# Merging and Inflating two PIDs from the ZooScan equipment
# v0.beta
# Merges PIDs from two aliquots into one PID, simple and step-by-step
# Before merging , the files are "inflated", i.e., the number of objects (data rows) in each PID file is multiplied by the Subsampling factor.
# Ralf Schwamborn, 2017
library(mefa) # needs package "mefa" (multivariate data handling)
## mefa 3.2-7 2016-01-11
# Creates 4 Sudirectories, one Direcory for each step.
### ALL INPUTS AND USER ACTIONS: search "PLEASE"
#. I Preparations
# Step I. 1. PLEASE Define your root working directory
# PLEASE INPUT HERE
setwd("~/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files")
# setwd("C://ZooScan")
# PLEASE INPUT HERE
mainDir <- "~/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files"
getwd()
## [1] "C:/Users/R/Documents/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files"
# this creates a Subdirectory "1_Raw_INPUT PIDs",if there is not one already.
subDir_1 <- "1_Raw_INPUT_PIDs"
if (file.exists(subDir_1)){
setwd(file.path(mainDir, subDir_1))
} else {
dir.create(file.path(mainDir, subDir_1))
}
# Step I.2. PLEASE COPY all your PID files into the Subdirectory "1_Raw_INPUT PIDs" : raw PID files with headers
# Step I.3. This Creates the other neessary Subdirectories (and checks if they already exist)
subDir_2 <- "2_Inflated_PIDs"
if (file.exists(subDir_2)){
setwd(file.path(mainDir, subDir_2))
} else {
dir.create(file.path(mainDir, subDir_2))
}
## Warning in dir.create(file.path(mainDir, subDir_2)): 'C:\Users\R
## \Documents\Recife\Orientandos Recife\Gabi Figueiredo_Doutorado\PID_Files
## \2_Inflated_PIDs' já existe
subDir_3 <- "3_Infl_renamed_PIDs"
if (file.exists(subDir_3)){
setwd(file.path(mainDir, subDir_3))
} else {
dir.create(file.path(mainDir, subDir_3))
}
## Warning in dir.create(file.path(mainDir, subDir_3)): 'C:\Users\R
## \Documents\Recife\Orientandos Recife\Gabi Figueiredo_Doutorado\PID_Files
## \3_Infl_renamed_PIDs' já existe
subDir_4 <- "4_Infl_merged_PIDs"
if (file.exists(subDir_4)){
setwd(file.path(mainDir, subDir_4))
} else {
dir.create(file.path(mainDir, subDir_4))
}
## Warning in dir.create(file.path(mainDir, subDir_4)): 'C:\Users\R
## \Documents\Recife\Orientandos Recife\Gabi Figueiredo_Doutorado\PID_Files
## \4_Infl_merged_PIDs' já existe
# CLEANUP, remove files that contain the string "concentrations"
setwd(file.path(mainDir, subDir_1))
getwd()
## [1] "C:/Users/R/Documents/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files/1_Raw_INPUT_PIDs"
file.remove(list.files(pattern = "concentrations") )
## logical(0)
# Step I.4. This copies your PID files into "2_Inflated_PIDs" and inflates them ( x SubPart)
# (duplicates all object, according to the SubPart factor,e.g. if SuBpart = 4, now you will have 4 times more lines in the data table )
#I.4.1 This lists all files in Input directory,copies them to subirectory "2_Inflated_PIDs"
setwd(file.path(mainDir, subDir_1))
getwd()
## [1] "C:/Users/R/Documents/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files/1_Raw_INPUT_PIDs"
list.files()
## [1] "abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [2] "abr1_atol_st12_300_d2_d2_1_dat1.txt"
## [3] "abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [4] "abr1_atol_st13_300_d2_d2_1_dat1.txt"
## [5] "abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [6] "abr1_atol_st14_300_d2_d2_1_dat1.txt"
## [7] "abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [8] "abr1_atol_st20_300_d2_d2_1_dat1.txt"
## [9] "abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [10] "abr1_atol_st22_300_d2_d2_1_dat1.txt"
## [11] "abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [12] "abr1_atol_st23_300_d2_d1_1_dat1.txt"
## [13] "abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [14] "abr1_noronha_st01_300_d2_d2_1_dat1.txt"
## [15] "abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [16] "abr1_noronha_st02_300_d2_d2_1_dat1.txt"
## [17] "abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [18] "abr1_noronha_st03_300_d2_d2_1_dat1.txt"
## [19] "abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [20] "abr1_noronha_st04_300_d2_d2_1_dat1.txt"
## [21] "abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [22] "abr1_noronha_st05_300_d2_d2_1_dat1.txt"
## [23] "abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [24] "abr1_noronha_st06_300_d2_d2_1_dat1.txt"
## [25] "abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [26] "abr1_noronha_st07_300_d2_d2_1_dat1.txt"
## [27] "abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [28] "abr1_noronha_st08_300_d2_d2_1_dat1.txt"
## [29] "abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [30] "abr1_noronha_st09_300_d2_d2_1_dat1.txt"
## [31] "abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [32] "abr1_noronha_st11_300_d2_d2_1_dat1.txt"
## [33] "abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [34] "abr1_plataforma_st25_300_d2_d2_1_dat1.txt"
## [35] "abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [36] "abr1_plataforma_st26_300_d2_d2_1_dat1.txt"
## [37] "abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [38] "abr1_plataforma_st27_300_d2_d2_1_dat1.txt"
## [39] "abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [40] "abr1_plataforma_st29_300_d2_d2_1_dat1.txt"
## [41] "abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [42] "abr1_plataforma_st31_300_d2_d2_1_dat1.txt"
## [43] "abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [44] "abr1_plataforma_st33_300_d2_d2_1_dat1.txt"
## [45] "abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [46] "abr1_plataforma_st34_300_d2_d2_1_dat1.txt"
