rarity <- check_rarity_atlantic_ants(dados, validate = FALSE, plot = FALSE)
#>
#> ********************************************************************************
#> 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
When the study involves several sampling units, the function
antclassify_community() applies the full classification pipeline to each
row of a community matrix and returns aggregated site‑by‑guild
information. This avoids manual loops and ensures consistent
classification across all sites.
The package includes a small built‑in dataset, ant_community, that
can be used to test this function.
data(ant_community)
# Run the pipeline on the built‑in dataset
res_com <- antclassify_community(ant_community, guild_col = "antclassify_guild",
validate = FALSE)
#> 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 10 50
#> Camponotus atriceps Camponotus atriceps 3 15
#> Pheidole megacephala Pheidole megacephala 2 10
#> Solenopsis saevissima Solenopsis saevissima 1 5
#> Nylanderia fulva Nylanderia fulva 4 20
#> antclassify_guild
#> Atta sexdens Fungus-growers (soil or leaf litter nesting)
#> Camponotus atriceps Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Pheidole megacephala Leaf litter omnivores and scavengers (cryptic or non-cryptic)
#> Solenopsis saevissima Leaf litter omnivores and scavengers (cryptic or non-cryptic)
#> Nylanderia fulva Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> silva_guild delabie_guild
#> Atta sexdens Unidentified Guild Attini (Fungus-growers)
#> Camponotus atriceps Unidentified Guild Omnivorous soil-and-litter species
#> Pheidole megacephala Unidentified Guild Omnivorous soil-and-litter species
#> Solenopsis saevissima Unidentified Guild Omnivorous soil-and-litter species
#> Nylanderia fulva Unidentified Guild Unidentified Guild
#> silvestre_guild
#> Atta sexdens Unidentified Guild
#> Camponotus atriceps Generalist patrolling Camponotines
#> Pheidole megacephala Dominant soil omnivores
#> Solenopsis saevissima Dominant soil omnivores
#> Nylanderia fulva Unidentified Guild
#> 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.
#> ********************************************************************************
#> 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 5 41.666667
#> Pheidole megacephala Pheidole megacephala 4 33.333333
#> Wasmannia auropunctata Wasmannia auropunctata 2 16.666667
#> Nylanderia fulva Nylanderia fulva 1 8.333333
#> antclassify_guild
#> Atta sexdens Fungus-growers (soil or leaf litter nesting)
#> Pheidole megacephala Leaf litter omnivores and scavengers (cryptic or non-cryptic)
#> Wasmannia auropunctata Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Nylanderia fulva Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> silva_guild delabie_guild
#> Atta sexdens Unidentified Guild Attini (Fungus-growers)
#> Pheidole megacephala Unidentified Guild Omnivorous soil-and-litter species
#> Wasmannia auropunctata Unidentified Guild Omnivorous soil-and-litter species
#> Nylanderia fulva Unidentified Guild Unidentified Guild
#> silvestre_guild
#> Atta sexdens Unidentified Guild
#> Pheidole megacephala Dominant soil omnivores
#> Wasmannia auropunctata Small arboreal species with massive recruitment
#> Nylanderia fulva Unidentified Guild
#> 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.
#> ********************************************************************************
#> Step 1: Preparing community data...
#> Step 2: Matching species to functional guilds...
#>
#> Guild classification results (first 6 rows):
#> species abundance percentage
#> Camponotus atriceps Camponotus atriceps 2 18.181818
#> Pheidole megacephala Pheidole megacephala 1 9.090909
#> Wasmannia auropunctata Wasmannia auropunctata 3 27.272727
#> Solenopsis saevissima Solenopsis saevissima 5 45.454545
#> antclassify_guild
#> Camponotus atriceps Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Pheidole megacephala Leaf litter omnivores and scavengers (cryptic or non-cryptic)
#> Wasmannia auropunctata Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Solenopsis saevissima Leaf litter omnivores and scavengers (cryptic or non-cryptic)
#> silva_guild delabie_guild
#> Camponotus atriceps Unidentified Guild Omnivorous soil-and-litter species
#> Pheidole megacephala Unidentified Guild Omnivorous soil-and-litter species
#> Wasmannia auropunctata Unidentified Guild Omnivorous soil-and-litter species
#> Solenopsis saevissima Unidentified Guild Omnivorous soil-and-litter species
#> silvestre_guild
#> Camponotus atriceps Generalist patrolling Camponotines
#> Pheidole megacephala Dominant soil omnivores
#> Wasmannia auropunctata Small arboreal species with massive recruitment
#> Solenopsis saevissima Dominant soil omnivores
#> 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.
#> ********************************************************************************
# Abundance matrix (sites × guilds)
res_com$guild_abundance
#> Fungus-growers (soil or leaf litter nesting)
#> Site1 10
#> Site2 5
#> Site3 0
#> Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal)
#> Site1 7
#> Site2 3
#> Site3 5
#> Leaf litter omnivores and scavengers (cryptic or non-cryptic)
#> Site1 3
#> Site2 4
#> Site3 6
# Guild richness per site
res_com$guild_richness
#> [1] 3 3 2
