Description Usage Arguments Details Value Note Author(s) References See Also Examples
Reads output file generated by the simulation programs and plots graphics
1 2 3 4 5 | read.plot.cerio.out(file.out.name,sens=F,pdfout=F)
read.plot.river.out(file.out.name,sens=F,pdfout=F)
read.plot.forsucc.out(file.out.name,sens=F,pdfout=F)
read.plot.zelig.out(fileout,spp,grp1,grp2,pdfout=F)
read.plot.semi.out(fileout,spp,label,pdfout=F,plotmarkov=F,ctd=F)
|
file.out.name |
name of output file to be read |
sens |
logical variable to decide whether the output includes sensitivity analysis |
pdfout |
logical variable to decide whether to produce PDF output |
fileout |
name of output file to be read |
spp |
array with codes for species |
grp1 |
array with members of group 1 of species |
grp2 |
array with members of group 2 of species |
label |
character string for label of plot |
plotmarkov |
optional logical to decide whether to plot the embedded Markov chain |
ctd |
optional logical variable to decide how to plot |
zelig: produces two figures, one for stand aggregates and one for basal area by species.
forsucc: produces two figures, one for basal area and the other for density. semi: produces two figures, one for Markov chain dynamics and one for semi-Markov dynamics.
From cerio, river, and forsucc:
t |
time sequence |
x |
state variable |
val.par |
values of parameters |
label.var |
labels for variables |
From semi:
X |
output from embedded Markov chain projection |
out |
output from semi-Markov simulator |
From zelig: None
Review documentation on how to use cerio.F, semi.F, zelig.F, river.C, and forsucc.C
The zelig model used here is based on the 2.3 version by D.L. Urban.
Miguel F. Acevedo Acevedo@unt.edu
Acevedo M.F. 2012. Simulation of Ecological and Environmental Models. CRC Press.
Acevedo, M.F., S. Pamarti, M. Ablan, D.L. Urban, and A. Mikler. 2001. Modeling forest landscapes: Parameter estimation from gap models over heterogeneous terrain. Simulation 77:53-68.
Acevedo, M.F., D.L. Urban, and M. Ablan, M. 1995. Transition and gap models of forest dynamics. Ecological Applications 5:1040-1055.
Interface functions .Fortran
, .C
, Wrappers F and C functions cerio.F
, semi.F
, zelig.F
, river.C
, forsucc.C
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 | ## Not run:
is.loaded("cerio", PACKAGE="seem")
fileout <- cerio.F("chp10","cerio")
x <- read.plot.cerio.out(fileout,pdfout=TRUE)
is.loaded("river", PACKAGE="seem")
fileout <- river.C("chp14","river-sens")
x <- read.plot.river.out(fileout,sens=TRUE)
spp <- c("Post oak", "Black jack oak", "Winged elm", "GreenAsh",
"CedarElm", "Hackberry", "BurOak", "Pecan")
grp1 <- c(1:3); grp2 <- c(4:8) #upland 3 spp and bottomland 5 spp
is.loaded("zelig", PACKAGE="seem")
fileout <- zelig.F("chp16","gbc")
x <- read.plot.zelig.out(fileout,spp, grp1, grp2)
fileout <- forsucc.C("chp16","forsucc") # forsucc is fileprefix
x <- read.plot.forsucc.out(fileout, sens=FALSE)
spp <- c("Role1", "Role2", "Role3", "Role4")
fileprefix <- "rolesm"; label <- "Semi-Markov Order 1"
fileout <- semi.F("chp16",fileprefix)
x <- read.plot.semi.out(fileout, spp, label)
## End(Not run)
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