Niche width of nearest phylogenetic neighbour

Includes analyses with 34 focal species (including T. alpinum)

Author: Tammy L. Elliott

Date:December 15, 2015

R version 3.2.0

Sample code

samp<-ANG.veg
for (c in 1:length(phy.dist)){
ANG.nn<-nn(ANG.veg, ANG.f, phy.dist[[c]])
ANG.nn.naomit<-na.omit(ANG.nn)
}
ANG.len<-length(ANG.nn)

for (i in ANG.nn){
ANG.sg.val<-sum(as.numeric(as.matrix(decode(ANG.nn.naomit, search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
ANG.val<-ANG.sg.val/ANG.len
}
ANG.val

## [1] 0.7968563

samp<-ALP.veg
for (c in 1:length(phy.dist)){
ALP.nn<-nn(ALP.veg, ALP.f, phy.dist[[c]])
ALP.nn.naomit<-na.omit(ALP.nn)
}
ALP.len<-length(ALP.nn.naomit)

for (i in ALP.nn){
ALP.sg.val<-sum(as.numeric(as.matrix(decode(ALP.nn.naomit, search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
ALP.val<-ALP.sg.val/ALP.len
}
ALP.val

## [1] 0.9179781

samp<-AQU.veg
for (c in 1:length(phy.dist)){
AQU.nn<-nn(AQU.veg, AQU.f, phy.dist[[c]])
AQU.nn.naomit<-na.omit(AQU.nn)
}
AQU.len<-length(AQU.nn.naomit)

for (i in AQU.nn){
AQU.sg.val<-sum(as.numeric(as.matrix(decode(AQU.nn.naomit, search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
AQU.val<-AQU.sg.val/AQU.len
}
AQU.val

## [1] 0.6894054

samp<-BIG.veg
for (c in 1:length(phy.dist)){
BIG.nn<-nn(BIG.veg, BIG.f, phy.dist[[c]])
BIG.nn.naomit<-as.matrix(na.omit(BIG.nn))
}
BIG.len<-length(BIG.nn.naomit)

for (i in BIG.nn){
BIG.sg.val<-sum(as.numeric(as.matrix(decode(BIG.nn.naomit, search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
BIG.val<-BIG.sg.val/BIG.len
}
BIG.val

## [1] 0.7450897

#remove DEF
samp<-BRU.veg
for (c in 1:length(phy.dist)){
BRU.nn<-nn(BRU.veg, BRU.f, phy.dist[[c]])
BRU.nn.naomit<-as.matrix(na.omit(BRU.nn))
}
BRU.len<-length(BRU.nn.naomit)

for (i in BRU.nn){
BRU.sg.val<-sum(as.numeric(as.matrix(decode(BRU.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
BRU.val<-BRU.sg.val/BRU.len
}
BRU.val

## [1] 0.901268

#remove GLA
samp<-CAP.veg
for (c in 1:length(phy.dist)){
CAP.nn<-nn(CAP.veg, CAP.f, phy.dist[[c]])
CAP.nn.naomit<-as.matrix(na.omit(CAP.nn))
}
CAP.len<-length(CAP.nn.naomit)

for (i in CAP.nn){
CAP.sg.val<-sum(as.numeric(as.matrix(decode(CAP.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
CAP.val<-CAP.sg.val/CAP.len
}
CAP.val

## [1] 0.7723294

samp<-CAN.veg
for (c in 1:length(phy.dist)){
CAN.nn<-nn(CAN.veg, CAN.f, phy.dist[[c]])
CAN.nn.naomit<-as.matrix(na.omit(CAN.nn))
}
CAN.len<-length(CAN.nn.naomit)

for (i in CAN.nn){
CAN.sg.val<-sum(as.numeric(as.matrix(decode(CAN.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
CAN.val<-CAN.sg.val/CAN.len
}
CAN.val

## [1] 0.7896825

#Remove ALP
samp<-CES.veg
for (c in 1:length(phy.dist)){
CES.nn<-nn(CES.veg, CES.f, phy.dist[[c]])
CES.nn.naomit<-as.matrix(na.omit(CES.nn))
}
CES.len<-length(CES.nn.naomit)

for (i in CES.nn){
CES.sg.val<-sum(as.numeric(as.matrix(decode(CES.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
CES.val<-CES.sg.val/CES.len
}
CES.val

