Description Usage Arguments Details Value Examples
rt_runGrid
is the main function of the rtsetse package to run a spatial simulation
1 2 3 4 5 6 7 8 9 10 11 12 13 | rt_runGrid(mVegCats = array(c("D", "T", "O", "S", "N", "N"), dim = c(2, 3)),
dfMortByVeg = data.frame(code = c("D", "T", "O", "S", "B", "G", "N"),
mortality = c(200, 150, 110, 100, 110, 210, 999), pupmortality = c(120, 110,
105, 100, 120, 170, 999), stringsAsFactors = FALSE),
dfMoveByVeg = data.frame(code = c("D", "T", "O", "S", "B", "G", "N"), move =
c(0.85, 0.9, 0.95, 1, 1.05, 1.1, 0)), iBestVeg = 4, pMoveF = 0.6,
pMoveM = 0.3, iDays = 4, iMaxAge = 120, iCarryCapF = 200,
fMperF = 0.5, fStartPopPropCC = 1, pMortF = 0.05, pMortM = 0.05,
iMortMinAgeStart = 10, iMortMinAgeStop = 50, fMortMinProp = 0.2,
fMortOldProp = 0.3, propMortAdultDD = 0.25, pMortPupa = 0.25,
propMortPupaDD = 0.25, iPupDurF = 26, iPupDurM = 28, iFirstLarva = 16,
iInterLarva = 10, pMortLarva = 0.05, propMortLarvaDD = 0.25,
pControl = 0, iControlBorder = 8, verbose = FALSE, report = NULL)
|
mVegCats |
a matrix or filepath for a map of vegetation codes |
dfMortByVeg |
a dataframe or filepath to a lookup table specifying mortality multiplier (percent) for each vegetation type |
dfMoveByVeg |
dataframe specifying a movement multiplier for each vegetation category |
iBestVeg |
the index of the preferred vegetation for this species, used in influencing movement |
pMoveF |
probability of F moving between cells |
pMoveM |
probability of M moving between cells |
iDays |
days to run simulation |
iMaxAge |
max age of fly allowed in model (will warn if flies age past this) |
iCarryCapF |
carrying capacity of adult females |
fMperF |
numbers of males per female, default 0.5 for half as many M as F |
fStartPopPropCC |
starting population as a proportion of carrying capacity, default = 1 option "sameAsAdults" to set tot pupae same as tot adults. |
pMortF |
adult female mortality on day1, rates on later days are determined by following parameters. |
pMortM |
adult male mortality on day1, rates on later days are determined by following parameters. |
iMortMinAgeStart |
Age at which min death rates start. |
iMortMinAgeStop |
Age at which min death rates stop. |
fMortMinProp |
What proportion of the maximum death rate on day 0 is the minimum death rate. |
fMortOldProp |
What proportion of the maximum death rate on day 0 is the death rate after iDeathMinAgeStop. |
propMortAdultDD |
proportion of adult mortality that is density dependent |
pMortPupa |
pupal mortality per period |
propMortPupaDD |
proportion of pupal mortality that is density dependent |
iPupDurF |
days it takes pupa(F) to develop |
iPupDurM |
days it takes pupa(M) to develop |
iFirstLarva |
Age that female produces first larva |
iInterLarva |
Inter-larval period |
pMortLarva |
larval mortality per period |
propMortLarvaDD |
proportion of larval mortality that is density dependent |
pControl |
extra mortality probability due to control, first go at implementing control. TODO improve this |
iControlBorder |
width (in cells) of border area not to control |
verbose |
print what it's doing T/F |
report |
filename for a report for this run, if not specified no report is produced |
This accepts a grid of vegetation and how mortality varies by vegetation.
a multi-dimensional array [day,y,x,sex,ages]
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
tst <- rt_runGrid()
rtPlotMapPop(tst)
#now try an unequal matrix
mCarryCapF <- matrix( 10*(1:16), 4, 4)
tst <- rt_runGrid(mCarryCapF)
rtPlotMapPop(tst)
#an unequal matrix starting at a fraction of CC
tst <- rt_runGrid(mCarryCapF, fStartPopPropCC = 0.5)
rtPlotMapPop(tst)
## End(Not run)
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