R Under development (unstable) (2026-03-23 r89685 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(AntClassify) > > # Force non-interactive mode to prevent "Press Enter" prompts during CRAN checks > options(interactive = FALSE) > > # Mock readline globally to ensure automated tests do not hang > assignInNamespace("readline", function(...) "", ns = "base") > > # Execute all tests in the package > test_check("AntClassify") ************************************************* Starting AntClassify ************************************************* >>> Running guild classification Step 1: Preparing community data... Step 2: Matching species to functional guilds... Guild classification results: species abundance percentage Pheidole megacephala Pheidole megacephala 10 30.303030 Strumigenys emmae Strumigenys emmae 5 15.151515 Paratrechina longicornis Paratrechina longicornis 8 24.242424 Hypoponera leninei Hypoponera leninei 3 9.090909 Camponotus fallatus Camponotus fallatus 2 6.060606 Ectatomma brunneum Ectatomma brunneum 1 3.030303 Ectatomma permagnum Ectatomma permagnum 1 3.030303 Pheidole aberrans Pheidole aberrans 1 3.030303 Pheidole fimbriata Pheidole fimbriata 1 3.030303 Pheidole obscurithorax Pheidole obscurithorax 1 3.030303 antclassify_guild Pheidole megacephala Leaf litter omnivores and scavengers (cryptic or non-cryptic) Strumigenys emmae Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal) Paratrechina longicornis Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal) Hypoponera leninei Specialist litter or soil predators (cryptic) Camponotus fallatus Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal) Ectatomma brunneum Generalist predators (dominant or cryptic in soil or leaf litter) Ectatomma permagnum Generalist predators (dominant or cryptic in soil or leaf litter) Pheidole aberrans Leaf litter omnivores and scavengers (cryptic or non-cryptic) Pheidole fimbriata Leaf litter omnivores and scavengers (cryptic or non-cryptic) Pheidole obscurithorax Leaf litter omnivores and scavengers (cryptic or non-cryptic) silva_guild Pheidole megacephala Unidentified Guild Strumigenys emmae Unidentified Guild Paratrechina longicornis Unidentified Guild Hypoponera leninei Small, generalist, low-agility ponerines living in the leaf litter Camponotus fallatus Unidentified Guild Ectatomma brunneum Generalist predatory ectaheteromorphs Ectatomma permagnum Generalist predatory ectaheteromorphs Pheidole aberrans Unidentified Guild Pheidole fimbriata Unidentified Guild Pheidole obscurithorax Unidentified Guild delabie_guild Pheidole megacephala Omnivorous soil-and-litter species Strumigenys emmae Cryptic species (Small specialized predators) Paratrechina longicornis Unidentified Guild Hypoponera leninei Cryptic species (Small specialized predators) Camponotus fallatus Omnivorous soil-and-litter species Ectatomma brunneum Large Ponerinae (Large epigeic predators) Ectatomma permagnum Large Ponerinae (Large epigeic predators) Pheidole aberrans Omnivorous soil-and-litter species Pheidole fimbriata Omnivorous soil-and-litter species Pheidole obscurithorax Omnivorous soil-and-litter species silvestre_guild Pheidole megacephala Dominant soil omnivores Strumigenys emmae Unidentified Guild Paratrechina longicornis Soil and vegetation opportunists Hypoponera leninei Cryptic Ponerinae Camponotus fallatus Generalist patrolling Camponotines Ectatomma brunneum Unidentified Guild Ectatomma permagnum Large predators Pheidole aberrans Dominant soil omnivores Pheidole fimbriata Dominant soil omnivores Pheidole obscurithorax 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. ******************************************************************************** >>> Checking exotic species Step 1: Preparing community data... Step 2: Generating results... ******************************************************************************** EXOTIC SPECIES DETECTED: species abundance percentage 1 Pheidole megacephala 10 30.30303 2 Strumigenys emmae 5 15.15152 3 Paratrechina longicornis 8 24.24242 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 Hypoponera leninei 3 9.090909 2 Camponotus fallatus 2 6.060606 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 Ectatomma brunneum Form 3 1 3.030303 2 Ectatomma permagnum Form 3 1 3.030303 3 Pheidole aberrans Form 2 1 3.030303 4 Pheidole fimbriata Form 2 1 3.030303 5 Pheidole obscurithorax Form 2 1 3.030303 