## [47] "abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [48] "abr1_plataforma_st36_300_d2_d2_1_dat1.txt"
## [49] "abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [50] "abr1_plataforma_st37_300_d2_d2_1_dat1.txt"
## [51] "abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [52] "abr1_plataforma_st40_300_d2_d2_1_dat1.txt"
## [53] "abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [54] "abr1_plataforma_st41_300_d2_d2_1_dat1.txt"
## [55] "abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [56] "abr1_plataforma_st43_300_d2_d2_1_dat1.txt"
## [57] "abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [58] "abr1_plataforma_st45_300_d2_d2_1_dat1.txt"
## [59] "abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [60] "abr1_plataforma_st48_300_d2_d2_1_dat1.txt"
## [61] "abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [62] "abr1_plataforma_st49_300_d2_d2_1_dat1.txt"
## [63] "abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [64] "abr1_plataforma_st51_300_d2_d2_1_dat1.txt"
## [65] "abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [66] "abr1_plataforma_st52_300_d2_d2_1_dat1.txt"
## [67] "abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
## [68] "abr1_plataforma_st54_300_d2_d2_1_dat1.txt"
filestocopy <- list.files()
filestocopy
## [1] "abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [2] "abr1_atol_st12_300_d2_d2_1_dat1.txt"
## [3] "abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [4] "abr1_atol_st13_300_d2_d2_1_dat1.txt"
## [5] "abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [6] "abr1_atol_st14_300_d2_d2_1_dat1.txt"
## [7] "abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [8] "abr1_atol_st20_300_d2_d2_1_dat1.txt"
## [9] "abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [10] "abr1_atol_st22_300_d2_d2_1_dat1.txt"
## [11] "abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [12] "abr1_atol_st23_300_d2_d1_1_dat1.txt"
## [13] "abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [14] "abr1_noronha_st01_300_d2_d2_1_dat1.txt"
## [15] "abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [16] "abr1_noronha_st02_300_d2_d2_1_dat1.txt"
## [17] "abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [18] "abr1_noronha_st03_300_d2_d2_1_dat1.txt"
## [19] "abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [20] "abr1_noronha_st04_300_d2_d2_1_dat1.txt"
## [21] "abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [22] "abr1_noronha_st05_300_d2_d2_1_dat1.txt"
## [23] "abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [24] "abr1_noronha_st06_300_d2_d2_1_dat1.txt"
## [25] "abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [26] "abr1_noronha_st07_300_d2_d2_1_dat1.txt"
## [27] "abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [28] "abr1_noronha_st08_300_d2_d2_1_dat1.txt"
## [29] "abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [30] "abr1_noronha_st09_300_d2_d2_1_dat1.txt"
## [31] "abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [32] "abr1_noronha_st11_300_d2_d2_1_dat1.txt"
## [33] "abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [34] "abr1_plataforma_st25_300_d2_d2_1_dat1.txt"
## [35] "abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [36] "abr1_plataforma_st26_300_d2_d2_1_dat1.txt"
## [37] "abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [38] "abr1_plataforma_st27_300_d2_d2_1_dat1.txt"
## [39] "abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [40] "abr1_plataforma_st29_300_d2_d2_1_dat1.txt"
## [41] "abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [42] "abr1_plataforma_st31_300_d2_d2_1_dat1.txt"
## [43] "abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [44] "abr1_plataforma_st33_300_d2_d2_1_dat1.txt"
## [45] "abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [46] "abr1_plataforma_st34_300_d2_d2_1_dat1.txt"
## [47] "abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [48] "abr1_plataforma_st36_300_d2_d2_1_dat1.txt"
## [49] "abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [50] "abr1_plataforma_st37_300_d2_d2_1_dat1.txt"
## [51] "abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [52] "abr1_plataforma_st40_300_d2_d2_1_dat1.txt"
## [53] "abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [54] "abr1_plataforma_st41_300_d2_d2_1_dat1.txt"
## [55] "abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [56] "abr1_plataforma_st43_300_d2_d2_1_dat1.txt"
## [57] "abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [58] "abr1_plataforma_st45_300_d2_d2_1_dat1.txt"
## [59] "abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [60] "abr1_plataforma_st48_300_d2_d2_1_dat1.txt"
## [61] "abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [62] "abr1_plataforma_st49_300_d2_d2_1_dat1.txt"
## [63] "abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [64] "abr1_plataforma_st51_300_d2_d2_1_dat1.txt"
## [65] "abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [66] "abr1_plataforma_st52_300_d2_d2_1_dat1.txt"
## [67] "abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
## [68] "abr1_plataforma_st54_300_d2_d2_1_dat1.txt"
targetdir <- file.path(mainDir, subDir_2)
file.copy(from=filestocopy, to=targetdir,
recursive = FALSE,
copy.mode = TRUE)
## [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [34] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [45] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [56] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [67] FALSE FALSE
#I.4.2 inflates, renames all files in subirectory "2_Inflated_PIDs", sets all Subparts to 1
