Description Usage Arguments Value Author(s) Examples
Converting regular survey data (long data, similar to the treedata and herbdata in the package) to species matrix, and attributes matrix (wide data).
1 2 | longtowide(longdata, left, up, inner = NULL,
fun = rep("sum", length(inner)), freq = FALSE)
|
longdata |
Regular survey data (long data, similar to the treedata and herbdata in the package) |
left |
Row names of matrix data after converted |
up |
Column names of matrix data after converted |
inner |
Attributes data need to converted |
fun |
Functions need to applied in the converting process |
freq |
Frequency of attributes |
Wide data,such species matrix, and attributes matrix, etc.
Zongzheng Chai
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | #####Example######
##Following two example data with different subject, pineoakTree
##is for the base data of individual trees, and the herb data is for
##the base data of cluster.
data(treedata)
data(herbdata)
####Merge a species matrix from base data
##Note: following calculation only for the base data of individual not cluster
pineoak.spematrix<-longtowide(longdata=treedata,left="plot.id",up="spe.id")
pineoak.spematrix
##Equivalent method to merge species matrix from base data
treedata$abundance<-1
head(treedata)
tree.spematrix<-longtowide(longdata=treedata,left="plot.id",up="spe.id",inner="abundance")
tree.spematrix
herb.spematrix<-longtowide(longdata=herbdata,left="plot.id",up="spe.id",inner="abundance")
herb.spematrix
####Compute the frequency of species in the multiple plots
##Merge a frequency matrix from base data
tree.freq<-longtowide(longdata=treedata,left="plot.id",up="spe.id",freq=TRUE)
tree.freq
herb.freq<-longtowide(longdata=herbdata,left="plot.id",up="spe.id",freq=TRUE)
herb.freq
####Compute the attribute matrix from base data
##Single attribute matrix
tree.dbh<-longtowide(longdata=treedata,left="plot.id",up="spe.id",inner="dbh.cm")
tree.dbh
herb.cover<-longtowide(longdata=herbdata,left="plot.id",up="spe.id",inner="coverage")
herb.cover
##Multiple attribute matrix
tree.multattr<-longtowide(longdata=treedata,left="plot.id",up="spe.id",
inner=c("dbh.cm","ht.m"))
tree.multattr
herb.multattr<-longtowide(longdata=herbdata,left="plot.id",up="spe.id",
inner=c("coverage","abundance"))
herb.multattr
#######Calculation of Importance value (IV) for species######
####Calculation of Importance value (IV) for individual tree data
##Covert long data to wide data
tree.freq<-longtowide(longdata=treedata,left="plot.id",up="spe.id",freq=TRUE)$frequency
tree.density<-longtowide(longdata=treedata,left="plot.id",up="spe.id")/(20*400)
treedata$base<-pi*(treedata$dbh.cm)^2/10000
tree.dominance<-longtowide(longdata=treedata,left="plot.id",up="spe.id",inner="base")/(20*400)
##Compute the relative value
tree.refreq<-tree.freq/rowSums(tree.freq)*100
tree.redensity<-tree.density/rowSums(tree.density)*100
tree.redominance<-tree.dominance/rowSums(tree.dominance)*100
##Compute the importance value matrix
treeIVmatirx<-(tree.refreq+tree.redensity+tree.redominance)/3
##Compute the total importance value for species
treeTIV<-colSums(treeIVmatirx)/20
##Order the total importance value for species
sortedtreeTIV<-sort(treeTIV,decreasing=TRUE)
sortedtreeTIV
####Calculation of Importance value (IV) for clust herb data
##Covert long data to wide data
herb.freq<-longtowide(longdata=herbdata,left="plot.id",up="spe.id",freq=TRUE)$frequency
herb.dencover<-longtowide(longdata=herbdata,left="plot.id",up="spe.id",
inner=c("abundance","coverage"))
herb.density<-herb.dencover$abundance/100
herb.coverage<-herb.dencover$coverage/100
##Compute the relative value
herb.refreq<-herb.freq/rowSums(herb.freq)*100
herb.redensity<-herb.density/rowSums(herb.density)*100
herb.recoverage<-herb.coverage/rowSums(herb.coverage)*100
##Compute the importance value matrix
herbIVmatirx<-(herb.refreq+herb.redensity+herb.recoverage)/3
##Compute the total importance value for species
herbTIV<-colSums(herbIVmatirx)/20
##Order the total importance value for species
sortedherbTIV<-sort(herbTIV,decreasing=TRUE)
sortedtreeTIV
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