## [1] 0.6866566

samp<-RUS.veg
for (c in 1:length(phy.dist)){
RUS.nn<-nn(RUS.veg, RUS.f, phy.dist[[c]])
RUS.nn.naomit<-as.matrix(na.omit(RUS.nn))
}
RUS.len<-length(RUS.nn.naomit)

for (i in RUS.nn){
RUS.sg.val<-sum(as.numeric(as.matrix(decode(RUS.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
RUS.val<-RUS.sg.val/RUS.len
}
RUS.val

## [1] 0.6780871

samp<-CHO.veg
for (c in 1:length(phy.dist)){
CHO.nn<-nn(CHO.veg, CHO.f, phy.dist[[c]])
CHO.nn.naomit<-as.matrix(na.omit(CHO.nn))
}
CHO.len<-length(CHO.nn.naomit)

for (i in CHO.nn){
CHO.sg.val<-sum(as.numeric(as.matrix(decode(CHO.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
CHO.val<-CHO.sg.val/CHO.len
}
CHO.val

## [1] 0.7009626

#samp<-DEF.veg
#for (c in 1:length(phy.dist)){
#DEF.nn<-nn(DEF.veg, DEF.f, phy.dist[[c]])
#DEF.nn.naomit<-as.matrix(na.omit(DEF.nn))
#}
#DEF.len<-length(DEF.nn.naomit)

#for (i in DEF.nn){
#DEF.sg.val<-sum(as.numeric(as.matrix(decode(DEF.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
#"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
#0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
#DEF.val<-DEF.sg.val/DEF.len
#}
#DEF.val

samp<-DIS.veg
for (c in 1:length(phy.dist)){
DIS.nn<-nn(DIS.veg, DIS.f, phy.dist[[c]])
DIS.nn.naomit<-as.matrix(na.omit(DIS.nn))
}
DIS.len<-length(DIS.nn.naomit)

for (i in DIS.nn){
DIS.sg.val<-sum(as.numeric(as.matrix(decode(DIS.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
DIS.val<-DIS.sg.val/DIS.len
}
DIS.val

## [1] 0.9255419

samp<-ECH.veg
for (c in 1:length(phy.dist)){
ECH.nn<-nn(ECH.veg, ECH.f, phy.dist[[c]])
ECH.nn.naomit<-as.matrix(na.omit(ECH.nn))
}
ECH.len<-length(ECH.nn.naomit)

for (i in ECH.nn){
ECH.sg.val<-sum(as.numeric(as.matrix(decode(ECH.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
ECH.val<-ECH.sg.val/ECH.len
}
ECH.val

## [1] 0.8168527

samp<-EXI.veg
for (c in 1:length(phy.dist)){
EXI.nn<-nn(EXI.veg, EXI.f, phy.dist[[c]])
EXI.nn.naomit<-as.matrix(na.omit(EXI.nn))
}
EXI.len<-length(EXI.nn.naomit)

for (i in EXI.nn){
EXI.sg.val<-sum(as.numeric(as.matrix(decode(EXI.nn.naomit, search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
EXI.val<-EXI.sg.val/EXI.len
}
EXI.val

## [1] 0.5550852

samp<-EVA.veg
for (c in 1:length(phy.dist)){
EVA.nn<-nn(EVA.veg, EVA.f, phy.dist[[c]])
EVA.nn.naomit<-as.matrix(na.omit(EVA.nn))
}
EVA.len<-length(EVA.nn.naomit)

for (i in EVA.nn){
EVA.sg.val<-sum(as.numeric(as.matrix(decode(EVA.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
EVA.val<-EVA.sg.val/EVA.len
}
EVA.val

## [1] 0.8981977

samp<-GYN.veg
for (c in 1:length(phy.dist)){
GYN.nn<-nn(GYN.veg, GYN.f, phy.dist[[c]])
GYN.nn.naomit<-as.matrix(na.omit(GYN.nn))
}
GYN.len<-length(GYN.nn.naomit)

for (i in GYN.nn){
GYN.sg.val<-sum(as.numeric(as.matrix(decode(GYN.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
GYN.val<-GYN.sg.val/GYN.len
}
GYN.val

