flower-package: Tools for characterizing flowering traits

In flower: Tools for characterizing flowering traits

Description

Flowering is an important life history trait of flowering plants. It has been mainly analyzed with respect to flowering onset and duration of flowering. This tools provide some functions to compute the temporal distribution of an flowering individual related to other population members. fCV() measures the temporal variation in flowering. RIind() measures the rank order of flowering for individual plants within a population. SI(), SI2(), SI3(), and SI4() calculate flowering synchrony with different methods.

Details

Package:	flower
Type:	Package
Version:	1.0
Date:	2015-01-23
License:	GPL(>=1.0)

Author(s)

WANG,Xie Maintainer: WANG,Xie <[e-mail]>

References

Michalski SG, Durka W. Synchronous Pulsed Flowering: Analysis of the Flowering Phenology in Juncus (Juncaceae). Annals of Botany 2007;100(6):1271-1285. doi:10.1093/aob/mcm206.

See Also

flower

Examples

a1=c(0,1,1,1,0,0,0)
a2=c(0,1,0,1,1,0,0)
a3=c(0,0,0,1,1,1,0)
a4=c(1,0,0,1,1,0,1)
a5=c(0,0,1,1,1,0,1)
a6=c(0,0,0,1,1,1,1)
pop=c("pop1","pop1","pop1","pop2","pop2","pop2")
ind=c(1,2,3,1,2,3)
dd=rbind(a1,a2,a3,a4,a5,a6)
colnames(dd)=c("D5/1","D5/2","D5/3","D5/4","D5/5","D5/6","D5/7")
#the flowering synchrony index
R0=SI(dd,pop)
R0
R1=SI2_onepop(dd,as.matrix(ind))
R1
R2=SI2(dd,as.matrix(pop),as.matrix(ind))
R2
R3=SI3(dd,as.matrix(pop),as.matrix(ind))
R3
R4=SI4(dd,as.matrix(pop),as.matrix(ind))
R4
#the rank order of flowering 
R5=RIind(dd,pop,ind)
R5
#the pulsed flowering phenology
R6=fCV(dd,pop)
R6

Example output

[1] "Result:S_mean= 0.9 S_sd= 0.14"
$m
[1] 7

$n
[1] 2

$f
[1] "pop1" "pop2"

$aij
     pop1 pop2
pop1    5    4
pop2    4    6

$bij
     pop1 pop2
pop1    5    5
pop2    5    6

$time
pop1 pop2 
   5    6 

$si
   pop1 pop2
Si  0.8    1

         si
1 0.6666667
2 0.8000000
3 0.7500000
         si
1 0.6666667
2 0.8000000
3 0.7500000
[1] "pop1"
         si
1 0.5000000
2 0.6666667
3 0.5000000
[1] "pop2"
    si
1 0.75
2 0.75
3 0.75
     n  min       max      mean         sd
pop1 3 0.50 0.6666667 0.5555556 0.09622504
pop2 3 0.75 0.7500000 0.7500000 0.00000000
[1] "pop1"
[1] "pop1 Xip- numbers of open flowers per day"
     pop1 - 1 pop1 - 2 pop1 - 3
D5.1        0        0        0
D5.2        1        1        0
D5.3        1        0        0
D5.4        1        1        1
D5.5        0        1        1
D5.6        0        0        1
[1] "pop1 ri-  all pairwise Pearson correlations coefficients (ri) of xit"
           pop1 - 1  pop1 - 2   pop1 - 3
pop1 - 1  1.0000000 0.3333333 -0.3333333
pop1 - 2  0.3333333 1.0000000  0.3333333
pop1 - 3 -0.3333333 0.3333333  1.0000000
[1] "pop2"
[1] "pop2 Xip- numbers of open flowers per day"
     pop2 - 1 pop2 - 2 pop2 - 3
D5.1        1        0        0
D5.2        0        0        0
D5.3        0        1        0
D5.4        1        1        1
D5.6        0        0        1
[1] "pop2 ri-  all pairwise Pearson correlations coefficients (ri) of xit"
          pop2 - 1  pop2 - 2  pop2 - 3
pop2 - 1 1.0000000 0.1666667 0.1666667
pop2 - 2 0.1666667 1.0000000 0.1666667
pop2 - 3 0.1666667 0.1666667 1.0000000
[1] "SI3:the mean of ri"
$Result
         pop1      pop2
SI3 0.1111111 0.1666667

[1] "pop1"
[1] "pop1 -SI4"
      pop1 - 1  pop1 - 2  pop1 - 3
[1,] 0.6666667 0.7777778 0.6666667
[1] "pop2"
[1] "pop2 -SI4"
      pop2 - 1  pop2 - 2  pop2 - 3
[1,] 0.8333333 0.8333333 0.8333333
$Result.si4
     n       min       max      mean         sd
pop1 3 0.6666667 0.7777778 0.7037037 0.06415003
pop2 3 0.8333333 0.8333333 0.8333333 0.00000000

     R.length R.min R.max R.mean R.sd
pop1        3     3     3      3    0
pop2        3     4     4      4    0
$res
     R.length R.min R.max R.mean R.sd
pop1        3     3     3      3    0
pop2        3     4     4      4    0

$NO.of.ind
[1] 6

$aij
   pop      fls D5/1 D5/2 D5/3 D5/4 D5/5 D5/6 D5/7
1 pop1 pop1 - 1    0    1    1    1    0    0    0
2 pop1 pop1 - 2    0    1    0    1    1    0    0
3 pop1 pop1 - 3    0    0    0    1    1    1    0
4 pop2 pop2 - 1    1    0    0    1    1    0    1
5 pop2 pop2 - 2    0    0    1    1    1    0    1
6 pop2 pop2 - 3    0    0    0    1    1    1    1

$bij
         [,1]
pop1 - 1    1
pop1 - 2    1
pop1 - 3    1
pop2 - 1    1
pop2 - 2    1
pop2 - 3    1

$xij
   pop      fls D5/1 D5/2 D5/3 D5/4 D5/5 D5/6 D5/7
1 pop1 pop1 - 1    0    1    1    1    0    0    0
2 pop1 pop1 - 2    0    1    0    1    1    0    0
3 pop1 pop1 - 3    0    0    0    1    1    1    0
4 pop2 pop2 - 1    1    0    0    1    1    0    1
5 pop2 pop2 - 2    0    0    1    1    1    0    1
6 pop2 pop2 - 3    0    0    0    1    1    1    1

$R
  population individual r
1       pop1   pop1 - 1 3
2       pop1   pop1 - 2 3
3       pop1   pop1 - 3 3
4       pop2   pop2 - 1 4
5       pop2   pop2 - 2 4
6       pop2   pop2 - 3 4

$CV.x
     pop1 pop2
D5/1    0    1
D5/2    2    0
D5/3    1    1
D5/4    3    3
D5/5    2    3
D5/6    1    1
D5/7    0    3

$CV.sd
         [,1]
pop1 1.290994
pop2 1.527525

$CV.mean
         [,1]
pop1 1.500000
pop2 1.333333

$CV
           cv
pop1 0.860663
pop2 1.145644

flower documentation built on May 1, 2019, 9:27 p.m.