vdswim_impute.R

In jmarca/calvad_impute_trucks: CalVAD impute trucks at VDS sites

## need node_modules directories
dot_is <- getwd()
node_paths <- dir(dot_is,pattern='\\.Rlibs',
                  full.names=TRUE,recursive=TRUE,
                  ignore.case=TRUE,include.dirs=TRUE,
                  all.files = TRUE)
path <- normalizePath(node_paths, winslash = "/", mustWork = FALSE)
lib_paths <- .libPaths()
.libPaths(c(path, lib_paths))

print(.libPaths())

pkg <- devtools::as.package('.')
ns_env <- devtools::load_all(pkg,quiet = TRUE)$env

## need env for test file
config_file <- Sys.getenv('R_CONFIG')

if(config_file ==  ''){
    config_file <- 'config.json'
}
print(paste ('using config file =',config_file))
config <- rcouchutils::get.config(config_file)

## pass it the raw data details, and either the raw data will get
## loaded and parsed and saved as a dataframe, or else the existing
## dataframe will get loaded.  In either case, the plots will get made
## and saved to couchdb


library('RPostgreSQL')
m <- dbDriver("PostgreSQL")
con <-  dbConnect(m
                  ,user=config$postgresql$auth$username
                  ,host=config$postgresql$host
                  ,port=config$postgresql$port
                  ,dbname=config$postgresql$db)

vds_id = Sys.getenv(c('CALVAD_VDS_ID'))[1]
if('' == vds_id){
  print('assign a vds_id to process to the CALVAD_VDS_ID environment variable')
  stop(1)
}
vds_id <- as.numeric(vds_id)

year = as.numeric(Sys.getenv(c('CALVAD_YEAR'))[1])
if('' == year){
  print('assign the year to process to the CALVAD_YEAR environment variable')
  stop(1)
}

vds_path = Sys.getenv(c('CALVAD_VDS_PATH'))[1]
if('' == vds_path){
    if(! is.null(config$calvad$vdspath) && config$calvad$vdspath != '' ){
        vds_path <- config$calvad$vdspath
    }
}
if('' == vds_path){
    print('assign a path to find the imputed vds data to the CALVAD_VDS_PATH environment variable or set calvad: {vdspath : /the/vds/path} in the config file')
    stop(1)
}

output_path <- Sys.getenv(c('CALVAD_OUTPUT_PATH'))[1]
if('' == output_path || is.null(output_path)){
    if(! is.null(config$calvad$outputpath) && config$calvad$outputpath != '' ){
        output_path <- config$calvad$outputpath
    }
}
if('' == output_path || is.null(output_path)){
    print(paste('CALVAD_OUTPUT_PATH environment variable is not set and no entry in config file under calvad:{outputpath:...}, so setting output path to',vds_path))
    output_path <- vds_path
}

maxiter = Sys.getenv(c('CALVAD_VDSWIM_IMPUTE_MAXITER'))[1]
if(is.null(maxiter)){
    maxiter=200
}
maxiter <- as.numeric(maxiter)

wim_pairs = Sys.getenv(c('CALVAD_WIM_PAIRS'))[1]
if(is.null(wim_pairs) || '' == wim_pairs){
    print(paste('assign the wim_pairs for site',vds_id,'to the CALVAD_WIM_PAIRS environment variable',collapse=' '))
    stop(1)
}
## need to convert the CSV string of wim_pairs info into a proper R list
w_p.df <- as.data.frame(matrix(data=strsplit(x=wim_pairs,split=',')[[1]],ncol=3,byrow=TRUE),stringsAsFactors=FALSE)
w_p.df[,1] <- as.numeric(w_p.df[,1])
w_p.df[,2] <- as.numeric(w_p.df[,2])


wim_pairs <- list()
for(i in 1:length(w_p.df[,1])){
    wim_pairs[[i]] <- list(vds_id=w_p.df[i,1],
                           wim_site=w_p.df[i,2],
                           direction=w_p.df[i,3])
}
print(paste('calling impute with options',
            paste(c(vds_id,
                    wim_pairs,
                    year,
                    vds_path,
                    output_path,
                    maxiter,
                    config$couchdb$trackingdb)
                    ,collapse=' ',sep=',')
                  ))

result <- impute.vds.site(vds_id=vds_id,
                          wim_pairs=wim_pairs,
                          year=year,
                          vds_path=vds_path,
                          output_path=output_path,
                          maxiter=maxiter,
                          trackingdb=config$couchdb$trackingdb
                          )

print(paste('imputation output saved to',result))
quit(save='no',status=10)