title: “AntClassify” output: rmarkdown::html_vignette vignette: > % % % ————————-
library(AntClassify)Introduction
The AntClassify package provides an integrated ecological pipeline to classify ant communities into functional guilds, identify exotic species, detect endemic and rare species of the Atlantic Forest, and quantify key ecological patterns.
This tool was developed to facilitate ecological analyses, standardize functional classification, and improve reproducibility in ant community studies. By integrating multiple ecological databases into a single workflow, AntClassify allows researchers to efficiently assess community structure, biological invasions, endemism, and rarity patterns.
The package is particularly useful for biodiversity monitoring, conservation planning, and macroecological research involving ant assemblages.
AntClassify aims to provide a standardized and reproducible framework for advancing ecological research on ant communities.
Example dataset
dados <- data.frame(
Atta_sexdens = 50,
Camponotus_atriceps = 40,
Crematogaster_sp = 35,
Cyphomyrmex_minutus = 30,
Cyphomyrmex_rimosus = 28,
Ectatomma_edentatum = 25,
Heteroponera_mayri = 22,
Holcoponera_striatula = 20,
Monomorium_floricola = 18,
Monomorium_pharaonis = 17,
Pheidole_megacephala = 16,
Strumigenys_emmae = 15,
Strumigenys_rogeri = 14,
Nylanderia_fulva = 13,
Odontomachus_chelifer = 12,
Oxyepoecus_reticulatus = 11,
Pachycondyla_striata = 10,
Apterostigma_serratum = 9,
Brachymyrmex_delabiei = 8,
Brachymyrmex_feitosai = 7,
Camponotus_fallatus = 6,
Camponotus_hermanni = 5,
Camponotus_xanthogaster = 4,
Pheidole_aberrans = 3,
Pheidole_fimbriata = 3,
Pheidole_obscurithorax = 2,
Pheidole_subarmata = 2,
Strumigenys_fridericimuelleri = 2,
Heteroponera_inermis = 2,
Oxyepoecus_browni = 2,
Sphinctomyrmex_stali = 1,
Strumigenys_sanctipauli = 1,
Brachymyrmex_micromegas = 1,
Camponotus_tripartitus = 1,
Diaphoromyrma_sofiae = 1
)
colnames(dados) <- gsub("_", " ", colnames(dados))
dados
#> Atta sexdens Camponotus atriceps Crematogaster sp Cyphomyrmex minutus
#> 1 50 40 35 30
#> Cyphomyrmex rimosus Ectatomma edentatum Heteroponera mayri
#> 1 28 25 22
#> Holcoponera striatula Monomorium floricola Monomorium pharaonis
#> 1 20 18 17
#> Pheidole megacephala Strumigenys emmae Strumigenys rogeri Nylanderia fulva
#> 1 16 15 14 13
#> Odontomachus chelifer Oxyepoecus reticulatus Pachycondyla striata
#> 1 12 11 10
#> Apterostigma serratum Brachymyrmex delabiei Brachymyrmex feitosai
#> 1 9 8 7
#> Camponotus fallatus Camponotus hermanni Camponotus xanthogaster
#> 1 6 5 4
#> Pheidole aberrans Pheidole fimbriata Pheidole obscurithorax
#> 1 3 3 2
#> Pheidole subarmata Strumigenys fridericimuelleri Heteroponera inermis
#> 1 2 2 2
#> Oxyepoecus browni Sphinctomyrmex stali Strumigenys sanctipauli
#> 1 2 1 1
#> Brachymyrmex micromegas Camponotus tripartitus Diaphoromyrma sofiae
#> 1 1 1 1Running the pipeline
resultado <- antclassify(dados)
#> *************************************************
#> Starting AntClassify
#> *************************************************
#>
#> >>> Running guild classification
#> Step 1: Preparing community data...
#> Step 2: Matching species to functional guilds...
