BioFTF: Biodiversity Assessment Using Functional Tools

> library(BioFTF)

バージョン: 1.0.0

関数名 概略
alltools Apply the whole analysis to the dataset.
arc Compute the arc length of beta profile for each community.
area Compute the area under the beta profile for each community.
beta Compute the values of beta profile for each community in every part of the beta domain.
beta_plot Plot the beta profile for each community.
betaprime Compute the values of the first derivative of beta profile for each community in every part of the beta domain.
betaprime_plot Plot the first derivative of the beta profile for each community.
betasecond Compute the values of the second derivative of beta profile for each community in every part of the beta domain.
betasecond_plot Plot the second derivative of the beta profile for each community.
curvature Compute the values of the curvature of the beta profile function for each community in every part of the beta domain.
curvature_plot Plot the curvature of the beta profiles for each community.
datirel Create a matrix with the relative frequencies for each community.
radius Compute the values for the radius of curvature of the beta profile for each community in every part of the beta domain.
radius_plot Plot the radius of curvature of the beta profiles for each community.
ranking Compute the communities ranking according to the biodiversity computed using the functional tools.
summary_species Create a species summary for each community. Based on the dataset with absolute abundance
summary_species_relative Create a species summary for each community. Based on the dataset with relative abundance.

ranking

> # 3つの群集を仮定
> c(0.3, 0.5, 0.1, 0.05, 0.05, 0.25, 0.25, 0.25, 0.25, 0, 0.35, 0.3, 0.35, 0, 0) %>% 
+   matrix(3, 5) %>% 
+   ranking()

              Richness  Shannon   Simpson      Arc     Area
community n.3        3 1.312765 0.7222222 3.146419 2.984527
community n.1        3 1.229655 0.6925208 3.201130 2.844371
community n.2        3 1.183976 0.6691871 3.234640 2.768054

summary_species

> # ５種の仮想データ
> c(3, 5, 5, 2, 1, 2, 6, 8, 5, 1) %>% 
+   matrix(2,5) %>% 
+   summary_species()

  species n.1   species n.2    species n.3    species n.4   species n.5
 Min.   :3.0   Min.   :2.00   Min.   :1.00   Min.   :6.0   Min.   :1   
 1st Qu.:3.5   1st Qu.:2.75   1st Qu.:1.25   1st Qu.:6.5   1st Qu.:2   
 Median :4.0   Median :3.50   Median :1.50   Median :7.0   Median :3   
 Mean   :4.0   Mean   :3.50   Mean   :1.50   Mean   :7.0   Mean   :3   
 3rd Qu.:4.5   3rd Qu.:4.25   3rd Qu.:1.75   3rd Qu.:7.5   3rd Qu.:4   
 Max.   :5.0   Max.   :5.00   Max.   :2.00   Max.   :8.0   Max.   :5