites = 1,
                        max_sites = 5,
                       step = 1,
                     reps = 5)
data <- ss
data  <- unlist(data, recursive = FALSE)
data <- do.call(rbind, data)

calc_delta_var(data,
             col_name = "richness",
           site_name = "num_sites",
        rep_name = "rep",
     visualize = TRUE)

Calculate biodiversity summary indices from count data

Description

Calculate biodiversity summary indices from count data

Usage

calc_diversity_indices(data)

Arguments

Value

A data frame with sites as rows and diversity indices as columns. The columns are: abundance, species richness, Shannon diveristy index, Simpson diversity index, Chao1, Difference between Choa1 and species richness.

Examples

ind <- calc_diversity_indices(BCI)

Create multiple resamples of a data set.

Description

Create multiple resamples of a data set.

Usage

create_resample(data, reps = 100, summary = TRUE, seed = sample(0:9999, 1))

Arguments

Value

A list of data frames, if summary = FALSE, each data frame is a resample of the original data set. If summary = TRUE, each data frame is a resample of the original data set with diversity indices calculated using calc_diversity_indices.

Examples

rs <- create_resample(BCI, reps = 10, summary = TRUE)

Generate subsamples of a data frame with a number of sites between a minimum and maximum value.

Description

Generate subsamples of a data frame with a number of sites between a minimum and maximum value.

Usage

generate_subsamples(
  data,
  min_sites = 1,
  max_sites = nrow(data),
  step = 1,
  reps = 100,
  summary = TRUE,
  seed = sample(0:9999, 1)
)

Arguments

Value

A list of lists of data frames, if summary = FALSE, each data frame is a subsample of the original data set. If summary = TRUE, each data frame is a subsample of the original data set with diversity indices calculated using calc_diversity_indices.

Examples

ss <- generate_subsamples(BCI,
                          min_sites = 1,
                          max_sites = 5,
                          step = 1,
                          reps = 2)

Calculate biodiversity measures and summary statistics for a data set using repeated sampling

Description

Calculate biodiversity measures and summary statistics for a data set using repeated sampling

Usage

get_sample_stats(data, sites_col = 1, reps = 100, indices = "all")

Arguments

Value

A list of two data frames. The first data frame contains site specific data with sites as rows and summary statistics as columns. The second contains an overall summary of the data.

Examples

stats <- get_sample_stats(BCI, reps = 5)