#>
#> Guild classification results (first 6 rows):
#> species abundance percentage
#> Atta sexdens Atta sexdens 50 11.467890
#> Camponotus atriceps Camponotus atriceps 40 9.174312
#> Crematogaster sp Crematogaster sp 35 8.027523
#> Cyphomyrmex minutus Cyphomyrmex minutus 30 6.880734
#> Cyphomyrmex rimosus Cyphomyrmex rimosus 28 6.422018
#> Ectatomma edentatum Ectatomma edentatum 25 5.733945
#> antclassify_guild
#> Atta sexdens Fungus-growers (soil or leaf litter nesting)
#> Camponotus atriceps Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Crematogaster sp Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Cyphomyrmex minutus Fungus-growers (soil or leaf litter nesting)
#> Cyphomyrmex rimosus Fungus-growers (soil or leaf litter nesting)
#> Ectatomma edentatum Generalist predators (dominant or cryptic in soil or leaf litter)
#> silva_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Unidentified Guild
#> Crematogaster sp Unidentified Guild
#> Cyphomyrmex minutus Unidentified Guild
#> Cyphomyrmex rimosus Unidentified Guild
#> Ectatomma edentatum Generalist predatory ectaheteromorphs
#> delabie_guild
#> Atta sexdens Attini (Fungus-growers)
#> Camponotus atriceps Omnivorous soil-and-litter species
#> Crematogaster sp Omnivorous soil-and-litter species
#> Cyphomyrmex minutus Attini (Fungus-growers)
#> Cyphomyrmex rimosus Attini (Fungus-growers)
#> Ectatomma edentatum Large Ponerinae (Large epigeic predators)
#> silvestre_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Generalist patrolling Camponotines
#> Crematogaster sp Small arboreal species with massive recruitment
#> Cyphomyrmex minutus Cryptic fungus-growing ants (Attines)
#> Cyphomyrmex rimosus Cryptic fungus-growing ants (Attines)
#> Ectatomma edentatum Large predators
#> Step 3: Generating plots...
#>
#> ********************************************************************************
#> IMPORTANT NOTICE:
#> Please verify all assigned guilds. 'Unidentified Guild' indicates that the
#> taxon was not found in the available reference databases.
#> Guild classification in this analysis follows:
#> - Literature-based criteria from:
#> Silvestre, R., Brandão, C. R. F., & Silva, R. R. (2003).
#> Grupos funcionales de hormigas: el caso de los gremios del Cerrado.
#> In F. Fernández (Ed.), *Introducción a las Hormigas de las Región Neotropical*
#> (pp. 113-148). Instituto Alexander Von Humboldt.
#> Silva, R. R., Silvestre, R., Brandão, C. R. F., Morini, M. S. C., & Delabie, J. H. C. (2015).
#> Grupos tróficos e guildas em formigas poneromorfas. In: Delabie, J. H. C. et al.
#> *As formigas poneromorfas do Brasil*. Ilhéus: Editus, 2015. p. 163-179.
#> Delabie, J. H. C., Agosti, D., & Nascimento, I. C. (2000).
#> Litter ant communities of the Brazilian Atlantic rain forest region.
#> *Sampling Ground-dwelling Ants: case studies from the world's rain forests.
#> Curtin University of Technology School of Environmental Biology Bulletin*, v. 18.
#> - The 'AntClassify Guilds' classification corresponds to the internal
#> classification system implemented in the AntClassify package.
#> ********************************************************************************
#>
#> >>> Checking exotic species
#> Step 1: Preparing community data...
#> Step 2: Generating results...
#>
#> ********************************************************************************
#> EXOTIC SPECIES DETECTED:
#> species abundance percentage
#> 1 Monomorium floricola 18 4.128440
#> 2 Monomorium pharaonis 17 3.899083
#> 3 Pheidole megacephala 16 3.669725
#> 4 Strumigenys emmae 15 3.440367
#> 5 Strumigenys rogeri 14 3.211009
#>
#> DATA SOURCE AND REFERENCE:
#> The exotic species list used in this function is sourced from:
#> VIEIRA, Vitoria Brunetta. 'Quem são e onde estão as formigas exóticas do Brasil?'
#> Dissertacao (Mestrado em Entomologia) – Universidade Federal do Parana (UFPR),
#> Curitiba, Brasil, 2025.
