## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(AntClassify)

## -----------------------------------------------------------------------------
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

## -----------------------------------------------------------------------------
resultado <- antclassify(dados, validate = FALSE, plot = FALSE)

## -----------------------------------------------------------------------------
names(resultado)

head(resultado$guilds$table)
resultado$exotics
resultado$endemics
resultado$rarity

## -----------------------------------------------------------------------------
guilds <- assign_guild_ants(dados, validate = FALSE, plot = FALSE)

head(guilds$table)

## -----------------------------------------------------------------------------
exotics <- check_exotic_ants(dados, validate = FALSE, plot = FALSE)
exotics

## -----------------------------------------------------------------------------
endemics <- check_endemic_atlantic_ants(dados, validate = FALSE, plot = FALSE)
endemics

## -----------------------------------------------------------------------------
rarity <- check_rarity_atlantic_ants(dados, validate = FALSE, plot = FALSE)
rarity

## -----------------------------------------------------------------------------
data(ant_community)

# Run the pipeline on the built‑in dataset
res_com <- antclassify_community(ant_community, guild_col = "antclassify_guild",
                                 validate = FALSE)

# Abundance matrix (sites × guilds)
res_com$guild_abundance

# Guild richness per site
res_com$guild_richness

## -----------------------------------------------------------------------------
data(ant_community)
ant_community

## ----eval=FALSE---------------------------------------------------------------
# dados <- read.csv("data.csv", check.names = FALSE)

## ----eval=FALSE---------------------------------------------------------------
# dados <- read.table("data.txt", header = TRUE, sep = "\t", check.names = FALSE)

## ----eval=FALSE---------------------------------------------------------------
# # install.packages("readxl")
# library(readxl)
# 
# dados <- read_excel("data.xlsx")
# dados <- as.data.frame(dados)

## ----eval=FALSE---------------------------------------------------------------
# colnames(dados) <- gsub("_", " ", colnames(dados))