## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", eval = FALSE, warning = FALSE ) ## ----------------------------------------------------------------------------- # library(florabr) # #Folder where you stored the data with the function get_florabr() # #Load data # bf <- load_florabr(data_dir = my_dir, # data_version = "Latest_available", # type = "short") #short version # #> Loading version 393.401 ## ----------------------------------------------------------------------------- # #Get available options to filter by lifeForm # get_attributes(data = bf, # attribute = "lifeForm")[[1]] # #> lifeForm # #> 1 Aquatic-Benthos # #> 2 Aquatic-Neuston # #> 3 Aquatic-Plankton # #> 4 Shrub # #> 5 Tree # #> 6 Bamboo # #> 7 Cushion # #> 8 Dendroid # #> 9 Unknown # #> 10 Dracaenoid # #> 13 Herb # #> 14 Flabellate # #> 15 Foliose # #> 16 Liana/scandent/vine # #> 19 Palm_tree # #> 21 Pendent # #> 23 Subshrub # #> 24 Succulent # #> 25 Thallose # #> 26 Mat # #> 27 Weft # #> 28 Tuft # # #Get available options to filter by Biome # get_attributes(data = bf, # attribute = "Biome")[[1]] # #> biome # #> 1 Amazon # #> 2 Atlantic_Forest # #> 3 Caatinga # #> 4 Cerrado # #> 5 Pampa # #> 6 Pantanal # #> 7 Not_found_in_brazil # # #Get available options to filter by vegetation # get_attributes(data = bf, # attribute = "vegetation")[[1]] # #> vegetation # #> 1 Anthropic_Area # #> 2 Caatinga # #> 3 Amazonian_Campinarana # #> 4 High_Altitude_Grassland # #> 5 Flooded_Field # #> 6 Grassland # #> 7 Highland_Rocky_Field # #> 8 Carrasco # #> 9 Cerrado # #> 10 Gallery_Forest # #> 11 Inundated_Forest_Igapo # #> 12 Terra_Firme_Forest # #> 13 Inundated_Forest # #> 14 Seasonallly_Deciduous_Forest # #> 15 Seasonal_Evergreen_Forest # #> 16 Seasonally_Semideciduous_Forest # #> 17 Rainforest # #> 18 Mixed_Ombrophyllous_Forest # #> 19 Mangrove # #> 20 Palm_Grove # #> 21 Restinga # #> 22 Amazonian_Savanna # #> 23 Aquatic_vegetation # #> 24 Rock_outcrop_vegetation # #> 25 Not_found_in_Brazil ## ----------------------------------------------------------------------------- # af_spp <- select_species(data = bf, # include_subspecies = FALSE, include_variety = FALSE, # kingdom = "Plantae", group = "All", subgroup = "All", # family = "All", genus = "All", # lifeForm = "Tree", #Specify tree species # filter_lifeForm = "in", # habitat = "All", filter_habitat = "in", # biome = "Atlantic_Forest", #Occuring in the At. Forest # filter_biome = "in", #In Atlantic Forest # state = "All", filter_state = "in", # vegetation = "All", filter_vegetation = "in", # endemism = "Endemic", #Only endemics to Brazil # origin = "Native", #Only natives # taxonomicStatus = "Accepted", # nomenclaturalStatus = "All") # nrow(af_spp) # #> [1] 2372 ## ----------------------------------------------------------------------------- # #First 7 unique values of biomes in the filtered dataset # unique(af_spp$biome)[1:7] # #> [1] "Atlantic_Forest" # #> [2] "Atlantic_Forest;Cerrado" # #> [3] "Atlantic_Forest;Caatinga" # #> [4] "Amazon;Atlantic_Forest;Caatinga;Cerrado" # #> [5] "Amazon;Atlantic_Forest;Cerrado" # #> [6] "Atlantic_Forest;Caatinga;Cerrado" # #> [7] "Amazon;Atlantic_Forest" ## ----------------------------------------------------------------------------- # only_af_spp <- select_species(data = bf, # include_subspecies = FALSE, include_variety = FALSE, # kingdom = "Plantae", group = "All", subgroup = "All", # family = "All", genus = "All", # lifeForm = "Tree", #Specify tree species # filter_lifeForm = "in", # habitat = "All", filter_habitat = "in", # biome = "Atlantic_Forest", #Occuring in the At. Forest # filter_biome = "only", #ONLY in Atlantic Forest # state = "All", filter_state = "in", # vegetation = "All", filter_vegetation = "in", # endemism = "Endemic", #Only endemics to Brazil # origin = "Native", #Only natives # taxonomicStatus = "Accepted", # nomenclaturalStatus = "All") # nrow(only_af_spp) # #> [1] 1858 # unique(only_af_spp$biome) # #> [1] "Atlantic_Forest" ## ----------------------------------------------------------------------------- # south_af_spp <- select_species(data = bf, # include_subspecies = FALSE, include_variety = FALSE, # kingdom = "Plantae", group = "All", subgroup = "All", # family = "All", genus = "All", # lifeForm = "Tree", #Specify tree species # filter_lifeForm = "in", # habitat = "All", filter_habitat = "in", # biome = "Atlantic_Forest", #Occuring in the At. Forest # filter_biome = "only", #Only in Atlantic Forest # state = c("PR", "SC", "RS"), #states - Use the acronynms # filter_state = "in", #IN at least one of these states # vegetation = "All", filter_vegetation = "in", # endemism = "Endemic", #Only endemics to Brazil # origin = "Native", #Only natives # taxonomicStatus = "Accepted", # nomenclaturalStatus = "All") # nrow(south_af_spp) # #> [1] 372 # # #First 10 unique values of states in the filtered dataset # unique(south_af_spp$states)[1:10] # #> [1] "BA;ES;PR;RJ;SC;SP" "AL;BA;CE;ES;MA;MG;PB;PE;PR;RJ;SE;SP" # #> [3] "PR;RS;SC" "BA;CE;ES;MA;MG;PE;PR;RJ;SP" # #> [5] "MG;PR;RJ;SC;SP" "MG;PR;RJ;RS;SC;SP" # #> [7] "BA;ES;MG;PR;RJ;SC;SP" "MG;PR;RS;SC;SP" # #> [9] "PR;RJ;RS;SC;SP" "ES;MG;PR;RJ;RS;SC;SP" ## ----------------------------------------------------------------------------- # south_af_spp2 <- select_species(data = bf, # include_subspecies = FALSE, include_variety = FALSE, # kingdom = "Plantae", group = "All", subgroup = "All", # family = "All", genus = "All", # lifeForm = "Tree", #Specify tree species # filter_lifeForm = "in", # habitat = "All", filter_habitat = "in", # biome = "Atlantic_Forest", #Occurring in the At. Forest # filter_biome = "only", #Only in Atlantic Forest # state = c("PR", "SC", "RS"), #states - Use the acronynms # filter_state = "and", #PR and SC and RS # vegetation = "All", filter_vegetation = "in", # endemism = "Endemic", #Only endemics to Brazil # origin = "Native", #Only natives # taxonomicStatus = "Accepted", # nomenclaturalStatus = "All") # nrow(south_af_spp2) # #> [1] 29 # # #All unique states in the filtered dataset # unique(south_af_spp2$states) # #> [1] "PR;RS;SC" "MG;PR;RS;SC;SP" "PR;RS;SC;SP" "ES;PR;RS;SC;SP" # #> [5] "MG;PR;RS;SC" ## ----------------------------------------------------------------------------- # south_af_spp3 <- select_species(data = bf, # include_subspecies = FALSE, include_variety = FALSE, # kingdom = "Plantae", group = "All", subgroup = "All", # family = "All", genus = "All", # lifeForm = "Tree", #Specify tree species # filter_lifeForm = "in", # habitat = "All", filter_habitat = "in", # biome = "Atlantic_Forest", #Occuring in the At. Forest # filter_biome = "only", #Only in Atlantic Forest # state = c("PR", "SC", "RS"), #states - Use the acronynms # filter_state = "only", #PR and SC and RS, no other else # vegetation = "All", filter_vegetation = "in", # endemism = "Endemic", #Only endemics to Brazil # origin = "Native", #Only natives # taxonomicStatus = "Accepted", # nomenclaturalStatus = "All") # nrow(south_af_spp3) # #> [1] 13 # # #The unique state in the filtered dataset # unique(south_af_spp3$states) # #> [1] "PR;RS;SC" ## ----------------------------------------------------------------------------- # complete_names <- c("Araucaria brasiliana var. ridolfiana (Pi.Savi) Gordon", # " Solanum restingae S.Knapp", # "Butia cattarinensis Noblick & Lorenzi ", # "Homo sapiens") # #Human specie was used just as an example that will be used to illustrate the # #next function # binomial_names <- get_binomial(species_names = complete_names) # binomial_names # #> [1] "Araucaria brasiliana" "Solanum restingae" "Butia cattarinensis" # #> [4] "Homo sapiens" ## ----------------------------------------------------------------------------- # #Create example # checked_names <- check_names(data = bf, # species = binomial_names, # max_distance = 0.1, # kingdom = "Plantae") # checked_names # # input_name Spelling Suggested_name Distance taxonomicStatus nomenclaturalStatus acceptedName family # # 1 Araucaria brasiliana Correct Araucaria brasiliana 0 Synonym Araucaria angustifolia Araucariaceae # # 2 Araucaria brasiliana Correct Araucaria brasiliana 0 Synonym Illegitimate Araucaria angustifolia Araucariaceae # # 3 Solanum restingae Correct Solanum restingae 0 Accepted Correct Solanum restingae Solanaceae # # 4 Butia cattarinensis Probably_incorrect Butia catarinensis 1 Accepted Butia catarinensis Arecaceae # # 5 Homo sapiens Not_found NA ## ----------------------------------------------------------------------------- # #Get only accepted names # accepted_names <- unique(checked_names$acceptedName) # accepted_names <- na.omit(accepted_names) #Remove NA # # #Subset species # my_sp <- subset_species(data = bf, species = accepted_names, # include_subspecies = FALSE, # include_variety = FALSE, # kingdom = "Plantae") # my_sp # #> species scientificName # #> 11785 Solanum restingae Solanum restingae S.Knapp # #> 26790 Araucaria angustifolia Araucaria angustifolia (Bertol.) Kuntze # #> 99881 Butia catarinensis Butia catarinensis Noblick & Lorenzi # #> acceptedName kingdom Group Subgroup family genus # #> 11785 Plantae Angiosperms Solanaceae Solanum # #> 26790 Plantae Gymnosperms Araucariaceae Araucaria # #> 99881 Plantae Angiosperms Arecaceae Butia # #> lifeForm habitat Biome States # #> 11785 Shrub Terrestrial Atlantic_Forest BA # #> 26790 Tree Terrestrial Atlantic_Forest;Pampa MG;PR;RJ;RS;SC;SP # #> 99881 Palm_tree Terrestrial Atlantic_Forest;Pampa RS;SC # #> vegetationType # #> 11785 Restinga # #> 26790 High_Altitude_Grassland;Mixed_Ombrophyllous_Forest; # #> Seasonally_Semideciduous_Forest # #> 99881 Restinga # #> origin endemism taxonomicStatus nomenclaturalStatus # #> 11785 Native Endemic Accepted Correct # #> 26790 Native Non-endemic Accepted