+++ /dev/null
-## File : 00_convertir-donnnes_2009.r
-## Description : Converts flat EDF's 32K data into a full data matrix
-## layout [individuals, variables]. Rownames are EDF's ids.
-## We process the original flat file sequentially by lines
-## to avoid exceding the available RAM memory (and so avoiding
-## swaping which is a computational burden).
-
-
-rm(list = ls())
-
-# setwd("~/ownCloud/projects/2014_EDF-Orsay-Lyon2/codes")
-
-
-## 1. Read auxiliar data files ####
-
-identifiants <- read.table("identifs.txt")[ ,1]
-dates0 <- read.table("datesall.txt")[, 1]
-dates <- dates0[grep("2009", dates0)]
-rm(dates0)
-
-n <- length(identifiants)
-p <- length(dates)
-
-blocks <- c(rep(6000, 3), 7011) # We'll process 1000 x p lines at each
- # iteration of the reading loop
-
-## 2. Process the large flat file ####
-## We want to check that every time step recorded for each id.
-
-con <- file("~/tmp/data/2009.csv") # Establish a connection to the file
-open(con, "r") # Open the connection
-rien <- readLines(con = con, n = 1); rm(rien) # Discard 1st line
-
-for(b in seq_along(blocks)){ # Reading loop
- nb <- blocks[b]
- actual <- readLines(con = con, n = nb * length(dates))
- auxmat <- matrix(unlist(strsplit(actual, ",")), ncol = 4, byrow = TRUE)
- rm(actual)
- auxdf <- data.frame(id = as.integer(auxmat[, 1]),
- date = auxmat[, 2],
- val = as.numeric(
- ifelse(auxmat[,3] == "", auxmat[, 4], auxmat[, 3])))
- rm(auxmat) # free up some space
-
- tab <- table(auxdf$id)
- idtt <- NULL
- for(tt in as.integer(names(which(tab < p)))) { # id with less than p records!
- print(tt)
- idtt <- c(idtt, which(auxdf$id == tt))
- }
-
- idmat <- matrix(auxdf$id[-idtt], ncol = p, byrow = TRUE)
- alldatesperid <- apply(idmat[-idtt, ], 1, sd) == 0
- valmat <- matrix(auxdf$val[-idtt], ncol = p, byrow = TRUE)
-
- # store separatelly full records from partial records
- write.table(file = paste0("~/tmp/2009_full_", b, ".txt"), valmat,
- row.names = idmat[, 1], col.names = FALSE)
- write.table(file = paste0("~/tmp/2009_partial_", b, ".txt"), auxdf[idtt, ])
-}
-
-close(con) # close connection to the file
-
-rm(auxdf, idmat, valmat, alldatesperid, b, # clean up some memory
- idtt, blocks, tab, tt, con)
-
-
-## 3. Complete partial records ####
-## After analysis, partial records are only 119 clients from which one only
-## time step (01JAN2009:00:00:00) is lacking.
-
-df_partial <- NULL
-for(f in list.files("~/tmp/", "2009_partial_*"))
- df_partial <- rbind(df_partial, read.table(paste0('~/tmp/', f)))
-
-tab <- table(df_partial$id)
-id_incomp <- as.integer(names(which(tab < p))) # Incomplete records
-
-df_partial_full <- rbind(df_partial,
- data.frame(id = id_incomp,
- date = "01JAN2009:00:00:00",
- val = NA))
-
-rm(df_partial)
-
-# tab2 <- table(df_partial_full$id) # Check that df_partial_full is full
-# head(sort(tab2))
-
-
-## 4. Reorder the lines to get the data matrix ####
-## As we paste chunks of partial records and impute some time steps,
-## the original order of the data is broken. We fix it by reordering
-## the ids and then the data.
-
-idx_ordered <- order(df_partial_full$id) # order ids
-df_partial_full2 <- df_partial_full[idx_ordered, ]
-rm(df_partial_full)
-
-# Order data values following the correct dates (as the date is a factor
-# we need to seek for each value: this is computationnaly innefficient).
-
-valmat <- matrix(df_partial_full2$val, ncol = p, byrow = TRUE)
-datemat <- matrix(df_partial_full2$date, ncol = p, byrow = TRUE)
-idmat <- matrix(df_partial_full2$id, ncol = p, byrow = TRUE)
-
-# Use this for as a check by running it twice. On the second run no
-# printing should be done (because records should be ordered).
-for(line in 1:nrow(datemat)) {
- if(any(datemat[line, ] != dates)) { # TRUE is line is not ordered
- cat(sprintf("\nline %i is not ordered", line))
-
- neworder <- match(dates, datemat[line, ])
- valmat[line , ] <- valmat[ line, neworder]
- datemat[line , ] <- datemat[line, neworder]
- }
-}
-
-
-## 5. Write on disk the full data matrix of partial records ####
-
-write.table(file = "~/tmp/2009_full_Z.txt", valmat,
- row.names = idmat[, 1], col.names = FALSE)
-rm(list = ls())
-gc()
-
-## 6. Compile data files in BASH ####
-
-# cat 2009_full*.txt > 2009_full.txt
-# rm 2009_full_*.txt 2009_partial_*.txt
-
-
-## A. data.table & reshape2 ####
-## When large RAM memory is available, one could use this code to process
-## everything in memory.
-
-#library(data.table)
-#library(reshape2)
-
-#dt <- fread(input = "~/tmp/data/2009_chunk.csv")
-
-#dt[, charge := ifelse(is.na(CPP_PUISSANCE_CORRIGEE),
-# CPP_PUISSANCE_BRUTE,
-# CPP_PUISSANCE_CORRIGEE), ]
-#dt[, CPP_PUISSANCE_CORRIGEE := NULL]
-#dt[, CPP_PUISSANCE_BRUTE := NULL]
-
-#dt2 <- dcast.data.table(data = dt, CPP_DATE_PUISSANCE + FK_CCU_ID ~ charge)
-
-
-## Z. Probably stuff to be deleted
-
-# searchpos <- function(row) {
-# str <- strsplit(row, ",")
-#
-# auxmat <- matrix(unlist(str), ncol = 4, byrow = TRUE); rm(str)
-#
-# auxdf <- data.frame(id = as.integer(auxmat[, 1]),
-# date = auxmat[, 2],
-# val = as.numeric(
-# ifelse(auxmat[,3] == "", auxmat[, 4], auxmat[, 3]))
-# )
-# rm(auxmat)
-#
-# idmat <- matrix(auxdf$id, ncol = length(dates), byrow = TRUE)
-# alldatesperid <- apply(idmat, 1, sd) == 0
-#
-#
-# # lines <- match(auxdf$id, identifiants)
-# # cols <- match(auxdf$date, dates)
-#
-# return(cbind(lines, cols, auxdf$val))
-# }
projects / epclust.git / blobdiff