# load some packages
# source some files
#
options(shiny.trace = F) # change to T for trace
require(shiny)
require(shinyFiles)
require(shinyIncubator)
require(igraph)
source("utils.R")
source("mig.matrix.R")
source("simcoal-history.R")
source("../skeleSim.classes.R")
source("../fastsimcoal/fsc.run.R")
source("../fastsimcoal/fsc.classes.R")
source("../fastsimcoal/fsc.scenarioCheck.R")
source("../rmetasim/rms.run.R")
source("../rmetasim/rms.classes.R")
source("../rmetasim/rms.scenarioCheck.R")
###these two globals record a record of the last
###click on the history graphs
lstclick <- NULL #last click
lstdblclick <- NULL #last double click
####### helper functions
#######
ssClassInit <- function(){ #Just creates a skelesim class instance with one scenario
ssClass <- new("skeleSim.params")
##### just a placeholder !!!!!!!! #######
##### need to include actual rep analyses
ssClass@rep.analysis.func <- function(params) {
result = rnorm(5)
names(result) <- paste("result", 1:5, sep = ".")
params@rep.result <- result
params
}
##############################################
ssClass@scenarios <- list(new("scenario.params"))
#default values for ssClass@scenarios (could be set in class definition)
ssClass@scenarios[[1]]@num.pops <- 1
ssClass@scenarios[[1]]@pop.size <- 100
ssClass@scenarios[[1]]@sample.size <- 10
ssClass@scenarios[[1]]@migration <- list(matrix(0,nrow=1,ncol=1))
ssClass@scenarios[[1]]@mig.helper <-
list(migModel="island",migRate=1,rows=1,cols=1,distfun="dexp")
ssClass@scenarios[[1]]@num.loci <- 1
ssClass@scenarios[[1]]@sequence.length <- 100
ssClass@scenarios[[1]]@mut.rate <- 10e-5
ssClass@scenarios[[1]]@simulator.params <-
new("fastsimcoal.params") #this will be changed if necessary reactively
ssClass
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.