#> ********************************************************************************
#>
#> >>> Checking Atlantic Forest endemic species
#>
#> **********************************************************************************
#> ATTENTION: This function identifies endemic species of the BRAZILIAN ATLANTIC FOREST.
#> If your data collection did not occur within this biome, this analysis may not
#> be appropriate for your study.
#> **********************************************************************************
#> Step 1: Preparing community data...
#> Step 2: Generating results...
#>
#> ********************************************************************************
#> ENDEMIC SPECIES DETECTED (ATLANTIC FOREST):
#> species abundance percentage
#> 1 Apterostigma serratum 9 2.064220
#> 2 Brachymyrmex delabiei 8 1.834862
#> 3 Brachymyrmex feitosai 7 1.605505
#> 4 Camponotus fallatus 6 1.376147
#> 5 Camponotus hermanni 5 1.146789
#>
#> DATA SOURCE AND REFERENCE:
#> The endemic species list is sourced from:
#> Silva, N. S., Goncalves, D. C. de O., Wazema, C. T., Barbosa, D. A., Prado, L. P. do,
#> Andrade-Silva, J., Fernandes, T. T., Silva, R. R., & Morini, M. S. de C. (2025).
#> 'Endemism and vulnerability of ants in the phytophysiognomies of the Brazilian
#> Atlantic Forest'. In: Brazilian Myrmecology: Exploring the World’s Richest Ant Fauna
#> (Chapter 16). Editora Cientifica Digital. DOI: 10.37885/250920259.
#> ********************************************************************************
#>
#> >>> Checking Atlantic Forest rarity patterns
#>
#> ********************************************************************************
#> ATTENTION:
#> This function identifies rare ant species and their rarity forms.
#> This classification is specific to the Brazilian Atlantic Forest and
#> may not be appropriate for other biomes.
#> ********************************************************************************
#> Step 1: Preparing community data and rarity database...
#> Step 2: Generating results...
#>
#> ********************************************************************************
#> RARE SPECIES DETECTED:
#> species rarity_form abundance percentage
#> 1 Brachymyrmex feitosai Form 4 7 1.6055046
#> 2 Brachymyrmex micromegas Form 7 1 0.2293578
#> 3 Camponotus atriceps Form 2 40 9.1743119
#> 4 Camponotus tripartitus Form 7 1 0.2293578
#> 5 Diaphoromyrma sofiae Form 7 1 0.2293578
#> 6 Heteroponera inermis Form 4 2 0.4587156
#> 7 Oxyepoecus browni Form 6 2 0.4587156
#> 8 Oxyepoecus reticulatus Form 1 11 2.5229358
#> 9 Pheidole aberrans Form 2 3 0.6880734
#> 10 Pheidole fimbriata Form 2 3 0.6880734
#> 11 Pheidole obscurithorax Form 2 2 0.4587156
#> 12 Pheidole subarmata Form 2 2 0.4587156
#> 13 Sphinctomyrmex stali Form 6 1 0.2293578
#> 14 Strumigenys fridericimuelleri Form 3 2 0.4587156
#> 15 Strumigenys sanctipauli Form 6 1 0.2293578
#>
#> DATA SOURCE AND REFERENCE:
#> Silva, N. S., Maciel, E. A., Prado, L. P., Silva, O. G., Barbosa, D. A.,
#> Andrade-Silva, J., ... & Morini, M. S. (2024).
#> 'Ant rarity and vulnerability in Brazilian Atlantic Forest fragments.'
#> Biological Conservation, 296, 110640.
