In AndySouth/rtsetse: simulating tsetse fly populations

This is a report on the outputs produced from one run of the rtsetse model run from the UI locally. See end of the document for the rtsetse code to repeat this run of the model on the command line.

#removed this because of trickiness in getting the vegetation matrix not to print out
#Parameter values used in this run :

#the arguments and their values passed to rtsetse function
#17/9/14 trying to reimplement this, yes it works
#23/12/14 problem with veg matrix which comes out as long matrix
#print(unlist(lNamedArgsGrid))


#old approach getting list of inputs from Shiny
#but that was a problem once I had multiple navbar tabs
# #getting the named input vars from shiny
# lNamedArgs <- isolate(reactiveValuesToList(input))
# #shinyapps adds extra input vars starting ss-net* or checkbox*
# #I don't want these to appear in the report
# lNamedArgsSub <- lNamedArgs[ substring(names(lNamedArgs),1,3)!='ss-' & substring(names(lNamedArgs),1,8)!='checkbox' ]
# #to order the params alphabetically
# lNamedArgsSub <- lNamedArgsSub[ order(names(lNamedArgsSub)) ]
# #to stop it from using sci notation
# print(unlist(format(lNamedArgsSub,scientific=FALSE)))

Figure 1 Adult population over time summed for the whole grid.

rtPlotPopGrid(v$gridResults)

Figure 2 Map of adults across the grid on final day of the simulation.

rtPlotMapPop(v$gridResults, days='final', sex='both')

Figure 3 Maps of adults across the grid over the days of the simulation.

rtPlotMapPop(v$gridResults, days='all', ifManyDays='spread', sex='both')

Figure 4 Age structure over time, summed for M&F across the whole grid.

rtPlotAgeStructure(v$gridResults)

Figure 5 Mean age of adults over time, summed for the whole grid.

rtPlotMeanAgeGrid(v$gridResults)

\pagebreak Code to repeat this run of the model locally (copy & paste the whole lot into the R console) :

# string is created in server.r/printParamsGrid

#have to be careful the code doesn't go across a page in the pdf otherwise the copied & pasted bit won't run in R

#replace ,space with ,newlines to wordwrap in pdf
string2 <- gsub(", ",",\n",stringCodeRepeat)
writeLines(string2, sep='')

#this fails because text isn't wrapped
#cat(stringCodeRepeat,"\n")
#this fails because prints in weird format
#print(stringCodeRepeat)

#cat("the code should be above this ...")

# old way of doing had problems with the veg matrix
# sCommand <- "rt_runGridTestSpread"
# #this creates a vector of 'name=value,'
# vArgs <- paste0(names(lNamedArgsGrid),"=",lNamedArgsGrid,", ")
# #to remove the final comma & space in args list
# vArgs[length(vArgs)] <- substr(vArgs[length(vArgs)],0,nchar(vArgs[length(vArgs)])-2)
# cat( sCommand,"( ",vArgs," )",sep="")