# new names : "Infl_..."
# inflate = duplicate data lines by the Subpart factor, each file has more lines now
setwd(file.path(mainDir, subDir_2))
getwd()
## [1] "C:/Users/R/Documents/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files/2_Inflated_PIDs"
# Read the data and Sub Part of all Files
### INPUT I.4.3. PLEASE define the number of files to import (default: 3 Files, files 1 to 3)
N_FILES <- (length(filestocopy)) #NUMBER OF FILES TO BE ANALYZED
# N_FILES <- 3 # NUMBER OF FILES TO BE ANALYZED
N_FILES
## [1] 68
# files.input <- list.files(pattern = "\\.txt$") #use this if your input file names are ".txt"
# files.input <- list.files(pattern = "\\.PID$") #use this if your input files nems are ".PID"
files.input <- filestocopy
files.input <- files.input[1:N_FILES] # SELECTS ONLY THE FIRST "N" FILES FOR ANLYSIS
files.input
## [1] "abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [2] "abr1_atol_st12_300_d2_d2_1_dat1.txt"
## [3] "abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [4] "abr1_atol_st13_300_d2_d2_1_dat1.txt"
## [5] "abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [6] "abr1_atol_st14_300_d2_d2_1_dat1.txt"
## [7] "abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [8] "abr1_atol_st20_300_d2_d2_1_dat1.txt"
## [9] "abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [10] "abr1_atol_st22_300_d2_d2_1_dat1.txt"
## [11] "abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [12] "abr1_atol_st23_300_d2_d1_1_dat1.txt"
## [13] "abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [14] "abr1_noronha_st01_300_d2_d2_1_dat1.txt"
## [15] "abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [16] "abr1_noronha_st02_300_d2_d2_1_dat1.txt"
## [17] "abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [18] "abr1_noronha_st03_300_d2_d2_1_dat1.txt"
## [19] "abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [20] "abr1_noronha_st04_300_d2_d2_1_dat1.txt"
## [21] "abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [22] "abr1_noronha_st05_300_d2_d2_1_dat1.txt"
## [23] "abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [24] "abr1_noronha_st06_300_d2_d2_1_dat1.txt"
## [25] "abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [26] "abr1_noronha_st07_300_d2_d2_1_dat1.txt"
## [27] "abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [28] "abr1_noronha_st08_300_d2_d2_1_dat1.txt"
## [29] "abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [30] "abr1_noronha_st09_300_d2_d2_1_dat1.txt"
## [31] "abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [32] "abr1_noronha_st11_300_d2_d2_1_dat1.txt"
## [33] "abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [34] "abr1_plataforma_st25_300_d2_d2_1_dat1.txt"
## [35] "abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [36] "abr1_plataforma_st26_300_d2_d2_1_dat1.txt"
## [37] "abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [38] "abr1_plataforma_st27_300_d2_d2_1_dat1.txt"
## [39] "abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [40] "abr1_plataforma_st29_300_d2_d2_1_dat1.txt"
## [41] "abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [42] "abr1_plataforma_st31_300_d2_d2_1_dat1.txt"
## [43] "abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [44] "abr1_plataforma_st33_300_d2_d2_1_dat1.txt"
## [45] "abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [46] "abr1_plataforma_st34_300_d2_d2_1_dat1.txt"
## [47] "abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [48] "abr1_plataforma_st36_300_d2_d2_1_dat1.txt"
## [49] "abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [50] "abr1_plataforma_st37_300_d2_d2_1_dat1.txt"
## [51] "abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [52] "abr1_plataforma_st40_300_d2_d2_1_dat1.txt"
## [53] "abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [54] "abr1_plataforma_st41_300_d2_d2_1_dat1.txt"
## [55] "abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [56] "abr1_plataforma_st43_300_d2_d2_1_dat1.txt"
## [57] "abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [58] "abr1_plataforma_st45_300_d2_d2_1_dat1.txt"
## [59] "abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [60] "abr1_plataforma_st48_300_d2_d2_1_dat1.txt"
## [61] "abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [62] "abr1_plataforma_st49_300_d2_d2_1_dat1.txt"
## [63] "abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [64] "abr1_plataforma_st51_300_d2_d2_1_dat1.txt"
## [65] "abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [66] "abr1_plataforma_st52_300_d2_d2_1_dat1.txt"
## [67] "abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
## [68] "abr1_plataforma_st54_300_d2_d2_1_dat1.txt"
# save & load Workspace
# save.image("ZooScan_NBSS_1.RData")
# load("ZooScan_NBSS_1.RData")
# Step II. Creates lists of Names for BATCH Import (Data, Vol.filtr, Sub.Part_)
# original names of all ZooScan PID files
zznames = paste((basename(files.input[1:N_FILES])))
# names of all ZooScan PID files with "zz_..."
zznames_Data = paste("zz_",substr(basename(files.input[1:N_FILES]), 0, nchar(basename(files.input[1:3])) ), sep="")
# Objects that will receive Sub.Part and Vol.filtr. values
zz_Sub.Part = paste("zzSub.Part_",substr(basename(files.input[1:N_FILES]), 10, nchar(basename(files.input[1:3])) - 4), sep="")
zz_Vol.f = paste("zzVol.f_",substr(basename(files.input[1:N_FILES]), 10, nchar(basename(files.input[1:3])) - 4), sep="")
# Step III. LOOP - BATCH IMPORT - Reads Data, Vol.filtr, Sub.Part (makes tables for Data, Vol.filtr, Sub.Part)
# file.index <- 3
setwd(file.path(mainDir, subDir_1))
getwd()
## [1] "C:/Users/R/Documents/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files/1_Raw_INPUT_PIDs"
# for (file.index in 21:30)
for (file.index in 1:length(zznames_Data))
{
#III.A. Read the file
setwd(file.path(mainDir, subDir_1))
full.textfileAll <- read.table(file = files.input[file.index], sep = ";", skip = 0, colClasses = "character", quote = "")
#III.B. Import the Data Table
#III.B.1 Searches, Finds and Gives the Line number of the Header, imports the Data Table
grep("Data", full.textfileAll$V1) # gives the line number of the line containing "SubPart"
Data.line.many = grep("Data", full.textfileAll$V1) # all line numbers containing "Data"
Data.line <- Data.line.many[3] # Line number of the third time "Data" appears in the file, above the Header of the Data Table.