#> ********************************************************************************
#>
#> ***********************************************
#> AntClassify finished successfully
#> *************************************************Accessing results
names(resultado)
#> [1] "guilds" "exotic" "endemic" "rarity"
head(resultado$guilds$table)
#> species abundance percentage
#> Atta sexdens Atta sexdens 50 11.467890
#> Camponotus atriceps Camponotus atriceps 40 9.174312
#> Crematogaster sp Crematogaster sp 35 8.027523
#> Cyphomyrmex minutus Cyphomyrmex minutus 30 6.880734
#> Cyphomyrmex rimosus Cyphomyrmex rimosus 28 6.422018
#> Ectatomma edentatum Ectatomma edentatum 25 5.733945
#> antclassify_guild
#> Atta sexdens Fungus-growers (soil or leaf litter nesting)
#> Camponotus atriceps Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Crematogaster sp Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Cyphomyrmex minutus Fungus-growers (soil or leaf litter nesting)
#> Cyphomyrmex rimosus Fungus-growers (soil or leaf litter nesting)
#> Ectatomma edentatum Generalist predators (dominant or cryptic in soil or leaf litter)
#> silva_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Unidentified Guild
#> Crematogaster sp Unidentified Guild
#> Cyphomyrmex minutus Unidentified Guild
#> Cyphomyrmex rimosus Unidentified Guild
#> Ectatomma edentatum Generalist predatory ectaheteromorphs
#> delabie_guild
#> Atta sexdens Attini (Fungus-growers)
#> Camponotus atriceps Omnivorous soil-and-litter species
#> Crematogaster sp Omnivorous soil-and-litter species
#> Cyphomyrmex minutus Attini (Fungus-growers)
#> Cyphomyrmex rimosus Attini (Fungus-growers)
#> Ectatomma edentatum Large Ponerinae (Large epigeic predators)
#> silvestre_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Generalist patrolling Camponotines
#> Crematogaster sp Small arboreal species with massive recruitment
#> Cyphomyrmex minutus Cryptic fungus-growing ants (Attines)
#> Cyphomyrmex rimosus Cryptic fungus-growing ants (Attines)
#> Ectatomma edentatum Large predators
resultado$exotics
#> NULL
resultado$endemics
#> NULL
resultado$rarity
#> $table
#> species abundance rarity_form percentage
#> 1 Brachymyrmex feitosai 7 Form 4 1.6055046
#> 2 Brachymyrmex micromegas 1 Form 7 0.2293578
#> 3 Camponotus atriceps 40 Form 2 9.1743119
#> 4 Camponotus tripartitus 1 Form 7 0.2293578
#> 5 Diaphoromyrma sofiae 1 Form 7 0.2293578
#> 6 Heteroponera inermis 2 Form 4 0.4587156
#> 7 Oxyepoecus browni 2 Form 6 0.4587156
#> 8 Oxyepoecus reticulatus 11 Form 1 2.5229358
#> 9 Pheidole aberrans 3 Form 2 0.6880734
#> 10 Pheidole fimbriata 3 Form 2 0.6880734
#> 11 Pheidole obscurithorax 2 Form 2 0.4587156
#> 12 Pheidole subarmata 2 Form 2 0.4587156
#> 13 Sphinctomyrmex stali 1 Form 6 0.2293578
#> 14 Strumigenys fridericimuelleri 2 Form 3 0.4587156
#> 15 Strumigenys sanctipauli 1 Form 6 0.2293578
#>
#> $plot
Using individual functions
Although antclassify() runs the full pipeline, users can
also apply each function separately depending on their research
goals.
Functional guild classification
guilds <- assign_guild_ants(dados)
#> Step 1: Preparing community data...
#> Step 2: Matching species to functional guilds...
