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r_function_century_simulations.R
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r_function_century_simulations.R
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##################################################################
#' Claudinei Oliveira dos Santos
#' Biologo | Msc. Ecologia | Dr. Ciências Ambientais
#' LAPIG - UFG
##################################################################
##
#' Packages, functions and configurations
options(scipen = 9999)
###
#' function century simulation
#' por padrão os argumentos opcionais são os últimos;
runCentury <- function(sch_eq_i = NULL,
cem_eq_i = NULL,
sch_lu_i = NULL,
cem_lu_i = NULL,
wth_lu_i = NULL,
dir_proj = NULL,
dir_ptos = NULL,
dir_cent = NULL,
dir_rest = NULL,
run_what = c("eq_cm",
"lu_cm",
"lu_cr"
)
){
path_proj <- dir_proj
if (run_what == "eq_cm") {
print("Rodar century para o equilibrio")
file.copy(from = sch_eq_i,
to = dir_cent
)
file.copy(from = cem_eq_i,
to = dir_cent
)
rename_eq_sch <- paste0(dir_cent,
'/eq_site.sch'
)
rename_eq_100 <- paste0(dir_cent,
'/eq_site.100'
)
file.rename(
str_replace(sch_eq_i,
dir_ptos,
dir_cent
),
rename_eq_sch
)
file.rename(
str_replace(cem_eq_i,
dir_ptos,
dir_cent
),
rename_eq_100
)
setwd(dir_cent)
system('century -s eq_site -n eq_site')
system('list100 eq_site eq_site output.txt')
setwd(path_proj)
bin_eq_site_i <- str_replace(rename_eq_sch,
'.sch',
'.bin'
)
lis_eq_site_i <- str_replace(rename_eq_sch,
'.sch',
'.lis'
)
bin_eq_i <- gsub("100",
"bin",
gsub(dir_ptos,
dir_rest,
cem_eq_i)
)
lis_eq_i <- gsub("100",
"lis",
gsub(dir_ptos,
dir_rest,
cem_eq_i)
)
file.copy(from = bin_eq_site_i,
to = bin_eq_i,
overwrite = FALSE
)
file.copy(from = lis_eq_site_i,
to = lis_eq_i,
overwrite = FALSE
)
file.remove(bin_eq_site_i,
lis_eq_site_i,
rename_eq_sch,
rename_eq_100
)
} else if (run_what == "lu_cm") {
print("Rodar century para o land use com clima medio")
file.copy(from = sch_eq_i,
to = dir_cent
)
file.copy(from = cem_eq_i,
to = dir_cent
)
file.copy(from = sch_lu_i,
to = dir_cent
)
file.copy(from = cem_lu_i,
to = dir_cent
)
rename_eq_sch <- paste0(dir_cent,
'/eq_site.sch'
)
rename_eq_100 <- paste0(dir_cent,
'/eq_site.100'
)
rename_lu_sch <- paste0(dir_cent,
'/lu_site.sch'
)
rename_lu_100 <- paste0(dir_cent,
'/lu_site.100'
)
file.rename(str_replace(sch_eq_i,
dir_ptos,
dir_cent
),
rename_eq_sch
)
file.rename(str_replace(cem_eq_i,
dir_ptos,
dir_cent
),
rename_eq_100
)
file.rename(str_replace(sch_lu_i,
dir_ptos,
dir_cent
),
rename_lu_sch
)
file.rename(str_replace(cem_lu_i,
dir_ptos,
dir_cent
),
rename_lu_100
)
setwd(dir_cent)
system('century -s eq_site -n eq_site')
system('list100 eq_site eq_site output.txt')
system('century -s lu_site -n lu_site -e eq_site')
system('list100 lu_site lu_site output.txt')
setwd(path_proj)
bin_eq_site_i <- str_replace(rename_eq_sch,
'.sch',
'.bin'
)
lis_eq_site_i <- str_replace(rename_eq_sch,
'.sch',
'.lis'
)
bin_lu_site_i <- str_replace(rename_lu_sch,
'.sch',
'.bin'
)
lis_lu_site_i <- str_replace(rename_lu_sch,
'.sch',
'.lis'
)
bin_eq_i <- gsub("100",
"bin",
gsub(dir_ptos,
dir_rest,
cem_eq_i)
)
lis_eq_i <- gsub("100",
"lis",
gsub(dir_ptos,
dir_rest,
cem_eq_i)
)
bin_lu_i <- gsub("100",
"bin",
gsub(dir_ptos,
dir_rest,
cem_lu_i)
)
lis_lu_i <- gsub("100",
"lis",
gsub(dir_ptos,
dir_rest,
cem_lu_i)
)
# file.copy(from = bin_eq_site_i,
# to = bin_eq_i,
# overwrite = FALSE
# )
# file.copy(from = lis_eq_site_i,
# to = lis_eq_i,
# overwrite = FALSE
# )
file.copy(from = bin_lu_site_i,
to = bin_lu_i,
overwrite = FALSE
)
file.copy(from = lis_lu_site_i,
to = lis_lu_i,
overwrite = FALSE
)
file.remove(bin_eq_site_i,
lis_eq_site_i,
bin_lu_site_i,
lis_lu_site_i,
rename_eq_sch,
rename_eq_100,
rename_lu_sch,
rename_lu_100
)
} else if (run_what == "lu_cr") {