## [1] 0.938656

samp<-HEL.veg
for (c in 1:length(phy.dist)){
HEL.nn<-nn(HEL.veg, HEL.f, phy.dist[[c]])
HEL.nn.naomit<-as.matrix(na.omit(HEL.nn))
}
HEL.len<-length(HEL.nn.naomit)

for (i in HEL.nn){
HEL.sg.val<-sum(as.numeric(as.matrix(decode(HEL.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
HEL.val<-HEL.sg.val/HEL.len
}
HEL.val

## [1] 0.6661949

samp<-LEN.veg
for (c in 1:length(phy.dist)){
LEN.nn<-nn(LEN.veg, LEN.f, phy.dist[[c]])
LEN.nn.naomit<-as.matrix(na.omit(LEN.nn))
}
LEN.len<-length(LEN.nn.naomit)

for (i in LEN.nn){
LEN.sg.val<-sum(as.numeric(as.matrix(decode(LEN.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
LEN.val<-LEN.sg.val/LEN.len
}
LEN.val

## [1] 0.8034113

samp<-LEP.veg
for (c in 1:length(phy.dist)){
LEP.nn<-nn(LEP.veg, LEP.f, phy.dist[[c]])
LEP.nn.naomit<-as.matrix(na.omit(LEP.nn))
}
LEP.len<-length(LEP.nn.naomit)

for (i in LEP.nn){
LEP.sg.val<-sum(as.numeric(as.matrix(decode(LEP.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
LEP.val<-LEP.sg.val/LEP.len
}
LEP.val

## [1] 0.985914

#remoe ALP
samp<-LIM.veg
for (c in 1:length(phy.dist)){
LIM.nn<-nn(LIM.veg, LIM.f, phy.dist[[c]])
LIM.nn.naomit<-as.matrix(na.omit(LIM.nn))
}
LIM.length<-length(LIM.nn.naomit)

for (i in LIM.nn){
LIM.sg.val<-sum(as.numeric(as.matrix(decode(LIM.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
LIM.val<-LIM.sg.val/LIM.length
}
LIM.val

## [1] 0.5635427

samp<-LIV.veg
for (c in 1:length(phy.dist)){
LIV.nn<-nn(LIV.veg, LIV.f, phy.dist[[c]])
LIV.nn.naomit<-as.matrix(na.omit(LIV.nn))
}
LIV.length<-length(LIV.nn.naomit)

for (i in LIV.nn){
LIV.sg.val<-sum(as.numeric(as.matrix(decode(LIV.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
LIV.val<-LIV.sg.val/LIV.length
}
LIV.val

## [1] 0.5690737

samp<-MAG.veg
for (c in 1:length(phy.dist)){
MAG.nn<-nn(MAG.veg, MAG.f, phy.dist[[c]])
MAG.nn.naomit<-as.matrix(na.omit(MAG.nn))
}
MAG.length<-length(MAG.nn.naomit)

for (i in MAG.nn){
MAG.sg.val<-sum(as.numeric(as.matrix(decode(MAG.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
MAG.val<-MAG.sg.val/MAG.length
}
MAG.val

## [1] 0.8309213

samp<-OLI.veg
for (c in 1:length(phy.dist)){
OLI.nn<-nn(OLI.veg, OLI.f, phy.dist[[c]])
OLI.nn.naomit<-as.matrix(na.omit(OLI.nn))
}
OLI.length<-length(OLI.nn.naomit)

for (i in OLI.nn){
OLI.sg.val<-sum(as.numeric(as.matrix(decode(OLI.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
OLI.val<-OLI.sg.val/OLI.length
}
OLI.val

## [1] 0.5420045

samp<-PAU.veg
for (c in 1:length(phy.dist)){
PAU.nn<-nn(PAU.veg, PAU.f, phy.dist[[c]])
PAU.nn.naomit<-as.matrix(na.omit(PAU.nn))
}
PAU.length<-length(PAU.nn.naomit)

for (i in PAU.nn){
PAU.sg.val<-sum(as.numeric(as.matrix(decode(PAU.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
PAU.val<-PAU.sg.val/PAU.length
}
PAU.val

## [1] 0.8549349

samp<-RAR.veg
for (c in 1:length(phy.dist)){
RAR.nn<-nn(RAR.veg, RAR.f, phy.dist[[c]])
RAR.nn.naomit<-as.matrix(na.omit(RAR.nn))
}
RAR.length<-length(RAR.nn.naomit)

for (i in RAR.nn){
RAR.sg.val<-sum(as.numeric(as.matrix(decode(RAR.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
RAR.val<-RAR.sg.val/RAR.length
}
RAR.val

