Mercurial > repos > siwaa > redelac_stics_s

comparison redelacSticsSimulator.R @ 4:70ae7516e925 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/94d9549470e1fe96ae832b04bea58b2f1c5663fc/tools/REDELACSticsSimulator commit 94d9549470e1fe96ae832b04bea58b2f1c5663fc-dirty"
author siwaa
date Tue, 27 Jun 2023 06:47:30 +0000
parents f262814e48a3
children 41f652e6616f
comparison
equal deleted inserted replaced
3:f262814e48a3 4:70ae7516e925
6 6
7 workspace <- paste0(getwd(), "/WS") 7 workspace <- paste0(getwd(), "/WS")
8 javastics_path <- getwd() 8 javastics_path <- getwd()
9 default_config_path <- paste0(javastics_path, "/config") 9 default_config_path <- paste0(javastics_path, "/config")
10 10
11 # copy of the var.mod and rap.mod into the config folder
12 # generalizing maybe should be inside a config folder
13
14 #file.copy(from = file.path(workspace, "var.mod"),
15 # to = file.path(default_config_path, "var.mod"),
16 # overwrite = TRUE)
17 #file.copy(from = file.path(workspace, "rap.mod"),
18 # to = file.path(default_config_path, "rap.mod"),
19 # overwrite = TRUE)
20
21 txt_path <- paste0(getwd(), "/WS/txt_files") 11 txt_path <- paste0(getwd(), "/WS/txt_files")
22 #dir.create(txt_path,recursive = T)
23
24 #gen_usms_xml2txt(javastics = javastics_path,
25 # workspace = workspace,
26 # out_dir = txt_path,
27 # check = FALSE)
28 12
29 print("==================================") 13 print("==================================")
30 14
31 print(paste0("Cores=", detectCores())) 15 print(paste0("Cores=", detectCores()))
32 print(paste0("javastics=", javastics_path)) 16 print(paste0("javastics=", javastics_path))
33 print(paste0("ws=", workspace)) 17 print(paste0("ws=", workspace))
34 print(paste0("out_dir=", txt_path)) 18 print(paste0("out_dir=", txt_path))
35 19
36 print("==================================") 20 print("==================================")
37
38 21
39 # List of successive USMs 22 # List of successive USMs
40 successive_usms_file <- ("successionPlan.csv") 23 successive_usms_file <- ("successionPlan.csv")
41 successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";") 24 successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";")
42 25
49 32
50 #result <- foreach(i=1:nrow(successive_usms_tab), 33 #result <- foreach(i=1:nrow(successive_usms_tab),
51 # .packages = c("SticsRFiles", "SticsOnR") ) %dopar% { 34 # .packages = c("SticsRFiles", "SticsOnR") ) %dopar% {
52 for(i in 1:nrow(successive_usms_tab)) { 35 for(i in 1:nrow(successive_usms_tab)) {
53 36
54 print(paste("coucou ", i))
55 nusms <- as.numeric(successive_usms_tab[i,2]) 37 nusms <- as.numeric(successive_usms_tab[i,2])
56 print(paste0("coco ", nusms))
57 38
58 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))]) 39 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))])
59 40
60 list_successive_usms <- list(vec) 41 list_successive_usms <- list(vec)
61 42
63 stics_exe = paste0(javastics_path,"/bin/stics_modulo"), 44 stics_exe = paste0(javastics_path,"/bin/stics_modulo"),
64 workspace = txt_path, 45 workspace = txt_path,
65 verbose = TRUE, 46 verbose = TRUE,
66 successive = list_successive_usms) 47 successive = list_successive_usms)
67 list_usms <- vec 48 list_usms <- vec
68 49
69 result = append(result, stics_wrapper(model_options = sim_options, situation = list_usms)) 50 singleResult = stics_wrapper(model_options = sim_options, situation = list_usms)
51
52 result = append(result, list(singleResult))
70 } 53 }
71 54
72 #stopCluster(cl) 55 #stopCluster(cl)
73 56
74 for (i in 1:nrow(successive_usms_tab)) { #i=1 57 for (i in 1:nrow(successive_usms_tab)) { #i=1
75 if (i == 1) { 58 if (i == 1) {
76 simPCP <- result[[i]] 59 simPCP <- result[[i]]
77 } else { 60 } else {