#>
#> Guild classification results (first 6 rows):
#> species abundance percentage
#> Atta sexdens Atta sexdens 50 11.467890
#> Camponotus atriceps Camponotus atriceps 40 9.174312
#> Crematogaster sp Crematogaster sp 35 8.027523
#> Cyphomyrmex minutus Cyphomyrmex minutus 30 6.880734
#> Cyphomyrmex rimosus Cyphomyrmex rimosus 28 6.422018
#> Ectatomma edentatum Ectatomma edentatum 25 5.733945
#> antclassify_guild
#> Atta sexdens Fungus-growers (soil or leaf litter nesting)
#> Camponotus atriceps Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Crematogaster sp Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Cyphomyrmex minutus Fungus-growers (soil or leaf litter nesting)
#> Cyphomyrmex rimosus Fungus-growers (soil or leaf litter nesting)
#> Ectatomma edentatum Generalist predators (dominant or cryptic in soil or leaf litter)
#> silva_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Unidentified Guild
#> Crematogaster sp Unidentified Guild
#> Cyphomyrmex minutus Unidentified Guild
#> Cyphomyrmex rimosus Unidentified Guild
#> Ectatomma edentatum Generalist predatory ectaheteromorphs
#> delabie_guild
#> Atta sexdens Attini (Fungus-growers)
#> Camponotus atriceps Omnivorous soil-and-litter species
#> Crematogaster sp Omnivorous soil-and-litter species
#> Cyphomyrmex minutus Attini (Fungus-growers)
#> Cyphomyrmex rimosus Attini (Fungus-growers)
#> Ectatomma edentatum Large Ponerinae (Large epigeic predators)
#> silvestre_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Generalist patrolling Camponotines
#> Crematogaster sp Small arboreal species with massive recruitment
#> Cyphomyrmex minutus Cryptic fungus-growing ants (Attines)
#> Cyphomyrmex rimosus Cryptic fungus-growing ants (Attines)
#> Ectatomma edentatum Large predators
#> Step 3: Generating plots...
#>
#> ********************************************************************************
#> IMPORTANT NOTICE:
#> Please verify all assigned guilds. 'Unidentified Guild' indicates that the
#> taxon was not found in the available reference databases.
#> Guild classification in this analysis follows:
#> - Literature-based criteria from:
#> Silvestre, R., Brandão, C. R. F., & Silva, R. R. (2003).
#> Grupos funcionales de hormigas: el caso de los gremios del Cerrado.
#> In F. Fernández (Ed.), *Introducción a las Hormigas de las Región Neotropical*
#> (pp. 113-148). Instituto Alexander Von Humboldt.
#> Silva, R. R., Silvestre, R., Brandão, C. R. F., Morini, M. S. C., & Delabie, J. H. C. (2015).
#> Grupos tróficos e guildas em formigas poneromorfas. In: Delabie, J. H. C. et al.
#> *As formigas poneromorfas do Brasil*. Ilhéus: Editus, 2015. p. 163-179.
#> Delabie, J. H. C., Agosti, D., & Nascimento, I. C. (2000).
#> Litter ant communities of the Brazilian Atlantic rain forest region.
#> *Sampling Ground-dwelling Ants: case studies from the world's rain forests.
#> Curtin University of Technology School of Environmental Biology Bulletin*, v. 18.
#> - The 'AntClassify Guilds' classification corresponds to the internal
#> classification system implemented in the AntClassify package.
#> ********************************************************************************
head(guilds$table)
#> species abundance percentage
#> Atta sexdens Atta sexdens 50 11.467890
#> Camponotus atriceps Camponotus atriceps 40 9.174312
#> Crematogaster sp Crematogaster sp 35 8.027523
#> Cyphomyrmex minutus Cyphomyrmex minutus 30 6.880734
#> Cyphomyrmex rimosus Cyphomyrmex rimosus 28 6.422018
#> Ectatomma edentatum Ectatomma edentatum 25 5.733945
#> antclassify_guild
#> Atta sexdens Fungus-growers (soil or leaf litter nesting)
#> Camponotus atriceps Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Crematogaster sp Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Cyphomyrmex minutus Fungus-growers (soil or leaf litter nesting)
#> Cyphomyrmex rimosus Fungus-growers (soil or leaf litter nesting)
#> Ectatomma edentatum Generalist predators (dominant or cryptic in soil or leaf litter)
#> silva_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Unidentified Guild
#> Crematogaster sp Unidentified Guild
#> Cyphomyrmex minutus Unidentified Guild
#> Cyphomyrmex rimosus Unidentified Guild
#> Ectatomma edentatum Generalist predatory ectaheteromorphs
#> delabie_guild
#> Atta sexdens Attini (Fungus-growers)
#> Camponotus atriceps Omnivorous soil-and-litter species
#> Crematogaster sp Omnivorous soil-and-litter species
#> Cyphomyrmex minutus Attini (Fungus-growers)
#> Cyphomyrmex rimosus Attini (Fungus-growers)
#> Ectatomma edentatum Large Ponerinae (Large epigeic predators)
#> silvestre_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Generalist patrolling Camponotines
#> Crematogaster sp Small arboreal species with massive recruitment
#> Cyphomyrmex minutus Cryptic fungus-growing ants (Attines)
#> Cyphomyrmex rimosus Cryptic fungus-growing ants (Attines)
#> Ectatomma edentatum Large predators
guilds$plot
#> [[1]]
#>
#> [[2]]
#>
#> [[3]]
#>
#> [[4]]
Exotic species detection
exotics <- check_exotic_ants(dados)
#> Step 1: Preparing community data...
