-
Notifications
You must be signed in to change notification settings - Fork 1
/
R_RunScript.R
84 lines (69 loc) · 3.18 KB
/
R_RunScript.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
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
setwd("~/EvonetC")
options(warn = 2)
source("ProcessDefaultParams.R") # Reads in default parameters from a text file and puts them into R format
# User-specific parameters. These will over-write any default parameters with the same name.
user_base_params <- c(
tfinal = 365+100, ##The duration of the run
N0 = 50,
Num_Loci = 5,
replicates = 1,
Infected0 = 26,
prop_mut_locus3 = 1.0, # proportion of population w/ K103N mutation
fast_metab_prop = 0.60,
inter_metab_prop = 0.10,
slow_metab_prop = 0.30,
fast_decay3_change=1.0, # value of decay change for drug3
inter_decay3_change=1.0, # value of decay change for drug3
slow_decay3_change=1.0, # value of decay change for drug3
DrugDose1 = 50.0,
DrugDose2 = 50.0,
DrugDose3 = 50.0,
BaseIC50Drug1 = 100, BaseIC50Drug2 = 100, BaseIC50Drug3 = 100, BaseIC50Drug4 = 100,
FC_D1_Mut1 = 200.0, FC_D1_Mut2 = 1.0, FC_D1_Mut3 = 1.0, FC_D1_Mut4 = 10.0, FC_D1_Mut5 = 1.0,
FC_D2_Mut1 = 1.0, FC_D2_Mut2 = 300.0, FC_D2_Mut3 = 1.0, FC_D2_Mut4 = 2.0, FC_D2_Mut5 = 20.0,
FC_D3_Mut1 = 1.0, FC_D3_Mut2 = 1.0, FC_D3_Mut3 = 400.0, FC_D3_Mut4 = 1.0, FC_D3_Mut5 = 1.0,
FC_D4_Mut1 = 1.0, FC_D4_Mut2 = 1.0, FC_D4_Mut3 = 1.0, FC_D4_Mut4 = 1.0, FC_D4_Mut5 = 1.0,
drug_decay1 = 0.1, drug_decay2 = 0.1, drug_decay3 = 0.1,
Adherence1 = 1.0, Adherence2 = 1.0, Adherence3 = 1.0,
Start_Spontaneous_Treatment = 100,
Start_TasP_Campaign =100,
# stockout = 11250,
# restart = 11300,
AverageLogSP0 = 4.0,
VarianceLogSP0 = 1.0,
plt_AD = 0,
plt_NS = 1,
plt_AM = 0,
mu = 1e-4,
print_frequency = 10
)
# Run program with different drug decay rates
par(mfrow=c(2,2))
V0_vec<-c(0.001)
for (ii in 1: length(V0_vec)) {
user_run_params <- list(V0 = V0_vec[ii]) # Run-specific parameters
#Add loops for task 1 - Aim 2
source("UpdateParams.R") # Create file with user_base_params and user_run_params
# Compile program: CSDE server C:/Rtools ... / mingw64...gcc, MacOS: system("gcc -O3 EvoNetC.c")
if (system("C:/Rtools40/mingw64/bin/gcc EvoNetC_Aim3.c") != 0) {stop("Halting program due to complier error\n!")}
#if (system("gcc -O3 EvoNetC_Aim3.c -o a.exe") != 0) {stop("Halting program due to complier error\n!")}
system("./a.exe")
if (plt_GS == 1) source("Plot_Time_Series.R")
if (plt_NS == 1) source("Plot_Network_Stats.R")
if (plt_AM == 1) source("Plot_Age_Matches.R")
if (plt_AD == 1) source("Plot_Age_Distribution.R")
source("Plot_Percent_Resistant.R")
}
date_time <- format(Sys.time(), "%b_%d_%Y_at_%H_%M_%S")
##export AgentHistory.txt file
agenthistory <- read.delim("AgentHistory.txt")
agent_filename<-"agenthistory"
file_name <- paste(agent_filename,date_time, "_", sep="")
write.csv(agenthistory,paste0(file_name, "_fastdecayhigh_slowdecaylow_adh100_2reps_n500_inf_175_1yr_.csv"), row.names=TRUE)
##export CheckSSCMax.txt file
checksscmax <- read.delim("CheckSSCMax.txt")
sscmax_filename<-"CheckSSCMax"
file_name <- paste(sscmax_filename,date_time,"_", sep="")
write.csv(checksscmax,paste0(file_name, "_fastdecayhigh_slowdecaylow_adh100_2reps_n500_inf_175_1yr_.csv"), row.names=TRUE)
source("Plotting_SSCMax_VerifyOutput.R")
#PatientRegistryOutput <- read.delim("PatientRegistryOutput.txt")