## [1] 0.8779437

samp<-ROS.veg
for (c in 1:length(phy.dist)){
ROS.nn<-nn(ROS.veg, ROS.f, phy.dist[[c]])
ROS.nn.naomit<-as.matrix(na.omit(ROS.nn))
}
ROS.length<-length(ROS.nn.naomit)

for (i in ROS.nn){
ROS.sg.val<-sum(as.numeric(as.matrix(decode(ROS.nn.naomit, search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
ROS.val<-ROS.sg.val/ROS.length
}
ROS.val

## [1] 0.4985495

ROS.val

## [1] 0.4985495

samp<-SAX.veg
for (c in 1:length(phy.dist)){
SAX.nn<-nn(SAX.veg, SAX.f, phy.dist[[c]])
SAX.nn.naomit<-as.matrix(na.omit(SAX.nn))
}
SAX.length<-length(SAX.nn.naomit)

for (i in SAX.nn){
SAX.sg.val<-sum(as.numeric(as.matrix(decode(SAX.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
SAX.val<-SAX.sg.val/SAX.length
}
SAX.val

## [1] 0.7999161

#remove GLA
samp<-SCI.veg
for (c in 1:length(phy.dist)){
SCI.nn<-nn(SCI.veg, SCI.f, phy.dist[[c]])
SCI.nn.naomit<-as.matrix(na.omit(SCI.nn))
}
SCI.length<-length(SCI.nn.naomit)

for (i in SCI.nn){
SCI.sg.val<-sum(as.numeric(as.matrix(decode(SCI.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
SCI.val<-SCI.sg.val/SCI.length
}
SCI.val

## [1] 0.7880885

samp<-STY.veg
for (c in 1:length(phy.dist)){
STY.nn<-nn(STY.veg, STY.f, phy.dist[[c]])
STY.nn.naomit<-as.matrix(na.omit(STY.nn))
}
STY.length<-length(STY.nn.naomit)

for (i in STY.nn){
STY.sg.val<-sum(as.numeric(as.matrix(decode(STY.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
STY.val<-STY.sg.val/STY.length
}
STY.val

## [1] 0.8154137

samp<-TEN.veg
for (c in 1:length(phy.dist)){
TEN.nn<-nn(TEN.veg, TEN.f, phy.dist[[c]])
TEN.nn.naomit<-as.matrix(na.omit(TEN.nn))
}
TEN.length<-length(TEN.nn.naomit)

for (i in TEN.nn){
TEN.sg.val<-sum(as.numeric(as.matrix(decode(TEN.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
TEN.val<-TEN.sg.val/TEN.length
}
TEN.val

## [1] 0.8292959

samp<-TRI.veg
for (c in 1:length(phy.dist)){
TRI.nn<-nn(TRI.veg, TRI.f, phy.dist[[c]])
TRI.nn.naomit<-as.matrix(na.omit(TRI.nn))
}
TRI.length<-length(TRI.nn.naomit)

for (i in TRI.nn){
TRI.sg.val<-sum(as.numeric(as.matrix(decode(TRI.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
TRI.val<-TRI.sg.val/TRI.length
}
TRI.val

## [1] 0.8903992

samp<-TRI.veg

samp<-UTR.veg
for (c in 1:length(phy.dist)){
UTR.nn<-nn(UTR.veg, UTR.f, phy.dist[[c]])
UTR.nn.naomit<-as.matrix(na.omit(UTR.nn))
}
UTR.length<-length(UTR.nn.naomit)

for (i in UTR.nn){
UTR.sg.val<-sum(as.numeric(as.matrix(decode(UTR.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
UTR.val<-UTR.sg.val/UTR.length
}
UTR.val

## [1] 0.8292518

samp<-VAG.veg
for (c in 1:length(phy.dist)){
VAG.nn<-nn(VAG.veg, VAG.f, phy.dist[[c]])
VAG.nn.naomit<-as.matrix(na.omit(VAG.nn))
}
VAG.length<-length(VAG.nn.naomit)

for (i in VAG.nn){
VAG.sg.val<-sum(as.numeric(as.matrix(decode(VAG.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
VAG.val<-VAG.sg.val/VAG.length
}
VAG.val

