Nothing
## ----vignette-setup, include = FALSE------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----load-pkg-----------------------------------------------------------------
library(fundiversity)
## ----panel-a------------------------------------------------------------------
data_a <- matrix(byrow = TRUE, ncol = 2,
c(
0.0, 1.0,
0.5, 1.0,
1.0, 1.0,
1.5, 1.0,
2.0, 1.0,
1.0, 0.0,
1.0, 0.5,
1.0, 1.5,
1.0, 2.0
)
)
rownames(data_a) <- paste0("species", seq_len(nrow(data_a)))
print(data_a)
## ----plot-data-a, out.width = '100%', fig.width=7, fig.asp=1------------------
plot(data_a, pch = 19, asp = 1, xlab = "Trait 1", ylab = "Trait 2")
## ----compute-a----------------------------------------------------------------
fric_a <- fd_fric(data_a)[["FRic"]]
feve_a <- fd_feve(data_a)[["FEve"]]
fdiv_a <- fd_fdiv(data_a)[["FDiv"]]
fdis_a <- fd_fdis(data_a)[["FDis"]]
raoq_a <- fd_raoq(data_a)[["Q"]]
## ----data-c-------------------------------------------------------------------
l <- 2 # common species
s <- 1 # rare species
wc <- matrix(c(l, s, l, s, l, l, s, s, l), nrow = 1)
colnames(wc) <- rownames(data_a)
rownames(wc) <- "site"
## ----compute-c----------------------------------------------------------------
fric_c <- fd_fric(data_a)[["FRic"]]
feve_c <- fd_feve(data_a, wc)[["FEve"]]
fdiv_c <- fd_fdiv(data_a, wc)[["FDiv"]]
fdis_c <- fd_fdis(data_a, wc)[["FDis"]]
raoq_c <- fd_raoq(data_a, wc)[["Q"]]
## ----data-b-------------------------------------------------------------------
l <- 2 # common species
s <- 1 # rare species
wb <- matrix(c(l, l, l, l, l, s, s, s, s), nrow = 1)
colnames(wb) <- rownames(data_a)
rownames(wb) <- "site"
## ----compute-b----------------------------------------------------------------
fric_b <- fd_fric(data_a)[["FRic"]]
feve_b <- fd_feve(data_a, wb)[["FEve"]]
fdiv_b <- fd_fdiv(data_a, wb)[["FDiv"]]
fdis_b <- fd_fdis(data_a, wb)[["FDis"]]
raoq_b <- fd_raoq(data_a, wb)[["Q"]]
## ----data-d-------------------------------------------------------------------
shift <- 1/(2*sqrt(2))
data_d <- matrix(c(
1-shift, 1-shift,
1-shift, 1+shift,
1+shift, 1-shift,
1+shift, 1+shift,
1.00 , 0.00 ,
2.00 , 1.00 ,
1.00 , 2.00 ,
0.00 , 1.00 ,
1.00 , 1.00),
byrow = TRUE,
ncol = 2
)
## ----compute-d----------------------------------------------------------------
fric_d <- fd_fric(data_d)[["FRic"]]
feve_d <- fd_feve(data_d)[["FEve"]]
fdiv_d <- fd_fdiv(data_d)[["FDiv"]]
fdis_d <- fd_fdis(data_d)[["FDis"]]
raoq_d <- fd_raoq(data_d)[["Q"]]
## ----data-e-------------------------------------------------------------------
data_e <- matrix(c(
0.0, 1.0,
0.5, 0.5,
1.0, 1.0,
1.5, 0.5,
2.0, 1.0,
1.0, 0.0,
0.5, 1.5,
1.5, 1.5,
1.0, 2.0),
byrow = TRUE,
ncol = 2
)
## ----compute-e----------------------------------------------------------------
fric_e <- fd_fric(data_e)[["FRic"]]
feve_e <- fd_feve(data_e)[["FEve"]]
fdiv_e <- fd_fdiv(data_e)[["FDiv"]]
fdis_e <- fd_fdis(data_e)[["FDis"]]
raoq_e <- fd_raoq(data_e)[["Q"]]
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