#> Step 2: Generating results...
#>
#> ********************************************************************************
#> EXOTIC SPECIES DETECTED:
#> species abundance percentage
#> 1 Monomorium floricola 18 4.128440
#> 2 Monomorium pharaonis 17 3.899083
#> 3 Pheidole megacephala 16 3.669725
#> 4 Strumigenys emmae 15 3.440367
#> 5 Strumigenys rogeri 14 3.211009
#>
#> DATA SOURCE AND REFERENCE:
#> The exotic species list used in this function is sourced from:
#> VIEIRA, Vitoria Brunetta. 'Quem são e onde estão as formigas exóticas do Brasil?'
#> Dissertacao (Mestrado em Entomologia) – Universidade Federal do Parana (UFPR),
#> Curitiba, Brasil, 2025.
#> ********************************************************************************
exotics
#> $table
#> species abundance percentage origin
#> 1 Monomorium floricola 18 4.128440 Exotic
#> 2 Monomorium pharaonis 17 3.899083 Exotic
#> 3 Pheidole megacephala 16 3.669725 Exotic
#> 4 Strumigenys emmae 15 3.440367 Exotic
#> 5 Strumigenys rogeri 14 3.211009 Exotic
#>
#> $plot
Endemic species (Atlantic Forest)
endemics <- check_endemic_atlantic_ants(dados)
#>
#> **********************************************************************************
#> ATTENTION: This function identifies endemic species of the BRAZILIAN ATLANTIC FOREST.
#> If your data collection did not occur within this biome, this analysis may not
#> be appropriate for your study.
#> **********************************************************************************
#> Step 1: Preparing community data...
#> Step 2: Generating results...
#>
#> ********************************************************************************
#> ENDEMIC SPECIES DETECTED (ATLANTIC FOREST):
#> species abundance percentage
#> 1 Apterostigma serratum 9 2.064220
#> 2 Brachymyrmex delabiei 8 1.834862
#> 3 Brachymyrmex feitosai 7 1.605505
#> 4 Camponotus fallatus 6 1.376147
#> 5 Camponotus hermanni 5 1.146789
#>
#> DATA SOURCE AND REFERENCE:
#> The endemic species list is sourced from:
#> Silva, N. S., Goncalves, D. C. de O., Wazema, C. T., Barbosa, D. A., Prado, L. P. do,
#> Andrade-Silva, J., Fernandes, T. T., Silva, R. R., & Morini, M. S. de C. (2025).
#> 'Endemism and vulnerability of ants in the phytophysiognomies of the Brazilian
#> Atlantic Forest'. In: Brazilian Myrmecology: Exploring the World’s Richest Ant Fauna
#> (Chapter 16). Editora Cientifica Digital. DOI: 10.37885/250920259.
#> ********************************************************************************
endemics
#> $table
#> species abundance percentage status
#> 1 Apterostigma serratum 9 2.064220 Endemic (AF)
#> 2 Brachymyrmex delabiei 8 1.834862 Endemic (AF)
#> 3 Brachymyrmex feitosai 7 1.605505 Endemic (AF)
#> 4 Camponotus fallatus 6 1.376147 Endemic (AF)
#> 5 Camponotus hermanni 5 1.146789 Endemic (AF)
#>
#> $plot
Rarity classification
rarity <- check_rarity_atlantic_ants(dados)
#>
#> ********************************************************************************
#> ATTENTION:
#> This function identifies rare ant species and their rarity forms.
#> This classification is specific to the Brazilian Atlantic Forest and
#> may not be appropriate for other biomes.
