Filters FORCIS data by a species list.
Examples
# Import example dataset ----
file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"),
package = "forcis")
net_data <- read.table(file_name, dec = ".", sep = ";")
# Add 'data_type' column ----
net_data$"data_type" <- "Net"
# Select a taxonomy ----
net_data <- select_taxonomy(net_data, taxonomy = "VT")
# Select only required columns (and taxa) ----
net_data <- select_forcis_columns(net_data)
# Dimensions of the data.frame ----
dim(net_data)
#> [1] 2451 77
# Get species names ----
get_species_names(net_data)
#> [1] "b_digitata_VT" "b_pumilio_VT"
#> [3] "b_variabilis_VT" "c_nitida_VT"
#> [5] "d_anfracta_VT" "g_adamsi_VT"
#> [7] "g_bulloides_VT" "g_calida_VT"
#> [9] "g_cavernula_VT" "g_conglobatus_VT"
#> [11] "g_conglomerata_VT" "g_crassaformis_VT"
#> [13] "g_elongatus_VT" "g_falconensis_VT"
#> [15] "g_glutinata_VT" "g_hexagona_VT"
#> [17] "g_hirsuta_VT" "g_inflata_VT"
#> [19] "g_cultrata_VT" "g_minuta_VT"
#> [21] "g_ruber_albus_VT" "g_ruber_albus_or_elongatus_VT"
#> [23] "g_ruber_any_VT" "g_ruber_ruber_VT"
#> [25] "g_rubescens_VT" "g_scitula_VT"
#> [27] "g_siphonifera_VT" "g_tenellus_VT"
#> [29] "g_theyeri_VT" "g_truncatulinoides_VT"
#> [31] "g_truncatulinoides_left_VT" "g_truncatulinoides_right_VT"
#> [33] "g_tumida_VT" "g_ungulata_VT"
#> [35] "g_uvula_VT" "n_vivans_VT"
#> [37] "h_digitata_VT" "h_pelagica_VT"
#> [39] "n_dutertrei_VT" "n_incompta_VT"
#> [41] "n_pachyderma_VT" "n_pachyderma_incompta_VT"
#> [43] "o_riedeli_VT" "o_universa_VT"
#> [45] "p_obliquiloculata_VT" "s_dehiscens_VT"
#> [47] "t_clarkei_VT" "t_fleisheri_VT"
#> [49] "t_humilis_VT" "t_iota_VT"
#> [51] "t_parkerae_VT" "t_quinqueloba_VT"
#> [53] "t_sacculifer_VT" "t_sacculifer_no_sac_VT"
#> [55] "t_sacculifer_sac_VT" "UnID_VT"
# Select records for three species ----
net_data_sub <- filter_by_species(data = net_data,
species = c("g_inflata_VT",
"g_elongatus_VT",
"g_glutinata_VT"))
# Dimensions of the data.frame ----
dim(net_data_sub)
#> [1] 2451 24
# Get species names ----
get_species_names(net_data_sub)
#> [1] "g_elongatus_VT" "g_glutinata_VT" "g_inflata_VT"