CTFSplot('bci',1:7)
CTFSmort()
CTFSgrowth()
CTFSabund(data=TRUE)
newtable = biomass.CTFSdb(RStemTable = bci.stem1, RTreeTable = bci.full1, plot = "bci", dbhunit = "mm") 
CTFSplot('bci',1:7,'stem')
newtable = biomass.CTFSdb(RStemTable = bci.stem1, RTreeTable = bci.full1, plot = "bci", dbhunit = "mm") 
head(newtable[, c("sp", "dbh", "agb")])
 sum(newtable$agb)/50
newtable7 = biomass.CTFSdb(RStemTable = bci.stem7, RTreeTable = bci.full7, plot = "bci", dbhunit = "mm") 
CTFSplot('bci',7)
newtable7 = biomass.CTFSdb(RStemTable = bci.stem7, RTreeTable = bci.full7, plot = "bci", dbhunit = "mm") 
head(newtable7[, c("sp", "dbh", "agb")])
 sum(newtable7$agb)/50
newtable5 = biomass.CTFSdb(RStemTable = bci.stem5, RTreeTable = bci.full5, plot = "bci", dbhunit = "mm") 
 sum(newtable5$agb)/50
deltaagb=pop.change(bci.full5,bci.full7,type='agb')
str(deltaagb)
deltaagb=pop.change.sp(bci.full5,bci.full7,type='agb')
deltaagb=pop.change.sp(bci.full5,bci.full7,type='agb',split=bci.full5$sp)
deltaagb=pop.change.dbh(bci.full5,bci.full7,type='agb',split=bci.full5$sp)
str(deltaagb)
head(deltaagb$agb)
plot('10_2'~'10_1',data=deltaagb)
plot(10_2~10_1,data=deltaagb)
plot(deltaagb[,1],deltaagb[,2])
plot(deltaagb$agb[,1],deltaagb$agb[,2])
plot(deltaagb$agb[,1],deltaagb$agb[,2],log='xy')
str(bci.full5)
str(bci.stem5)
table(bci.full5$nostems)
options(width=130)
data.frame(table(bci.full5$nostems))
subset(bci.full5,nostems>25)
options(width=80)
subset(bci.full5,nostems>25)
options(width=90)
subset(bci.full5,nostems>25)
subset(bci.stem5,tag=='114636')
str(bci.stem5)
dim(subset(bci.stem5,tag %in% subset(bci.full5,nostes>10)$tag & status=='A')) 
dim(subset(bci.stem5,tag %in% subset(bci.full5,nostems>10)$tag & status=='A')) 
dim(subset(bci.stem5,tag %in% subset(bci.full5,nostems>20)$tag & status=='A')) 
dim(subset(bci.stem5,tag %in% subset(bci.full5,nostems>22)$tag & status=='A')) 
head(subset(bci.stem5,tag %in% subset(bci.full5,nostems>22)$tag & status=='A')) 
head(subset(bci.stem5,tag %in% subset(bci.full5,nostems==3)$tag & status=='A')) 
head(subset(bci.stem5,tag %in% subset(bci.full5,nostems==3)$tag & status=='A'),9) 
head(subset(bci.full5,nostems==3)$tag)
subset(bci.full5,tag=='00015')
subset(bci.full5,tag=='000015')
search()
ls(11)
ls(10)
str(wsg.ctfs2)
head(wsg.ctfs2)
args(biomass.CTFSdb)
newtable2 = biomass.CTFSdb(RStemTable = bci.stem2, RTreeTable = bci.full2, plot = "bci", dbhunit = "mm") 
str(newtable2)
sum(newtable5$agb)
newtable2 = biomass.CTFSdb(RStemTable = bci.stem2, RTreeTable = bci.full2, plot = "bci", dbhunit = "mm") 
total=abundance(bci.full5,mindbh=10)
total
total=abundance(bci.full5,mindbh=10,type='agb')
total
total=abundance(bci.full5,mindbh=10,type='agb')/50
total=abundance(bci.full5,mindbh=10,type='agb')$agb/50
abundance(bci.full5,mindbh=10,type='agb')$agb/50
abundance(bci.full5,mindbh=10,type='agb')$agb
abundance(bci.full7,mindbh=10,type='agb')$agb
abundance(bci.full7,mindbh=10,type='agb')$agb/50
totalsp=abundance(bci.full5,mindbh=10,type='agb',split1=bci.full5$sp)$agb/50
head(totalsp)
tail(totalsp)
dim(totalsp)
which.max(totalsp$all)
totals[250,]
totalsp[250,]
subset(totalsp,all>15)
subset(totalsp,all>10)
totalsp=abundance(bci.full5,mindbh=10,type='agb',split1=bci.full5$sp)$agb/50
totalsp=abundance(bci.full5,mindbh=10,type='agb',split1=bci.full5$sp)$agb
save.history(file='~/meeting_workshops/Rmodeling/FrontRoyal/histR23July2013.txt')
