estab: Bioentity establishment or not at each node

In GarrettLab/SeaMonster2: Test

Description

This function determines whether a bioentity establishes or not at each node. It is similar in some ways to the function makedec, which determines whether management is adopted.

Usage

estab(
  decvec,
  dispvec,
  probestabmean4,
  probestabsd4,
  maneffdir4,
  maneffmean4n,
  maneffsd4n,
  plotmp = F,
  geocoords4n,
  readprobestabvec4,
  probestabvec4
)

Arguments

decvec	vector of 1=management, 0=no management
dispvec	vector of 1=sp has dispersed to node, 0=sp has not dispersed to node
probestabmean4	mean probability of establishment (new or CONTINUED) in absence of management (used if readprobestabvec4 = F)
probestabsd4	sd in probability of establishment in absence of management (used if readprobestabvec4 = F)
maneffdir4	if maneffdir4='decrease_estab', the management reduces the probability of establishment; if maneffdir4='increase_estab', the management reduces the probability that establishment does NOT occur
maneffmean4n	mean effect of management (proportional change in estabp, where the combination of maneffmean4n = 1 and maneffsd4n = 0 makes establishment impossible)
maneffsd4n	sd of management effect
plotmp	if T, then map of establishment is plotted
geocoords4n	matrix of x,y coordinates of nodes (used if plotmp = T)
readprobestabvec4	if T, then a vector probestabvec4 is read in; otherwise the vector is generated using probestabmean4 and probestabsd4
probestabvec4	vector of probabilities of establishment (read in or generated when the function is run, depending on readprobestabvec4 equal to T or F)

Details

Updated 2020-09-05

Examples

x6decrease <- estab(decvec=c(1,1,1,0,0,0), dispvec=c(1,1,1,1,1,0), geocoords4n=matrix(c(1,1, 1,2, 1,3, 2,1, 2,2, 2,3), byrow=T, ncol=2), readprobestabvec4=F, probestabmean4=0.5, probestabsd4=0.1, maneffdir4='decrease_estab', maneffmean4n=0.1, maneffsd4n=0.1, plotmp=T)
x7decrease <- estab(decvec=c(1,1,1,0,0,0), dispvec=c(1,1,1,1,1,0), geocoords4n=matrix(c(1,1, 1,2, 1,3, 2,1, 2,2, 2,3), byrow=T, ncol=2), readprobestabvec4=F, probestabmean4=0.5, probestabsd4=0.1, maneffdir4='decrease_estab', maneffmean4n=0.9, maneffsd4n=0.1, plotmp=T)
x8decrease <- estab(decvec=c(1,1,1,0,0,0), dispvec=c(1,1,1,1,1,0), geocoords4n=matrix(c(1,1, 1,2, 1,3, 2,1, 2,2, 2,3), byrow=T, ncol=2), readprobestabvec4=T, probestabvec4=c(0.9,0.1,0.1,0.1,0.1,0.9), maneffdir4='decrease_estab', maneffmean4n=0.9, maneffsd4n=0.1, plotmp=T)
x9decrease <- estab(decvec=c(1,1,1,0,0,0), dispvec=c(1,1,1,1,1,0), geocoords4n=matrix(c(1,1, 1,2, 1,3, 2,1, 2,2, 2,3), byrow=T, ncol=2), readprobestabvec4=T, probestabvec4=c(0.9,0.1,0.1,0.1,0.1,0.9), maneffdir4='decrease_estab', maneffmean4n=0.1, maneffsd4n=0.1, plotmp=T)
x6increase <- estab(decvec=c(1,1,1,0,0,0), dispvec=c(1,1,1,1,1,0), geocoords4n=matrix(c(1,1, 1,2, 1,3, 2,1, 2,2, 2,3), byrow=T, ncol=2), readprobestabvec4=F, probestabmean4=0.5, probestabsd4=0.1, maneffdir4='increase_estab', maneffmean4n=0.1, maneffsd4n=0.1, plotmp=T)
x7increase <- estab(decvec=c(1,1,1,0,0,0), dispvec=c(1,1,1,1,1,0), geocoords4n=matrix(c(1,1, 1,2, 1,3, 2,1, 2,2, 2,3), byrow=T, ncol=2), readprobestabvec4=F, probestabmean4=0.5, probestabsd4=0.1, maneffdir4='increase_estab', maneffmean4n=0.9, maneffsd4n=0.1, plotmp=T)
x8increase <- estab(decvec=c(1,1,1,0,0,0), dispvec=c(1,1,1,1,1,0), geocoords4n=matrix(c(1,1, 1,2, 1,3, 2,1, 2,2, 2,3), byrow=T, ncol=2), readprobestabvec4=T, probestabvec4=c(0.9,0.1,0.1,0.1,0.1,0.9), maneffdir4='increase_estab', maneffmean4n=0.9, maneffsd4n=0.1, plotmp=T)
x9increase <- estab(decvec=c(1,1,1,0,0,0), dispvec=c(1,1,1,1,1,0), geocoords4n=matrix(c(1,1, 1,2, 1,3, 2,1, 2,2, 2,3), byrow=T, ncol=2), readprobestabvec4=T, probestabvec4=c(0.9,0.1,0.1,0.1,0.1,0.9), maneffdir4='increase_estab', maneffmean4n=0.1, maneffsd4n=0.1, plotmp=T)

GarrettLab/SeaMonster2 documentation built on Dec. 17, 2021, 9:27 p.m.