Data.line # Line number of the text "Data", above the Header of the Data Table
#III. B.2. Read the Data Table,save it as "Data_(filename)"
# assign(zznames_Data[2], read.table(file = files.input[2], sep = "\t", skip = (Data.line), header = TRUE)) # Imports the ZooScan Data Table
temp.obj <- assign(zznames_Data[file.index], read.table(file = files.input[file.index], sep = "\t", skip = (Data.line), header = TRUE)) # Imports the ZooScan Data Table
#View (temp.obj)
#III.C.Searches, Finds and Gives the Line number of the Subsampling Factor
#III. C1. Search and Find the SubSampling Factor
SP.line = grep("SubPart", full.textfileAll$V1) # gives the line number of the line containing "SubPart"
SP.line
# III.C2. Read the SubSampling Factor
#full.textfileSP <- read.table(file = files.input[2], sep = "=", skip = (SP.line - 1), nrows= 1, colClasses = "character")
full.textfileSP <- read.table(file = files.input[file.index], sep = "=", skip = (SP.line - 1), nrows= 1, colClasses = "character")
zz_Sub.Part[file.index] <- as.numeric(full.textfileSP[1,2]);
zz_Sub.Part[file.index] # gives the SubSampling Factor
#zz_Sub.Part[2] <- as.numeric(full.textfileSP[1,2]);
#zz_Sub.Part[2] # gives the SubSampling Factor
full.textfileSP <- zz_Sub.Part[file.index]
# full.textfileSP <- zz_Sub.Part[2]
# III.D. now inflate
library(mefa)
infl.temp<- temp.obj
infl.temp2<- mefa:::rep.data.frame(infl.temp, full.textfileSP)
# View(infl.temp)
length(infl.temp[,1]) # no de objetos pr?-infl.
length(infl.temp2[,1]) # no de objetos p?s-infl.
#View(infl.temp2)
###
# III.E. Rename the textfiles, merge inflated data with old header,change SubPart to 1
# III.E.1 merge inflated data with old header
#read the old header
header.temp <- read.table(file = files.input[file.index], col.names = "V1", comment="", quote= NULL,sep = "\t", header = FALSE) # Imports the Header
header.temp <- as.vector( header.temp)
#View(header.temp)
header.temp2 <- as.data.frame(header.temp[1:(Data.line+1),])
# View(header.temp2)
# merge header and data
names(header.temp2) <- "V1"
names(infl.temp2) <- "V1"
newfile <- rbind.data.frame(header.temp2, (infl.temp2), make.row.names = FALSE, stringsAsFactors = FALSE)
newfile$V1 <- as.character(newfile$V1)
# View(newfile)
# III.E.2 CHANGE SUBPART TO 1
newfile[SP.line,1] <- "SubPart= 1"
setwd(file.path(mainDir, subDir_2))
# III.E.3 save inflated file with old name
write.table(newfile, file = paste("zz_Infl_" ,zznames[file.index] ),
row.names = FALSE, quote=FALSE, col.names = FALSE)
} # END OF first LOOP (inflate and rename)
# OK
###
# MERGE pairs of inflated PIDs #
# STEP IV. (USER ACTION): PLEASE check carefully (or manually rename) all pairs of inflated aliquots, place them in subdirectory " 3_Infl_renamed_PIDs "
# Example without renaming : "...300_d1..." (Aliq. 1) and "...300_d2..." (Aliq. 1) search these stings in old filenames, no renaming necessary
# Example with renaming: New file names: "Ali1_Infl_..." and "Ali2_Infl_..."
# file name "..." has to be identical for each pair of aliquots
# STEP V: now merge "Ali1_Infl_" and "Ali2_Infl_" Files, keep Header (SubPart = 1)
# Creates one "Merged_Infl_..." file for each pair
# copy all inflated pairs from "2_Inflated_PIDs" into "3_Infl_renamed_PIDs", then check (or manually rename, if necessary)
subDir_2 <- "2_Inflated_PIDs"
subDir_3 <- "3_Infl_renamed_PIDs"
subDir_4 <- "4_Infl_merged_PIDs"
setwd(file.path(mainDir, subDir_2))
getwd()
## [1] "C:/Users/R/Documents/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files/2_Inflated_PIDs"
filestocopy <- list.files()
filestocopy
## [1] "abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [2] "abr1_atol_st12_300_d2_d2_1_dat1.txt"
## [3] "abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [4] "abr1_atol_st13_300_d2_d2_1_dat1.txt"
## [5] "abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [6] "abr1_atol_st14_300_d2_d2_1_dat1.txt"
## [7] "abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [8] "abr1_atol_st20_300_d2_d2_1_dat1.txt"
## [9] "abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [10] "abr1_atol_st22_300_d2_d2_1_dat1.txt"
## [11] "abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [12] "abr1_atol_st23_300_d2_d1_1_dat1.txt"
## [13] "abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [14] "abr1_noronha_st01_300_d2_d2_1_dat1.txt"
## [15] "abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [16] "abr1_noronha_st02_300_d2_d2_1_dat1.txt"
## [17] "abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [18] "abr1_noronha_st03_300_d2_d2_1_dat1.txt"
## [19] "abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [20] "abr1_noronha_st04_300_d2_d2_1_dat1.txt"
## [21] "abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [22] "abr1_noronha_st05_300_d2_d2_1_dat1.txt"
## [23] "abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [24] "abr1_noronha_st06_300_d2_d2_1_dat1.txt"
## [25] "abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [26] "abr1_noronha_st07_300_d2_d2_1_dat1.txt"
## [27] "abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [28] "abr1_noronha_st08_300_d2_d2_1_dat1.txt"
## [29] "abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [30] "abr1_noronha_st09_300_d2_d2_1_dat1.txt"
## [31] "abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [32] "abr1_noronha_st11_300_d2_d2_1_dat1.txt"
## [33] "abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [34] "abr1_plataforma_st25_300_d2_d2_1_dat1.txt"
## [35] "abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [36] "abr1_plataforma_st26_300_d2_d2_1_dat1.txt"
## [37] "abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [38] "abr1_plataforma_st27_300_d2_d2_1_dat1.txt"
## [39] "abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [40] "abr1_plataforma_st29_300_d2_d2_1_dat1.txt"
## [41] "abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [42] "abr1_plataforma_st31_300_d2_d2_1_dat1.txt"
