seem (version 1.0)

Read and plot .F .C output: Read and plot output from Fortran and C simulation programs

Description

Reads output file generated by the simulation programs and plots graphics

Usage

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)

Arguments

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

Value

• 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

Details

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.

References

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.

See Also

Interface functions .Fortran, .C, Wrappers F and C functions cerio.F, semi.F, zelig.F, river.C, forsucc.C

Examples

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)