docs/countryside_workings.R

In txm676/mmSAR2: Fit and Compare Species-Area Relationship Models Using Multimodel Inference

#add starting parameters for sar_habitat: docs

#Add in logarithmic version and maybe logistic?
#say to users to contact us

#some sort of plot function that looks at extinction
#rates if you change amount of habitat!?

#sar_matrix?

library(sars)
library(dplyr)
data <- read.table("D:\\documents\\Work\\On-going projects\\Habitat SAR Models\\Countryside files\\Vania\\MatrixMHUb.txt", 1)
data <- data[,c(2:4, 6,8,7,9)]


f <- sar_countryside(data, ubiSp = TRUE,
                     habNam = c("AG", "SH", "F"),
                     grid_start = "partial")

countryside_extrap(f, 1:3)

##user startPar

SP <- matrix(rep(c(3.061161e+08, 2.104536e-01,
               1.074748e+00, 1.223700e-01),4),
             ncol = 4) %>% t()

f <- sar_countryside(data, ubiSp = TRUE,
                     habNam = c("AG", "SH", "F"),
                     startPar  = SP)

SP2 <- matrix(rep(c(5, 1,
                   0.5),2),
             ncol = 2) %>% t()

data(habitat)
#Fit the models in log-log space
s <- sar_habitat(data = habitat, 
                 modType = "power",
                 con = NULL, logT = log,
                 startPar = SP2)


SP2 <- matrix(rep(c(5, 1, 0.5),2), ncol = 2) %>% t()
s <- sar_habitat(data = habitat, modType = "power",
                con = NULL, logT = log, startPar = SP2)


#define CSAR 2 - used to estimate total species
CountrysideSAR2<-function(a1,a2,a3,par)
{
  species<-(a1*par[1]+par[2]*a2+par[3]*a3)^par[4]
  names(species)<-NULL
  species
}

# determine total species
TotalCSAR <- function (a1,a2,a3, f)
{
  sp.AG<-CountrysideSAR2(a1,a2,a3,coef(f[[1]]))
  sp.UB<-CountrysideSAR2(a1,a2,a3,coef(f[[4]]))	
  sp.SH<-CountrysideSAR2(a1,a2,a3,coef(f[[2]]))
  sp.QF<-CountrysideSAR2(a1,a2,a3,coef(f[[3]]))
  sp.AG+sp.SH+sp.QF+sp.UB
}

TotalCSAR(1,2,3,f)