## [43] "abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [44] "abr1_plataforma_st33_300_d2_d2_1_dat1.txt"
## [45] "abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [46] "abr1_plataforma_st34_300_d2_d2_1_dat1.txt"
## [47] "abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [48] "abr1_plataforma_st36_300_d2_d2_1_dat1.txt"
## [49] "abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [50] "abr1_plataforma_st37_300_d2_d2_1_dat1.txt"
## [51] "abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [52] "abr1_plataforma_st40_300_d2_d2_1_dat1.txt"
## [53] "abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [54] "abr1_plataforma_st41_300_d2_d2_1_dat1.txt"
## [55] "abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [56] "abr1_plataforma_st43_300_d2_d2_1_dat1.txt"
## [57] "abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [58] "abr1_plataforma_st45_300_d2_d2_1_dat1.txt"
## [59] "abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [60] "abr1_plataforma_st48_300_d2_d2_1_dat1.txt"
## [61] "abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [62] "abr1_plataforma_st49_300_d2_d2_1_dat1.txt"
## [63] "abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [64] "abr1_plataforma_st51_300_d2_d2_1_dat1.txt"
## [65] "abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [66] "abr1_plataforma_st52_300_d2_d2_1_dat1.txt"
## [67] "abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
## [68] "abr1_plataforma_st54_300_d2_d2_1_dat1.txt"
## [69] "zz_Infl_ abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [70] "zz_Infl_ abr1_atol_st12_300_d2_d2_1_dat1.txt"
## [71] "zz_Infl_ abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [72] "zz_Infl_ abr1_atol_st13_300_d2_d2_1_dat1.txt"
## [73] "zz_Infl_ abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [74] "zz_Infl_ abr1_atol_st14_300_d2_d2_1_dat1.txt"
## [75] "zz_Infl_ abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [76] "zz_Infl_ abr1_atol_st20_300_d2_d2_1_dat1.txt"
## [77] "zz_Infl_ abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [78] "zz_Infl_ abr1_atol_st22_300_d2_d2_1_dat1.txt"
## [79] "zz_Infl_ abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [80] "zz_Infl_ abr1_atol_st23_300_d2_d1_1_dat1.txt"
## [81] "zz_Infl_ abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [82] "zz_Infl_ abr1_noronha_st01_300_d2_d2_1_dat1.txt"
## [83] "zz_Infl_ abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [84] "zz_Infl_ abr1_noronha_st02_300_d2_d2_1_dat1.txt"
## [85] "zz_Infl_ abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [86] "zz_Infl_ abr1_noronha_st03_300_d2_d2_1_dat1.txt"
## [87] "zz_Infl_ abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [88] "zz_Infl_ abr1_noronha_st04_300_d2_d2_1_dat1.txt"
## [89] "zz_Infl_ abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [90] "zz_Infl_ abr1_noronha_st05_300_d2_d2_1_dat1.txt"
## [91] "zz_Infl_ abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [92] "zz_Infl_ abr1_noronha_st06_300_d2_d2_1_dat1.txt"
## [93] "zz_Infl_ abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [94] "zz_Infl_ abr1_noronha_st07_300_d2_d2_1_dat1.txt"
## [95] "zz_Infl_ abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [96] "zz_Infl_ abr1_noronha_st08_300_d2_d2_1_dat1.txt"
## [97] "zz_Infl_ abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [98] "zz_Infl_ abr1_noronha_st09_300_d2_d2_1_dat1.txt"
## [99] "zz_Infl_ abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [100] "zz_Infl_ abr1_noronha_st11_300_d2_d2_1_dat1.txt"
## [101] "zz_Infl_ abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [102] "zz_Infl_ abr1_plataforma_st25_300_d2_d2_1_dat1.txt"
## [103] "zz_Infl_ abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [104] "zz_Infl_ abr1_plataforma_st26_300_d2_d2_1_dat1.txt"
## [105] "zz_Infl_ abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [106] "zz_Infl_ abr1_plataforma_st27_300_d2_d2_1_dat1.txt"
## [107] "zz_Infl_ abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [108] "zz_Infl_ abr1_plataforma_st29_300_d2_d2_1_dat1.txt"
## [109] "zz_Infl_ abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [110] "zz_Infl_ abr1_plataforma_st31_300_d2_d2_1_dat1.txt"
## [111] "zz_Infl_ abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [112] "zz_Infl_ abr1_plataforma_st33_300_d2_d2_1_dat1.txt"
## [113] "zz_Infl_ abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [114] "zz_Infl_ abr1_plataforma_st34_300_d2_d2_1_dat1.txt"
## [115] "zz_Infl_ abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [116] "zz_Infl_ abr1_plataforma_st36_300_d2_d2_1_dat1.txt"
## [117] "zz_Infl_ abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [118] "zz_Infl_ abr1_plataforma_st37_300_d2_d2_1_dat1.txt"
## [119] "zz_Infl_ abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [120] "zz_Infl_ abr1_plataforma_st40_300_d2_d2_1_dat1.txt"
## [121] "zz_Infl_ abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [122] "zz_Infl_ abr1_plataforma_st41_300_d2_d2_1_dat1.txt"
## [123] "zz_Infl_ abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [124] "zz_Infl_ abr1_plataforma_st43_300_d2_d2_1_dat1.txt"
## [125] "zz_Infl_ abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [126] "zz_Infl_ abr1_plataforma_st45_300_d2_d2_1_dat1.txt"
## [127] "zz_Infl_ abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [128] "zz_Infl_ abr1_plataforma_st48_300_d2_d2_1_dat1.txt"
## [129] "zz_Infl_ abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [130] "zz_Infl_ abr1_plataforma_st49_300_d2_d2_1_dat1.txt"
## [131] "zz_Infl_ abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [132] "zz_Infl_ abr1_plataforma_st51_300_d2_d2_1_dat1.txt"
## [133] "zz_Infl_ abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [134] "zz_Infl_ abr1_plataforma_st52_300_d2_d2_1_dat1.txt"
## [135] "zz_Infl_ abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
## [136] "zz_Infl_ abr1_plataforma_st54_300_d2_d2_1_dat1.txt"
targetdir <- file.path(mainDir, subDir_3)