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 ************************************************* ************************************************* Starting AntClassify ************************************************* >>> Running guild classification Step 1: Preparing community data... Step 2: Matching species to functional guilds... Guild classification results: species abundance percentage Pheidole megacephala Pheidole megacephala 10 30.303030 Strumigenys emmae Strumigenys emmae 5 15.151515 Paratrechina longicornis Paratrechina longicornis 8 24.242424 Hypoponera leninei Hypoponera leninei 3 9.090909 Camponotus fallatus Camponotus fallatus 2 6.060606 Ectatomma brunneum Ectatomma brunneum 1 3.030303 Ectatomma permagnum Ectatomma permagnum 1 3.030303 Pheidole aberrans Pheidole aberrans 1 3.030303 Pheidole fimbriata Pheidole fimbriata 1 3.030303 Pheidole obscurithorax Pheidole obscurithorax 1 3.030303 antclassify_guild Pheidole megacephala Leaf litter omnivores and scavengers (cryptic or non-cryptic) Strumigenys emmae Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal) Paratrechina longicornis Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal) Hypoponera leninei Specialist litter or soil predators (cryptic) Camponotus fallatus Generalist omnivores (dominant or opportunistic in soil, leaf litter, or arboreal) Ectatomma brunneum Generalist predators (dominant or cryptic in soil or leaf litter) Ectatomma permagnum Generalist predators (dominant or cryptic in soil or leaf litter) Pheidole aberrans Leaf litter omnivores and scavengers (cryptic or non-cryptic) Pheidole fimbriata Leaf litter omnivores and scavengers (cryptic or non-cryptic) Pheidole obscurithorax Leaf litter omnivores and scavengers (cryptic or non-cryptic) silva_guild Pheidole megacephala Unidentified Guild Strumigenys emmae Unidentified Guild Paratrechina longicornis Unidentified Guild Hypoponera leninei Small, generalist, low-agility ponerines living in the leaf litter Camponotus fallatus Unidentified Guild Ectatomma brunneum Generalist predatory ectaheteromorphs Ectatomma permagnum Generalist predatory ectaheteromorphs Pheidole aberrans Unidentified Guild Pheidole fimbriata Unidentified Guild Pheidole obscurithorax Unidentified Guild delabie_guild Pheidole megacephala Omnivorous soil-and-litter species Strumigenys emmae Cryptic species (Small specialized predators) Paratrechina longicornis Unidentified Guild Hypoponera leninei Cryptic species (Small specialized predators) Camponotus fallatus Omnivorous soil-and-litter species Ectatomma brunneum Large Ponerinae (Large epigeic predators) Ectatomma permagnum Large Ponerinae (Large epigeic predators) Pheidole aberrans Omnivorous soil-and-litter species Pheidole fimbriata Omnivorous soil-and-litter species Pheidole obscurithorax Omnivorous soil-and-litter species silvestre_guild Pheidole megacephala Dominant soil omnivores Strumigenys emmae Unidentified Guild Paratrechina longicornis Soil and vegetation opportunists Hypoponera leninei Cryptic Ponerinae Camponotus fallatus Generalist patrolling Camponotines Ectatomma brunneum Unidentified Guild Ectatomma permagnum Large predators Pheidole aberrans Dominant soil omnivores Pheidole fimbriata Dominant soil omnivores Pheidole obscurithorax 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. ******************************************************************************** >>> Checking exotic species Step 1: Preparing community data... Step 2: Generating results... ******************************************************************************** EXOTIC SPECIES DETECTED: species abundance percentage 1 Pheidole megacephala 10 30.30303 2 Strumigenys emmae 5 15.15152 3 Paratrechina longicornis 8 24.24242 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 Hypoponera leninei 3 9.090909 2 Camponotus fallatus 2 6.060606 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 Ectatomma brunneum Form 3 1 3.030303 2 Ectatomma permagnum Form 3 1 3.030303 3 Pheidole aberrans Form 2 1 3.030303 4 Pheidole fimbriata Form 2 1 3.030303 5 Pheidole obscurithorax Form 2 1 3.030303 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 ************************************************* [ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ] > > # Restore readline to its original state (safety measure) > assignInNamespace("readline", base::readline, ns = "base") > > proc.time() user system elapsed 4.18 0.25 4.42