A data frame containing 20 tree species from Anatolian forests, distributed across three sample plots with varying community compositions. Species abundances follow the Westhoff & van der Maarel (1973) scale (1–9). Taxonomic classification includes seven ranks from species to kingdom.
Format
A data frame with 33 rows and 9 columns:
- Site
Sample plot name (character)
- Species
Binomial species name with underscore separator (character)
- Genus
Genus (character)
- Family
Family (character)
- Order
Order (character)
- Class
Class (character)
- Phylum
Phylum / Division (character)
- Kingdom
Kingdom (character)
- Abundance
Westhoff abundance value, integer 1–9 (numeric)
Details
The three sites represent different forest types:
- Karisik_Orman
Mixed forest – both conifers and broadleaves (12 species)
- Yaprakli_Orman
Broadleaf-dominated forest (13 species)
- Konifer_Orman
Conifer-dominated forest (8 species)
This dataset can be used directly with batch_analysis
for multi-site analysis:
batch_analysis(anatolian_trees)To extract a single community for use with ozkan_pto
or compare_indices:
References
Westhoff, V. & van der Maarel, E. (1973). The Braun-Blanquet approach. In: R.H. Whittaker (ed.), Ordination and classification of communities. Handbook of Vegetation Science 5, 617–726.
See also
batch_analysis for multi-site analysis,
gazi_comm and gazi_gytk for a
single-community example.
Examples
data(anatolian_trees)
head(anatolian_trees)
#> Site Species Genus Family Order Class
#> 1 Karisik_Orman Pinus_nigra Pinus Pinaceae Pinales Pinopsida
#> 2 Karisik_Orman Cedrus_libani Cedrus Pinaceae Pinales Pinopsida
#> 3 Karisik_Orman Abies_nordmanniana Abies Pinaceae Pinales Pinopsida
#> 4 Karisik_Orman Quercus_cerris Quercus Fagaceae Fagales Magnoliopsida
#> 5 Karisik_Orman Quercus_petraea Quercus Fagaceae Fagales Magnoliopsida
#> 6 Karisik_Orman Fagus_orientalis Fagus Fagaceae Fagales Magnoliopsida
#> Phylum Kingdom Abundance
#> 1 Pinophyta Plantae 5
#> 2 Pinophyta Plantae 4
#> 3 Pinophyta Plantae 3
#> 4 Magnoliophyta Plantae 7
#> 5 Magnoliophyta Plantae 6
#> 6 Magnoliophyta Plantae 8
# Multi-site analysis
batch_analysis(anatolian_trees)
#> taxdiv -- Batch Analysis
#> Sites: 3
#> Indices: 14
#>
#> Site N_Species Shannon Simpson Delta Delta_star AvTD
#> Karisik_Orman 12 2.317570 0.889414 3.826087 4.208289 4.575758
#> Konifer_Orman 8 1.868458 0.824142 2.526882 2.967172 4.071429
#> Yaprakli_Orman 13 2.399399 0.897929 2.822775 3.083196 3.435897
#> VarTD uTO TO uTO_plus TO_plus uTO_max TO_max uTO_plus_max
#> 2.335170 8.984158 15.56321 9.717193 16.29644 8.984158 15.56321 9.717193
#> 3.066327 7.236543 13.80194 8.416052 14.99530 7.236543 13.80194 8.416052
#> 0.733070 6.887741 10.05336 7.872282 11.05034 6.887741 10.05336 7.872282
#> TO_plus_max
#> 16.29644
#> 14.99530
#> 11.05034
# Single site extraction
site1 <- anatolian_trees[anatolian_trees$Site == "Karisik_Orman", ]
comm <- setNames(site1$Abundance, site1$Species)
tax <- site1[, c("Species", "Genus", "Family", "Order",
"Class", "Phylum", "Kingdom")]
ozkan_pto(comm, tax)
#> taxdiv -- Ozkan pTO Result
#>
#> All levels:
#> uTO : 8.984158
#> TO : 15.56321
#> uTO+ : 9.717193
#> TO+ : 16.29644
#>
#> Max informative level (level 5):
#> uTO_max : 8.984158
#> TO_max : 15.56321
#> uTO+_max : 9.717193
#> TO+_max : 16.29644
#>
#> Deng entropy by level:
#> Species: 2.484907
#> Genus: 2.552484
#> Family: 3.137316
#> Order: 3.685721
#> Class: 5.233373
#> Phylum: 5.233373
#> Kingdom: 0