file.copy(from=filestocopy, to=targetdir,
recursive = FALSE,
copy.mode = TRUE)
## [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [34] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [45] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [56] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [67] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [78] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [89] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [100] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [111] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [122] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE
setwd(file.path(mainDir, subDir_3))
getwd()
## [1] "C:/Users/R/Documents/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files/3_Infl_renamed_PIDs"
list.files()
## [1] "abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [2] "abr1_atol_st12_300_d2_d2_1_dat1.txt"
## [3] "abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [4] "abr1_atol_st13_300_d2_d2_1_dat1.txt"
## [5] "abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [6] "abr1_atol_st14_300_d2_d2_1_dat1.txt"
## [7] "abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [8] "abr1_atol_st20_300_d2_d2_1_dat1.txt"
## [9] "abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [10] "abr1_atol_st22_300_d2_d2_1_dat1.txt"
## [11] "abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [12] "abr1_atol_st23_300_d2_d1_1_dat1.txt"
## [13] "abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [14] "abr1_noronha_st01_300_d2_d2_1_dat1.txt"
## [15] "abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [16] "abr1_noronha_st02_300_d2_d2_1_dat1.txt"
## [17] "abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [18] "abr1_noronha_st03_300_d2_d2_1_dat1.txt"
## [19] "abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [20] "abr1_noronha_st04_300_d2_d2_1_dat1.txt"
## [21] "abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [22] "abr1_noronha_st05_300_d2_d2_1_dat1.txt"
## [23] "abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [24] "abr1_noronha_st06_300_d2_d2_1_dat1.txt"
## [25] "abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [26] "abr1_noronha_st07_300_d2_d2_1_dat1.txt"
## [27] "abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [28] "abr1_noronha_st08_300_d2_d2_1_dat1.txt"
## [29] "abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [30] "abr1_noronha_st09_300_d2_d2_1_dat1.txt"
## [31] "abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [32] "abr1_noronha_st11_300_d2_d2_1_dat1.txt"
## [33] "abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [34] "abr1_plataforma_st25_300_d2_d2_1_dat1.txt"
## [35] "abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [36] "abr1_plataforma_st26_300_d2_d2_1_dat1.txt"
## [37] "abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [38] "abr1_plataforma_st27_300_d2_d2_1_dat1.txt"
## [39] "abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [40] "abr1_plataforma_st29_300_d2_d2_1_dat1.txt"
## [41] "abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [42] "abr1_plataforma_st31_300_d2_d2_1_dat1.txt"
## [43] "abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [44] "abr1_plataforma_st33_300_d2_d2_1_dat1.txt"
## [45] "abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [46] "abr1_plataforma_st34_300_d2_d2_1_dat1.txt"
## [47] "abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [48] "abr1_plataforma_st36_300_d2_d2_1_dat1.txt"
## [49] "abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [50] "abr1_plataforma_st37_300_d2_d2_1_dat1.txt"
## [51] "abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [52] "abr1_plataforma_st40_300_d2_d2_1_dat1.txt"
## [53] "abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [54] "abr1_plataforma_st41_300_d2_d2_1_dat1.txt"
## [55] "abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [56] "abr1_plataforma_st43_300_d2_d2_1_dat1.txt"
## [57] "abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [58] "abr1_plataforma_st45_300_d2_d2_1_dat1.txt"
## [59] "abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [60] "abr1_plataforma_st48_300_d2_d2_1_dat1.txt"
## [61] "abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [62] "abr1_plataforma_st49_300_d2_d2_1_dat1.txt"
## [63] "abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [64] "abr1_plataforma_st51_300_d2_d2_1_dat1.txt"
## [65] "abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [66] "abr1_plataforma_st52_300_d2_d2_1_dat1.txt"
## [67] "abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
## [68] "abr1_plataforma_st54_300_d2_d2_1_dat1.txt"
## [69] "zz_Infl_ abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [70] "zz_Infl_ abr1_atol_st12_300_d2_d2_1_dat1.txt"
## [71] "zz_Infl_ abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [72] "zz_Infl_ abr1_atol_st13_300_d2_d2_1_dat1.txt"
## [73] "zz_Infl_ abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [74] "zz_Infl_ abr1_atol_st14_300_d2_d2_1_dat1.txt"
## [75] "zz_Infl_ abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [76] "zz_Infl_ abr1_atol_st20_300_d2_d2_1_dat1.txt"
## [77] "zz_Infl_ abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [78] "zz_Infl_ abr1_atol_st22_300_d2_d2_1_dat1.txt"
## [79] "zz_Infl_ abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [80] "zz_Infl_ abr1_atol_st23_300_d2_d1_1_dat1.txt"
## [81] "zz_Infl_ abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [82] "zz_Infl_ abr1_noronha_st01_300_d2_d2_1_dat1.txt"
## [83] "zz_Infl_ abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [84] "zz_Infl_ abr1_noronha_st02_300_d2_d2_1_dat1.txt"
## [85] "zz_Infl_ abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [86] "zz_Infl_ abr1_noronha_st03_300_d2_d2_1_dat1.txt"
## [87] "zz_Infl_ abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [88] "zz_Infl_ abr1_noronha_st04_300_d2_d2_1_dat1.txt"
## [89] "zz_Infl_ abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [90] "zz_Infl_ abr1_noronha_st05_300_d2_d2_1_dat1.txt"
## [91] "zz_Infl_ abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [92] "zz_Infl_ abr1_noronha_st06_300_d2_d2_1_dat1.txt"
## [93] "zz_Infl_ abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [94] "zz_Infl_ abr1_noronha_st07_300_d2_d2_1_dat1.txt"
## [95] "zz_Infl_ abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [96] "zz_Infl_ abr1_noronha_st08_300_d2_d2_1_dat1.txt"
## [97] "zz_Infl_ abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [98] "zz_Infl_ abr1_noronha_st09_300_d2_d2_1_dat1.txt"
## [99] "zz_Infl_ abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [100] "zz_Infl_ abr1_noronha_st11_300_d2_d2_1_dat1.txt"
## [101] "zz_Infl_ abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [102] "zz_Infl_ abr1_plataforma_st25_300_d2_d2_1_dat1.txt"
## [103] "zz_Infl_ abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [104] "zz_Infl_ abr1_plataforma_st26_300_d2_d2_1_dat1.txt"
## [105] "zz_Infl_ abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [106] "zz_Infl_ abr1_plataforma_st27_300_d2_d2_1_dat1.txt"
## [107] "zz_Infl_ abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [108] "zz_Infl_ abr1_plataforma_st29_300_d2_d2_1_dat1.txt"
## [109] "zz_Infl_ abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [110] "zz_Infl_ abr1_plataforma_st31_300_d2_d2_1_dat1.txt"
## [111] "zz_Infl_ abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [112] "zz_Infl_ abr1_plataforma_st33_300_d2_d2_1_dat1.txt"
## [113] "zz_Infl_ abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [114] "zz_Infl_ abr1_plataforma_st34_300_d2_d2_1_dat1.txt"
## [115] "zz_Infl_ abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [116] "zz_Infl_ abr1_plataforma_st36_300_d2_d2_1_dat1.txt"
## [117] "zz_Infl_ abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [118] "zz_Infl_ abr1_plataforma_st37_300_d2_d2_1_dat1.txt"
## [119] "zz_Infl_ abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [120] "zz_Infl_ abr1_plataforma_st40_300_d2_d2_1_dat1.txt"
## [121] "zz_Infl_ abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [122] "zz_Infl_ abr1_plataforma_st41_300_d2_d2_1_dat1.txt"
## [123] "zz_Infl_ abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [124] "zz_Infl_ abr1_plataforma_st43_300_d2_d2_1_dat1.txt"
## [125] "zz_Infl_ abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [126] "zz_Infl_ abr1_plataforma_st45_300_d2_d2_1_dat1.txt"
## [127] "zz_Infl_ abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [128] "zz_Infl_ abr1_plataforma_st48_300_d2_d2_1_dat1.txt"
## [129] "zz_Infl_ abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [130] "zz_Infl_ abr1_plataforma_st49_300_d2_d2_1_dat1.txt"
## [131] "zz_Infl_ abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [132] "zz_Infl_ abr1_plataforma_st51_300_d2_d2_1_dat1.txt"
## [133] "zz_Infl_ abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [134] "zz_Infl_ abr1_plataforma_st52_300_d2_d2_1_dat1.txt"
## [135] "zz_Infl_ abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
## [136] "zz_Infl_ abr1_plataforma_st54_300_d2_d2_1_dat1.txt"
list.temp<-list.files()
nfiles <- length(list.temp)
# STEP V.1: prepares file lists for aliquots 1 (filesAli1) and 2 (filesAli2)
# filesAli1 <- list.temp[1:(nfiles/2)]
# filesAli2 <- list.temp[((nfiles/2)+1):nfiles]
filesAli1 <- list.files(pattern="300_d1") # search string
filesAli2 <- list.files(pattern="300_d2") # search string
# Step V.II. FINAL LOOP - MERGE FILES
# file.index <- 1
for (file.index in 1:length(filesAli1))
{
#V.II.A. Read the fileS
setwd(file.path(mainDir, subDir_3))
full.textfileAl1 <- read.table(file = filesAli1[file.index], sep = ";", skip = 0, colClasses = "character", quote = "")
full.textfileAl2 <- read.table(file = filesAli2[file.index], sep = ";", skip = 0, colClasses = "character", quote = "")
#V.II.B. Import the Data Table
#V.II.B.1 Searches, Finds and Gives the Line number of the Header, imports the Data Table
grep("Data", full.textfileAl1$V1) # gives the line number of the line containing "DATA"
Data.line.many = grep("Data", full.textfileAl1$V1) # all line numbers containing "Data"
Data.line <- Data.line.many[3] # Line number of the third time "Data" appears in the file, above the Header of the Data Table.
Data.line # Line number of the text "Data", above the Header of the Data Table
#V.II. B.2. Read the Data Table,save it as "Data_(filename)"
# assign(zznames_Data[2], read.table(file = files.input[2], sep = "\t", skip = (Data.line), header = TRUE)) # Imports the ZooScan Data Table
temp.obj1 <- read.table(file = filesAli1[file.index], sep = "\t", skip = (Data.line), header = TRUE) # Imports the ZooScan Data Table
temp.obj2 <- read.table(file = filesAli2[file.index], sep = "\t", skip = (Data.line), header = TRUE) # Imports the ZooScan Data Table
# V.II.B.3. Merge obj1 and and obj2
names(temp.obj1) <- "V1"
names(temp.obj2) <- "V1"
temp.obj1_2merged <- rbind.data.frame(temp.obj1, temp.obj2, make.row.names = FALSE, stringsAsFactors = FALSE)
temp.obj1_2merged$V1 <- as.character(temp.obj1_2merged$V1)
# V.II.B.4. Merge merged data with header
#read the old header
header.temp <- read.table(file = filesAli1[file.index], col.names = "V1", comment="", quote= NULL,sep = "\t", header = FALSE) # Imports the Header
header.temp <- as.vector( header.temp)
#View(header.temp)
header.temp2 <- as.data.frame(header.temp[1:(Data.line+1),])
# View(header.temp2)
# merge header and data
names(header.temp2) <- "V1"
names(temp.obj1_2merged) <- "V1"
newfile <- rbind.data.frame(header.temp2, (temp.obj1_2merged), make.row.names = FALSE, stringsAsFactors = FALSE)