Correct # #> 99881 Native Endemic Accepted # #> vernacularName # #> 11785 # #> 26790 araucaria, pinheiro-do-parana, curi, pinheiro-brasileiro, # #> pinho-do-parana # #> 99881 # #> taxonRank # #> 11785 Species # #> 26790 Species # #> 99881 Species ## ----------------------------------------------------------------------------- # my_sp2 <- subset_species(data = bf, species = accepted_names, # include_subspecies = TRUE, # include_variety = TRUE, # kingdom = "Plantae") # my_sp2[1:5,] # #> species scientificName # #> 11785 Solanum restingae Solanum restingae S.Knapp # #> 26790 Araucaria angustifolia Araucaria angustifolia (Bertol.) Kuntze # #> 35204 Araucaria angustifolia Araucaria angustifolia var. alba Reitz # #> 35205 Araucaria angustifolia Araucaria angustifolia var. caiova Reitz # #> 35206 Araucaria angustifolia Araucaria angustifolia var. caiuva Mattos # #> acceptedName kingdom Group Subgroup family # #> 11785 Plantae Angiosperms Solanaceae # #> 26790 Plantae Gymnosperms Araucariaceae # #> 35204 Araucaria angustifolia Plantae Gymnosperms Araucariaceae # #> 35205 Araucaria angustifolia Plantae Gymnosperms Araucariaceae # #> 35206 Araucaria angustifolia Plantae Gymnosperms Araucariaceae # #> genus lifeForm habitat Biome States # #> 11785 Solanum Shrub Terrestrial Atlantic_Forest BA # #> 26790 Araucaria Tree Terrestrial Atlantic_Forest;Pampa MG;PR;RJ;RS;SC;SP # #> 35204 Araucaria # #> 35205 Araucaria # #> 35206 Araucaria # #> vegetationType # #> 11785 Restinga # #> 26790 High_Altitude_Grassland;Mixed_Ombrophyllous_Forest; # #> Seasonally_Semideciduous_Forest # #> 35204 # #> 35205 # #> 35206 # #> origin endemism taxonomicStatus nomenclaturalStatus # #> 11785 Native Endemic Accepted Correct # #> 26790 Native Non-endemic Accepted Correct # #> 35204 Synonym # #> 35205 Synonym # #> 35206 Synonym # #> vernacularName # #> 11785 # #> 26790 araucaria, pinheiro-do-parana, curi, pinheiro-brasileiro, # #> pinho-do-parana # #> 35204 # #> 35205 # #> 35206 # #> taxonRank # #> 11785 Species # #> 26790 Species # #> 35204 Variety # #> 35205 Variety # #> 35206 Variety ## ----------------------------------------------------------------------------- # spp <- c("Araucaria angustifolia", "Adesmia paranensis") # spp_syn <- get_synonym(data = bf, species = spp) # spp_syn # #> synonym acceptedName taxonomicStatus nomenclaturalStatus # #> 35323 Araucaria brasiliana Araucaria angustifolia Synonym # #> 35325 Araucaria brasiliensis Araucaria angustifolia Synonym # #> 35327 Araucaria dioica Araucaria angustifolia Synonym # #> 35328 Araucaria elegans Araucaria angustifolia Synonym # #> 35329 Araucaria ridolfiana Araucaria angustifolia Synonym # #> 35330 Araucaria saviana Araucaria angustifolia Synonym # #> 35332 Columbea angustifolia Araucaria angustifolia Synonym Legitimate_but_incorrect # #> 35333 Columbea brasiliana Araucaria angustifolia Synonym Legitimate_but_incorrect # #> 60644 Pinus dioica Araucaria angustifolia Synonym # #> 141020 Araucaria bibbiani Araucaria angustifolia Synonym # #> 141021 Araucaria lindleyana Araucaria angustifolia Synonym # #> 141041 Araucaria brasiliana Araucaria angustifolia Synonym Illegitimate # #> 85308 Adesmia psoraleoides Adesmia paranensis Synonym Legitimate_but_incorrect