print("Rodar century para o land use com clima real")
file.copy(from = sch_eq_i,
to = dir_cent
)
file.copy(from = cem_eq_i,
to = dir_cent
)
file.copy(from = sch_lu_i,
to = dir_cent
)
file.copy(from = cem_lu_i,
to = dir_cent
)
file.copy(from = wth_lu_i,
to = dir_cent
)
rename_eq_sch <- paste0(dir_cent,
'/eq_site.sch'
)
rename_eq_100 <- paste0(dir_cent,
'/eq_site.100'
)
rename_lu_sch <- paste0(dir_cent,
'/lu_site.sch'
)
rename_lu_100 <- paste0(dir_cent,
'/lu_site.100'
)
rename_lu_wth <- paste0(dir_cent,
'/lu_site.wth'
)
file.rename(str_replace(sch_eq_i,
dir_ptos,
dir_cent
),
rename_eq_sch
)
file.rename(str_replace(cem_eq_i,
dir_ptos,
dir_cent
),
rename_eq_100
)
file.rename(str_replace(sch_lu_i,
dir_ptos,
dir_cent
),
rename_lu_sch
)
file.rename(str_replace(cem_lu_i,
dir_ptos,
dir_cent
),
rename_lu_100
)
file.rename(str_replace(wth_lu_i,
dir_ptos,
dir_cent
),
rename_lu_wth
)
setwd(dir_cent)
system('century -s eq_site -n eq_site')
system('list100 eq_site eq_site output.txt')
system('century -s lu_site -n lu_site -e eq_site')
system('list100 lu_site lu_site output.txt')
setwd(dir_proj)
bin_eq_site_i <- str_replace(rename_eq_sch,
'.sch',
'.bin'
)
lis_eq_site_i <- str_replace(rename_eq_sch,
'.sch',
'.lis'
)
bin_lu_site_i <- str_replace(rename_lu_sch,
'.sch',
'.bin'
)
lis_lu_site_i <- str_replace(rename_lu_sch,
'.sch',
'.lis'
)
bin_eq_i <- gsub("100",
"bin",
gsub(dir_ptos,
dir_rest,
cem_eq_i
)
)
lis_eq_i <- gsub("100",
"lis",
gsub(dir_ptos,
dir_rest,
cem_eq_i
)
)
bin_lu_i <- gsub("100",
"bin",
gsub(dir_ptos,
dir_rest,
cem_lu_i
)
)
lis_lu_i <- gsub("100",
"lis",
gsub(dir_ptos,
dir_rest,
cem_lu_i
)
)
# file.copy(from = bin_eq_site_i,
# to = bin_eq_i,
# overwrite = FALSE
# )
# file.copy(from = lis_eq_site_i,
# to = lis_eq_i,
# overwrite = FALSE
# )
file.copy(from = bin_lu_site_i,
to = bin_lu_i,
overwrite = FALSE
)
file.copy(from = lis_lu_site_i,
to = lis_lu_i,
overwrite = FALSE
)
file.remove(bin_eq_site_i,
lis_eq_site_i,
bin_lu_site_i,
lis_lu_site_i,
rename_eq_sch,
rename_eq_100,
rename_lu_sch,
rename_lu_100,
rename_lu_wth
)
} else {
print("choose a option to century simulation: eq_cm, lu_cm or lu_cr")
}
}
###
#' change files
changFILES <- function(changeFrom, changeTo, l1, l2){
newFile <- readLines(changeFrom)
newFile[l1:l2] <- changeTo
write.table(newFile, changeFrom, quote = FALSE, row.names = FALSE, col.names = FALSE)
}
###
#'alterar parâmetros nos arquivos 100 por linhas
changFILES_linhaI <- function(changeFrom, changeTo, linha){
newFile <- readLines(changeFrom)
newFile[linha] <- changeTo
write.table(newFile, changeFrom, quote = FALSE, row.names = FALSE, col.names = FALSE)
}
###
#' gerar o wth
createCenturyWth <- function(x) {
if(!ncol(x) == 5){
print("The data frame must have five columns")
} else{
climateData = x
#reshape data (long to wide)
reshapeClimateData = as.data.frame(
t(
stats::reshape(climateData,
idvar = c("mes"),
v.names = c( "prec", "tmin", "tmax"),
timevar = "ano", direction = "wide")
)
)
names(reshapeClimateData) = 1:12
reshapeClimateData$Var = substr(rownames(reshapeClimateData), 1, 4)
reshapeClimateData$ano = substr(rownames(reshapeClimateData), 6, 9)
reshapeClimateData = reshapeClimateData[-1, c(13:14,1:12)]
# Format rows output to the same number of character
rowsClimateData = list()
for (i in 1:nrow(reshapeClimateData))
{
linha = reshapeClimateData[i,]
v_linha = as.vector(linha)
v_linha[,3:14] = sprintf("%.2f", round(v_linha[,3:14], 2))
v_linha = as.vector(as.character(v_linha))
for (j in 3:14) {
v_linha[j] = ifelse(nchar(v_linha[j]) < 5, paste0(" ", v_linha[j]), v_linha[j] )
}
v_linha = paste(v_linha, collapse = " ")
rowsClimateData[[i]] = v_linha
}
dfClimateData = do.call("rbind", rowsClimateData)
return(dfClimateData)
}
}
####################################################
#####################################################################