newfile$V1 <- as.character(newfile$V1)
# CHANGE SUBPART TO 1
newfile[SP.line,1] <- "SubPart= 1"
# V.II.C. save MERGED file with NEW name in subDirerctory 4
setwd(file.path(mainDir, subDir_4))
getwd()
write.table(newfile, file = paste("zz_Merged_", filesAli1[file.index] ),
row.names = FALSE, quote=FALSE, col.names = FALSE)
} # End of Last Loop #
## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string
## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string
# PLease verify your final (inflated and merged) files in the subdiretory "4_Infl_merged_PIDs"
setwd(file.path(mainDir, subDir_4))
getwd()
## [1] "C:/Users/R/Documents/Recife/Orientandos Recife/Gabi Figueiredo_Doutorado/PID_Files/4_Infl_merged_PIDs"
list.files()
## [1] "zz_Merged_ abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [2] "zz_Merged_ abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [3] "zz_Merged_ abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [4] "zz_Merged_ abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [5] "zz_Merged_ abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [6] "zz_Merged_ abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [7] "zz_Merged_ abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [8] "zz_Merged_ abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [9] "zz_Merged_ abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [10] "zz_Merged_ abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [11] "zz_Merged_ abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [12] "zz_Merged_ abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [13] "zz_Merged_ abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [14] "zz_Merged_ abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [15] "zz_Merged_ abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [16] "zz_Merged_ abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [17] "zz_Merged_ abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [18] "zz_Merged_ abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [19] "zz_Merged_ abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [20] "zz_Merged_ abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [21] "zz_Merged_ abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [22] "zz_Merged_ abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [23] "zz_Merged_ abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [24] "zz_Merged_ abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [25] "zz_Merged_ abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [26] "zz_Merged_ abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [27] "zz_Merged_ abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [28] "zz_Merged_ abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [29] "zz_Merged_ abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [30] "zz_Merged_ abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [31] "zz_Merged_ abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [32] "zz_Merged_ abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [33] "zz_Merged_ abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [34] "zz_Merged_ abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
## [35] "zz_Merged_ zz_Infl_ abr1_atol_st12_300_d1_d1_1_dat1.txt"
## [36] "zz_Merged_ zz_Infl_ abr1_atol_st13_300_d1_d1_1_dat1.txt"
## [37] "zz_Merged_ zz_Infl_ abr1_atol_st14_300_d1_d1_1_dat1.txt"
## [38] "zz_Merged_ zz_Infl_ abr1_atol_st20_300_d1_d1_1_dat1.txt"
## [39] "zz_Merged_ zz_Infl_ abr1_atol_st22_300_d1_d1_1_dat1.txt"
## [40] "zz_Merged_ zz_Infl_ abr1_atol_st23_300_d1_d1_1_dat1.txt"
## [41] "zz_Merged_ zz_Infl_ abr1_noronha_st01_300_d1_d1_1_dat1.txt"
## [42] "zz_Merged_ zz_Infl_ abr1_noronha_st01_300_d1_d1_1_dat1_corr_excl_OK.CSV"
## [43] "zz_Merged_ zz_Infl_ abr1_noronha_st02_300_d1_d1_1_dat1.txt"
## [44] "zz_Merged_ zz_Infl_ abr1_noronha_st03_300_d1_d1_1_dat1.txt"
## [45] "zz_Merged_ zz_Infl_ abr1_noronha_st04_300_d1_d1_1_dat1.txt"
## [46] "zz_Merged_ zz_Infl_ abr1_noronha_st05_300_d1_d1_1_dat1.txt"
## [47] "zz_Merged_ zz_Infl_ abr1_noronha_st06_300_d1_d1_1_dat1.txt"
## [48] "zz_Merged_ zz_Infl_ abr1_noronha_st07_300_d1_d1_1_dat1.txt"
## [49] "zz_Merged_ zz_Infl_ abr1_noronha_st08_300_d1_d1_1_dat1.txt"
## [50] "zz_Merged_ zz_Infl_ abr1_noronha_st09_300_d1_d1_1_dat1.txt"
## [51] "zz_Merged_ zz_Infl_ abr1_noronha_st11_300_d1_d1_1_dat1.txt"
## [52] "zz_Merged_ zz_Infl_ abr1_plataforma_st25_300_d1_d1_1_dat1.txt"
## [53] "zz_Merged_ zz_Infl_ abr1_plataforma_st26_300_d1_d1_1_dat1.txt"
## [54] "zz_Merged_ zz_Infl_ abr1_plataforma_st27_300_d1_d1_1_dat1.txt"
## [55] "zz_Merged_ zz_Infl_ abr1_plataforma_st29_300_d1_d1_1_dat1.txt"
## [56] "zz_Merged_ zz_Infl_ abr1_plataforma_st31_300_d1_d1_1_dat1.txt"
## [57] "zz_Merged_ zz_Infl_ abr1_plataforma_st33_300_d1_d1_1_dat1.txt"
## [58] "zz_Merged_ zz_Infl_ abr1_plataforma_st34_300_d1_d1_1_dat1.txt"
## [59] "zz_Merged_ zz_Infl_ abr1_plataforma_st36_300_d1_d1_1_dat1.txt"
## [60] "zz_Merged_ zz_Infl_ abr1_plataforma_st37_300_d1_d1_1_dat1.txt"
## [61] "zz_Merged_ zz_Infl_ abr1_plataforma_st40_300_d1_d1_1_dat1.txt"
## [62] "zz_Merged_ zz_Infl_ abr1_plataforma_st41_300_d1_d1_1_dat1.txt"
## [63] "zz_Merged_ zz_Infl_ abr1_plataforma_st41_300_d1_d1_1_dat1__CORR_lines EXCL_OK.csv"
## [64] "zz_Merged_ zz_Infl_ abr1_plataforma_st43_300_d1_d1_1_dat1.txt"
## [65] "zz_Merged_ zz_Infl_ abr1_plataforma_st45_300_d1_d1_1_dat1.txt"
## [66] "zz_Merged_ zz_Infl_ abr1_plataforma_st45_300_d1_d1_1_dat1_CORR_lines_EXCL_OK.csv"
## [67] "zz_Merged_ zz_Infl_ abr1_plataforma_st48_300_d1_d1_1_dat1.txt"
## [68] "zz_Merged_ zz_Infl_ abr1_plataforma_st49_300_d1_d1_1_dat1.txt"
## [69] "zz_Merged_ zz_Infl_ abr1_plataforma_st51_300_d1_d1_1_dat1.txt"
## [70] "zz_Merged_ zz_Infl_ abr1_plataforma_st52_300_d1_d1_1_dat1.txt"
## [71] "zz_Merged_ zz_Infl_ abr1_plataforma_st54_300_d1_d1_1_dat1.txt"
### End of Script ###