savehistory(file='~/meeting_workshops/Rmodeling/FrontRoyal/histR23July2013.txt')
dir('/home/condit/meeting_workshops')
savehistory(file='~/meetings_workshops/Rmodeling/FrontRoyal/histR23July2013.txt')
dir('/home/condit/meetings_workshops/Rmodeling')
dir('/home/condit/meetings_workshops/Rmodeling/FrontRoyal')
system(ls -ll /home/condit/meetings_workshops/Rmodeling/FrontRoyal)
system('ls -ll /home/condit/meetings_workshops/Rmodeling/FrontRoyal')
system('ls -ll /home/condit/meetings_workshops/Rmodeling/FrontRoyal/history')
savehistory(file='~/meetings_workshops/Rmodeling/FrontRoyal/history/histR23July2013.txt')
abundance(bci.full5,mindbh=10,type='agb',split1=bci.full5$status)$agb
abundance(bci.full5,mindbh=10,type='agb',split1=bci.full5$status)$agb/50
half=bci.full5$gx<500
abundance(bci.full5,mindbh=10,type='agb',split1=bci.full5$status,split2=half)$agb/50
half=character()
half[bci.full5$gx<500]='west'
half[bci.full5$gx>=500]='east'
abundance(bci.full5,mindbh=10,type='agb',split1=bci.full5$status,split2=half)$agb/50
abundance(bci.full2,mindbh=10,type='agb',split1=bci.full5$status,split2=half)$agb/50
39.9/(39.9+132.4)
36.7/(36.7+105)
abundance(bci.full2,mindbh=10,type='agb',split1=bci.full5$status,split2=bci.full5$sp)$agb/50
abundance(bci.full2,mindbh=10,type='agb',split2=bci.full5$status,split1=bci.full5$sp)$agb/50
agbmort=abundance(bci.full2,mindbh=10,type='agb',split2=bci.full5$status,split1=bci.full5$sp)$agb/50
head(agbmort)
str(agbmort)
agbmort$rate=agb$D/(agb$D+agb$A)
agbmort$rate=agbmort$D/(agbmort$D+agbmort$A)
head(agbmort)
agbmort$total=(agbmort$D+agbmort$A)
head(agbmort)
plot(rate~total,data=agbmort)
plot(rate~total,data=agbmort,log='x')
agbmort=abundance(bci.full2,mindbh=10,type='agb',split2=bci.full5$status,split1=bci.full5$sp)$agb/50
agbmort$rate=agbmort$D/(agbmort$D+agbmort$A)
agbmort$total=(agbmort$D+agbmort$A)
plot(rate~total,data=agbmort,log='x')
bcichange=pop.change(bci.full5,bci.full6,type='abund',split1=bci.full5$sp,mindbh=10)
bcichange=pop.change(bci.full2,bci.full5,type='abund',split1=bci.full5$sp,mindbh=10)
names(bcichange)
str(bcichange)
bcichange=pop.change(bci.full2,bci.full5,type='agb',split1=bci.full5$sp,mindbh=10)
str(bcichange)
assemble.demography(bcichange,type='agb')
deltaagb=assemble.demography(bcichange,type='agb')
head(deltaagb)
bcichange=pop.change(bci.full2,bci.full5,type='agb',split1=bci.full5$sp,mindbh=10)
deltaagb=assemble.demography(bcichange,type='agb')
head(deltaagb)
subset(deltaagb,little.r>.05)
subset(deltaagb,little.r>.1)
bcichange=pop.change(bci.full2,bci.full5,type='agb',split1=bci.full5$sp,mindbh=10)
deltaagb=assemble.demography(bcichange,type='agb')
head(deltaagb)
plot(AGB.2~AGB.1,data=deltaagb)
plot(AGB.2~AGB.1,data=deltaagb,log='xy')
abline(1,0)
plot(AGB.2~AGB.1,data=deltaagb,log='xy')
abline(0,1)
identify(deltaagb$AGB.1,deltaagb$AGB.2,rownames(deltaagb))
plot(deltaagb$AGB.1,deltaagb$AGB.2)
identify(deltaagb$AGB.1,deltaagb$AGB.2,rownames(deltaagb))
abline(0,1)
bcichange=pop.change(bci.full2,bci.full5,type='agb',split1=bci.full5$sp,mindbh=10)
plot(AGB.2~AGB.1,data=deltaagb,log='xy')
bcichange=pop.change(bci.full2,bci.full5,type='agb',split1=bci.full5$sp,mindbh=10)
deltaagb=assemble.demography(bcichange,type='agb')
plot(deltaagb$AGB.1,deltaagb$AGB.2)
abline(0,1)
identify(deltaagb$AGB.1,deltaagb$AGB.2,rownames(deltaagb))
savehistory(file='~/meetings_workshops/Rmodeling/FrontRoyal/history/histR23July2013.txt')