#> ********************************************************************************
#> Step 1: Preparing community data and rarity database...
#> Step 2: Generating results...
#>
#> ********************************************************************************
#> RARE SPECIES DETECTED:
#> species rarity_form abundance percentage
#> 1 Brachymyrmex feitosai Form 4 7 1.6055046
#> 2 Brachymyrmex micromegas Form 7 1 0.2293578
#> 3 Camponotus atriceps Form 2 40 9.1743119
#> 4 Camponotus tripartitus Form 7 1 0.2293578
#> 5 Diaphoromyrma sofiae Form 7 1 0.2293578
#> 6 Heteroponera inermis Form 4 2 0.4587156
#> 7 Oxyepoecus browni Form 6 2 0.4587156
#> 8 Oxyepoecus reticulatus Form 1 11 2.5229358
#> 9 Pheidole aberrans Form 2 3 0.6880734
#> 10 Pheidole fimbriata Form 2 3 0.6880734
#> 11 Pheidole obscurithorax Form 2 2 0.4587156
#> 12 Pheidole subarmata Form 2 2 0.4587156
#> 13 Sphinctomyrmex stali Form 6 1 0.2293578
#> 14 Strumigenys fridericimuelleri Form 3 2 0.4587156
#> 15 Strumigenys sanctipauli Form 6 1 0.2293578
#>
#> DATA SOURCE AND REFERENCE:
#> Silva, N. S., Maciel, E. A., Prado, L. P., Silva, O. G., Barbosa, D. A.,
#> Andrade-Silva, J., ... & Morini, M. S. (2024).
#> 'Ant rarity and vulnerability in Brazilian Atlantic Forest fragments.'
#> Biological Conservation, 296, 110640.
#> ********************************************************************************
rarity
#> $table
#> species abundance rarity_form percentage
#> 1 Brachymyrmex feitosai 7 Form 4 1.6055046
#> 2 Brachymyrmex micromegas 1 Form 7 0.2293578
#> 3 Camponotus atriceps 40 Form 2 9.1743119
#> 4 Camponotus tripartitus 1 Form 7 0.2293578
#> 5 Diaphoromyrma sofiae 1 Form 7 0.2293578
#> 6 Heteroponera inermis 2 Form 4 0.4587156
#> 7 Oxyepoecus browni 2 Form 6 0.4587156
#> 8 Oxyepoecus reticulatus 11 Form 1 2.5229358
#> 9 Pheidole aberrans 3 Form 2 0.6880734
#> 10 Pheidole fimbriata 3 Form 2 0.6880734
#> 11 Pheidole obscurithorax 2 Form 2 0.4587156
#> 12 Pheidole subarmata 2 Form 2 0.4587156
#> 13 Sphinctomyrmex stali 1 Form 6 0.2293578
#> 14 Strumigenys fridericimuelleri 2 Form 3 0.4587156
#> 15 Strumigenys sanctipauli 1 Form 6 0.2293578
#>
#> $plot
Input data format
The package expects a community matrix where:
- Rows represent sampling units (or a single community)
- Columns represent species
- Values represent abundance (or presence/absence)
Species names must be provided as column names.
Example structure
dados_exemplo <- data.frame(
"Atta sexdens" = 10,
"Camponotus atriceps" = 5
)
dados_exemplo
#> Atta.sexdens Camponotus.atriceps
#> 1 10 5Importing data from external files
CSV files
dados <- read.csv("data.csv", check.names = FALSE)TXT files
dados <- read.table("data.txt", header = TRUE, sep = "\t", check.names = FALSE)Excel files
# install.packages("readxl")
library(readxl)
dados <- read_excel("data.xlsx")
dados <- as.data.frame(dados)Important note
colnames(dados) <- gsub("_", " ", colnames(dados))This step guarantees compatibility with the internal species name standardization used in AntClassify.
Final considerations
The AntClassify package provides a flexible workflow that can be used either as a fully automated pipeline or through modular functions, allowing users to adapt analyses to different ecological questions.
By integrating functional classification, invasion biology, endemism, and rarity into a single framework, the package enhances reproducibility and facilitates ecological interpretation of ant communities.