-
Notifications
You must be signed in to change notification settings - Fork 0
/
GA_prep.R
124 lines (97 loc) · 4.51 KB
/
GA_prep.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
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
### hisafe-calibration
### GA PREP
### Author: Kevin J. Wolz
ga.path <- "/Users/kevinwolz/Desktop/RESEARCH/ACTIVE_PROJECTS/HI-SAFE/hisafe-GA/"
input.path <- "/Users/kevinwolz/Desktop/RESEARCH/ACTIVE_PROJECTS/HI-SAFE/hisafe-calibration/raw_data/"
default.path <- paste0(ga.path, "default_folders/")
dir.create(default.path, showWarnings = FALSE, recursive = TRUE)
A3 <- define_hisafe(path = default.path,
profiles = "all-private",
template = "restinclieres_agroforestry_A3",
SimulationName = "A3",
weatherFile = A3.WEATHER)
A2 <- define_hisafe(path = default.path,
profiles = "all-private",
template = "restinclieres_agroforestry_A2",
SimulationName = "A2",
weatherFile = A2.WEATHER)
A4 <- define_hisafe(path = default.path,
profiles = "all-private",
template = "restinclieres_forestry_A4",
SimulationName = "A4",
weatherFile = A4.WEATHER)
A2.MC <- define_hisafe(path = default.path,
profiles = "all-private",
template = "restinclieres_monocrop_A2",
SimulationName = "A2MC",
weatherFile = A2.WEATHER)
##### BULID DEFAULT FOLDERS #####
default.files <- c("tec", "plt", "pro", "par", "pld", "wth")
build_hisafe(hip = A3,
files = default.files,
plot.scene = FALSE,
summary.files = FALSE)
dum <- file.copy(from = paste0(input.path, "A3.rootcal"),
to = paste0(default.path, "A3/A3.rootcal"))
dum <- file.copy(from = paste0(input.path, "A3.dbhcal"),
to = paste0(default.path, "A3/A3.dbhcal"))
build_hisafe(hip = A2,
files = default.files,
plot.scene = FALSE,
summary.files = FALSE)
dum <- file.copy(from = paste0(input.path, "A2.dbhcal"),
to = paste0(default.path, "A2/A2.dbhcal"))
build_hisafe(hip = A4,
files = default.files,
plot.scene = FALSE,
summary.files = FALSE)
dum <- file.copy(from = paste0(input.path, "A4.dbhcal"),
to = paste0(default.path, "A4/A4.dbhcal"))
build_hisafe(hip = A2.MC,
files = default.files,
plot.scene = FALSE,
summary.files = FALSE)
##### BULID TEMPLATE FOLDERS #####
template.path <- paste0(ga.path, "templates/")
dir.create(template.path, showWarnings = FALSE, recursive = TRUE)
A2$path <- A3$path <- A4$path <- A2.MC$path <- template.path
A3$profiles <- c("annualDBH")
A2$profiles <- c("annualDBH", "annualCellsYield")
A4$profiles <- c("annualDBH")
A2.MC$profiles <- c("annualCellsYield")
template.files <- c("sim", "tree")
build_hisafe(hip = A3,
files = template.files,
plot.scene = FALSE,
summary.files = FALSE)
build_hisafe(hip = A2,
files = template.files,
plot.scene = FALSE,
summary.files = FALSE)
build_hisafe(hip = A4,
files = template.files,
plot.scene = FALSE,
summary.files = FALSE)
build_hisafe(hip = A2.MC,
files = "sim",
plot.scene = FALSE,
summary.files = FALSE)
##### CREATE INITIAL POP FOR REOUND 2 #####
pop.archive1 <- read_csv("/Users/kevinwolz/Desktop/RESEARCH/ACTIVE_PROJECTS/HI-SAFE/SUPPORT/hisafe-GA-ROUND1/output/pop_archive.csv")
new.init.pop <- pop.archive1 %>%
filter(A2 != A3 & A2 != A4) %>%
distinct(gen.id, .keep_all = TRUE) %>%
arrange(VOL) %>%
filter(VOL < 23)# %>%
#select(lueMax:treeMinTranspirationPotential)
#write_csv(new.init.pop, "/Users/kevinwolz/Desktop/RESEARCH/ACTIVE_PROJECTS/HI-SAFE/hisafe-GA/input/INITIAL_POP.csv")
# new.init.pop %>%
# select(orig.gen, gen.id) %>%
# dplyr::mutate(gen = 27, id = 1:nrow(.)) %>%
# write_csv("/Users/kevinwolz/Desktop/RESEARCH/ACTIVE_PROJECTS/HI-SAFE/SUPPORT/hisafe-GA-ROUND1/round2_initial_pop_info.csv")
end.GA1.pop <- pop.archive1 %>%
filter(gen == max(gen))
init.surv <- read_csv("/Users/kevinwolz/Desktop/RESEARCH/ACTIVE_PROJECTS/HI-SAFE/hisafe-GA/inital_gen_surv_ids.csv")
nrow(init.surv)
hist(end.GA1.pop$orig.gen) #end of GA1 orig hist
hist(new.init.pop$orig.gen[init.surv$gen.id]) #end of GA2 first round of selection hist