## [1] 0.9059512

#remove diandra
samp<-VES.veg
for (c in 1:length(phy.dist)){
VES.nn<-nn(VES.veg, VES.f, phy.dist[[c]])
VES.nn.naomit<-as.matrix(na.omit(VES.nn))
}
VES.length<-length(VES.nn.naomit)

for (i in VES.nn){
VES.sg.val<-sum(as.numeric(as.matrix(decode(VES.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
VES.val<-VES.sg.val/VES.length
}
VES.val

## [1] 0.8540848

samp<-VIR.veg
for (c in 1:length(phy.dist)){
VIR.nn<-nn(VIR.veg, VIR.f, phy.dist[[c]])
VIR.nn.naomit<-as.matrix(na.omit(VIR.nn))
}
VIR.length<-length(VIR.nn.naomit)

for (i in VIR.nn){
VIR.sg.val<-sum(as.numeric(as.matrix(decode(VIR.nn.naomit,  search  = c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP","CAP", "CES", "CHO", "DIS", "ECH", "EXI", "GYN", "LEP", "LIM", "LIV", "MAG", "PAU", "RAR", "RUS", "SCI",
"STY", "VAG"),replace = c(1.0000000, 0.7257200, 0.7466363, 0.3166945, 0.0000000, 0.6537528, 0.6545460, 0.6592725, 0.9121210, 0.9752128, 0.2915727, 0.6228344, 0.8574476, 0.7733402, 0.7505228, 0.4437916, 0.7259687,0.6467988, 0.9002497, 0.3742042,
0.4531321, 0.7505226, 0.0000000, 0.9609642, 0.9079703, 0.3255431, 0.1730651, 0.9555671, 0.7593922, 0.8374707, 0.5371735, 0.6607605, 0.7568643, 0.9917777)))))
VIR.val<-VIR.sg.val/VIR.length
}
VIR.val

## [1] 0.808422

vegcom.row.names=c("AQU", "BIG", "LEN", "OLI", "ROS", "SAX", "UTR", "VES", "BRU", "CAN", "HEL", "TEN", "TRI", "ANG", "EVA", "VIR", "ALP", "CAP", "CES",
 "CHO",  "DIS", "ECH", "EXI", "GYN","LEP", "LIM", "LIV", "MAG" ,"PAU", "RAR", "RUS", "SCI", "STY" ,"VAG")
veg.val<-c(AQU.val, BIG.val, LEN.val, OLI.val, ROS.val, SAX.val, UTR.val, VES.val, BRU.val, CAN.val, HEL.val, TEN.val, TRI.val, ANG.val, EVA.val, VIR.val, ALP.val, CAP.val, CES.val,
 CHO.val, DIS.val, ECH.val, EXI.val, GYN.val, LEP.val, LIM.val, LIV.val, MAG.val,PAU.val, RAR.val, RUS.val, SCI.val, STY.val,VAG.val)

veg.sp.gen<-as.matrix(cbind(vegcom.row.names, veg.val))

#write.csv(file="C:/Users/Tammy Elliott/Documents/PhD/Year6/Sedges2/Oikos_submission/Analysis/Sedges_2_gen_spec_neighbour_FNTI_Oikos.csv", x=veg.sp.gen)

#veg.hinv<-read.csv("Sedges_2_gen_spec_neighbour_hinv.csv", row.names=1, head=TRUE)

veg.hinv<-read.csv("Sedges_2_gen_spec_neighbour_hinv.csv", row.names=1, head=TRUE)
h.inv.cor<-veg.hinv[,2]
veg.vals<-veg.hinv[,3]
names<-row.names(veg.hinv)
no.plots<-veg.hinv[,4]

library(caper)

## Loading required package: MASS
## Loading required package: mvtnorm

for (e in 1:length(Cyperaceae.samp)){
sedge.traits<-comparative.data(Cyperaceae.samp[[e]], veg.hinv, X.1, vcv=TRUE, vcv.dim=3)
}

Show different types of models

 #incorporate correction for different sampling of number of plots

veg.vals.lm<-lm(veg.vals~h.inv.cor)
veg.vals.lm.weights<-lm(veg.vals~h.inv.cor, weights=no.plots)
veg.vals.pgls<-pgls(veg.val~h.inv.cor, sedge.traits, lambda="ML")

OLS model

summary(veg.vals.lm)

