longtowide: A R function for converting to long data to wide data

In Zongzheng/forestHES: Forest health evaluation system at the forest stand level in China

Description

Converting regular survey data (long data, similar to the treedata and herbdata in the package) to species matrix, and attributes matrix (wide data).

Usage

longtowide(longdata, left, up, inner = NULL,
fun = rep("sum", length(inner)), freq = FALSE)

Arguments

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

Value

Wide data,such species matrix, and attributes matrix, etc.

Author(s)

Zongzheng Chai

Examples

#####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

Zongzheng/forestHES documentation built on May 10, 2019, 1:59 a.m.