-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathLutjanus_kasmira_ctrl_Marquesas_parameters.R
61 lines (52 loc) · 4.99 KB
/
Lutjanus_kasmira_ctrl_Marquesas_parameters.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
#### Parameters for seaINVADERS.R model #####
NP <- 20 #Number of processors to use
MODEL_DURATION <- 2 #Number of years to run the model
NUM_BOOTSTRAPS <- 2 #Number of simulations to run with each source
#### Population Genetic Parameters ####
species <- "LutKas"
source.name <- "Marquesas"
#source.hap <- c(3,1,0,0,0,0,1,0,0,0,1,1,0,0,0,1,1,1,1,0,0,0,0,0,0,1,0,0,0,0,1,0,1,1,1,0,0,0,0,0,1,0,0,0,0,1,1,0,0,1,0,1,1,0,1,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,0,0,0,0,1,1,1,0,0,0,2,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,1,0,1,1,0,1,0,0,0,1,0,0,1,0,0,1,1,0,1,1,0,1)
source.hap <- c(1,2,0,0,0,0,3,1,1,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,0,0,0,0,1,1,0,1,0,1,0,0,0,0,1,1,1,0,1,0,0,0,1,0,1,0,0,1,1,0,1,1,0,1,1,0,0,0,0,1,0,0,0,1,0,0,0,1,1,1,1,0,0,0,0,0,0,1,0,0,0,0,1,0,1,1,1,0,0,0,0,0,1,0,0,0,0,1,1,0,0,1,0,1,1,0,1,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0)
#source.thetas <- c(14.958010 + (seq(-2,2,2)* 4.455406) #theta(S)
#source.thetas <- c(149,376,1062) #list of thetas to run, must comment out source.theta and source.theta.sd or this will be ignored, use Theta(k) from Arlequin
destination.name <- "Hawaii"
#destination.hap <- c(10,3,1,2,2,3,2,9,3,3,0,0,3,1,2,0,0,1,0,2,4,2,1,4,3,0,4,3,1,1,2,2,0,0,0,6,4,2,1,2,0,2,1,1,1,0,2,2,3,0,1,1,1,1,0,1,1,3,1,4,1,1,1,3,1,1,3,0,5,1,1,2,1,1,0,1,1,1,1,4,1,1,2,1,1,1,2,1,4,1,1,1,1,2,2,1,1,1,1,3,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,2,0,4,1,2,1,1,2,0,0,3,0,4,18,0,0,1,0,1,2,0,5,1,2,1,0,2,3,1,2,2,4,0,0,3,0,3,4,1,0,2,3,0,2,1,0,0,1,4,1,1,0)
destination.hap <- c(3,0,1,5,4,3,10,0,1,4,4,3,3,1,3,1,1,1,1,1,2,0,4,1,2,1,1,2,0,0,1,2,1,0,2,3,1,2,2,0,0,3,0,3,4,1,0,2,0,2,1,0,0,1,4,1,1,0,3,1,2,2,3,2,9,3,3,0,3,1,2,0,0,1,0,2,4,2,1,4,3,0,4,3,1,1,2,2,0,0,0,6,4,2,1,2,0,2,1,1,1,0,2,2,3,0,1,1,1,1,0,1,1,3,1,4,1,1,1,3,1,1,3,0,5,1,2,1,1,0,1,1,1,1,1,1,2,1,1,1,2,1,1,1,1,1,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)
dest.gendiv <- c(0.9926,0.0011) #(mean,stdev)
#dest.theta <- c(119.017997) #c() list of thetas to run, use Theta(k) from Arlequin, comment out if haplotype vector adequately describes diversity of entire population
#### Demographic Parameters for Model ####
MONTHS <- 12 #Number of "months" or portions to divide a year into (age repro mat)
thin <- FALSE # Save only first and last month of simulated pops?
min_prop <- 4 #This is the minimum proportion of successful recruits relative to that of the demographic parameters in the literature
max_prop <- 10 #This is the maximum proportion of successful recruits relative to that of the demographic parameters in the literature
prop_bins <- 2 #ex. If prop_increment=4, then 4 different props will be run, ex: (.25,.5,.75,1)
min_f_number <- 20 #This is the minimum # of colonizing females.
max_f_number <- 100 #This is the maximum # of colonizing females.
f_bins <- 19 #ex. If f_increment=3, then three different numbers of female colonists will be run (min, min+(max-min)/2,max)
BIN <- 12 # Number of different age-classes
JUVI.MORT <- 0.395 # Juvenile mortality ***too high?
ADULT.MORT <- 0.0083 # Adult mortality
ADULT.FRAC <- 1 # Fraction of starting population that are adults*
ADULT.FEM.FRAC <- 0.54128 # Proportion of adults that are females
ADULT.FEM.MAT <- 0.6004 # Proportion of females that are mature
FE <- 11986.11 # Fecundity - number of eggs per female per month ***too low?
ME <- 0.1583 # Egg mortality (per day)
DE <- 0.778 # Egg duration (days)
ML <- 0.34884 # Larval mortality (per day)
DL <- 20.4 # Larval duration (days)
K <- 1000000 #Carrying capacity, used to modulate "birth rate" for logistic pop growth
## Standard deviations of each parameter (not in Jason's model)
# Most recently updated by Gray on 4_8_2019
#SR.sd <- ? #Spawning rate standard deviation
#FE.sd <- 6279.28 #Fecundinty standard deviation
#ME.sd <- 2.5 #Egg mortality standard deviation
#DE.sd <- 0.339 #Egg duration standard deviation
#ML.sd <- 0.03453 #Larval mortality standard deviation
#DL.sd <- 0.5 #Larval duration standard deviation
#JUVI.MORT.sd <- ? #Juvenile mortality standard deviation
#JD.sd <- ? #Juvenile duration standard deviation
#ARM.sd <- ? #Age of reproductive maturity standard deviation
#ADULT.MORT.sd <- ? #Adult mortality standard deviation
#ADULT.FRAC.sd <- 0 #Proportion of starting population that are adults standard deviation
#ADULT.FEM.MAT.sd <- ? #Proportion of females that are mature standard deviation
#ADULT.FEM.FRAC.sd <- ? #Fraction of population that are females