## 
## Call:
## lm(formula = veg.vals ~ h.inv.cor)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.20646 -0.04798  0.01221  0.05628  0.22352 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  0.54270    0.03905  13.896 4.18e-15 ***
## h.inv.cor    0.35316    0.05548   6.365 3.79e-07 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.08736 on 32 degrees of freedom
## Multiple R-squared:  0.5587, Adjusted R-squared:  0.5449 
## F-statistic: 40.51 on 1 and 32 DF,  p-value: 3.788e-07

OLS weighted for number of plots

summary(veg.vals.lm.weights)

## 
## Call:
## lm(formula = veg.vals ~ h.inv.cor, weights = no.plots)
## 
## Weighted Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.86974 -0.19208  0.04342  0.24129  0.99663 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  0.54275    0.03864  14.047 3.10e-15 ***
## h.inv.cor    0.35454    0.05593   6.339 4.08e-07 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.3769 on 32 degrees of freedom
## Multiple R-squared:  0.5567, Adjusted R-squared:  0.5428 
## F-statistic: 40.19 on 1 and 32 DF,  p-value: 4.081e-07

PGLS

summary(veg.vals.pgls)

## 
## Call:
## pgls(formula = veg.val ~ h.inv.cor, data = sedge.traits, lambda = "ML")
## 
## Residuals:
##       Min        1Q    Median        3Q       Max 
## -0.031267 -0.007065 -0.003682  0.004983  0.020325 
## 
## Branch length transformations:
## 
## kappa  [Fix]  : 1.000
## lambda [ ML]  : 0.000
##    lower bound : 0.000, p = 1    
##    upper bound : 1.000, p = 1.1472e-05
##    95.0% CI   : (NA, 0.607)
## delta  [Fix]  : 1.000
## 
## Coefficients:
##             Estimate Std. Error t value  Pr(>|t|)    
## (Intercept) 0.542702   0.039055 13.8959 4.219e-15 ***
## h.inv.cor   0.353164   0.055485  6.3651 3.788e-07 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.01118 on 32 degrees of freedom
## Multiple R-squared: 0.5587,  Adjusted R-squared: 0.5449 
## F-statistic: 40.51 on 1 and 32 DF,  p-value: 3.788e-07

Show figure

#dev.new(width=3.15, height=4.2)
par(oma=c(0.05,0.05, 0.05, 0.05),mai=c(0.25,0.25,0, 0.05), omi=c(0.3, 0.4,0,0))
par(mgp=c(0.4,0.4,0))
plot(veg.vals~h.inv.cor,type="n", axes=FALSE, ann=FALSE,xlim=c(0,1), ylim=c(0.4,1), cex.lab=1.25, font.lab=4 )
axis(1, lwd=3, cex.axis=1, tck=0.03)
axis(2, las=2, lwd=3, cex.axis=1, tck=0.03)
mtext("Niche width", side=1, line=1.75, cex.lab=1.25,font.lab=4 )
mtext("Niche width of nearest taxon in plot", side=2, line=2, cex.lab=1.25,font.lab=4 )
points(h.inv.cor, veg.vals, cex=1.25, col="black", pch=16)
box(lwd=3, col = 'black')
#text(h.inv.cor, veg.vals,labels=names, cex=0.4, pos=1, offset=0.2)
abline(veg.vals.pgls, lwd=3)

#dev.new(width=3.15, height=4.2)
par(oma=c(0.05,0.05, 0.05, 0.05),mai=c(0.25,0.25,0, 0.05), omi=c(0.3, 0.4,0,0))
par(mgp=c(0.4,0.4,0))
plot(veg.vals~h.inv.cor,type="n", axes=FALSE, ann=FALSE,xlim=c(0,1), ylim=c(0.4,1), cex.lab=1.25, font.lab=4 )
axis(1, lwd=3, cex.axis=1, tck=0.03)
axis(2, las=2, lwd=3, cex.axis=1, tck=0.03)
mtext("Niche width of focal", side=1, line=1.75, cex.lab=1.25,font.lab=4 )
mtext("Mean niche width of nearest neighbour", side=2, line=2, cex.lab=1.25,font.lab=4 )
points(h.inv.cor, veg.vals, cex=1.25, col="black", pch=16)
box(lwd=3, col = 'black')
text(h.inv.cor, veg.vals,labels=names, cex=0.4, pos=1, offset=0.2)
abline(veg.vals.pgls, lwd=3)