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# Regression testing script for GCAT.
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# Yury V Bukhman, 17 Nov 2014
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# This script tests outputs generated from the example dataset "YPDAFEXglucoseTests_2-25-10" with default GCAT settings.
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INPUT.DIR = system.file("extdata/YPDAFEXglucoseTests_2-25-10",package="GCAT")
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OUTPUT.DIR = paste(INPUT.DIR,"temp",sep="/")
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INPUT.FILE = "YPDAFEXglucoseTests_2-25-10.csv"
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# Run GCAT
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library(GCAT)
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setwd(INPUT.DIR)
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time.input=1/3600
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out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,
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out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR,
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add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
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use.linear.param=F, use.loess=F, smooth.param=0.1,
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points.to.remove = integer(), remove.jumps = F, time.input=time.input,
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silent = F, verbose = T, return.fit = T, overview.jpgs = T)
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# Read in old and new output spreadsheets
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old.output.table = read.table("default_output.txt",header=T,sep="\t")
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new.output.file = list.files(path=OUTPUT.DIR, pattern = "^output_gcat\\.fit_.+\\.txt$")
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new.output.table = read.table(paste("temp",new.output.file,sep="/"),header=T,sep="\t",nrows=96)
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# Remove "pdf.file" column
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old.output.table = old.output.table[names(old.output.table) != "pdf.file"]
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new.output.table = new.output.table[names(new.output.table) != "pdf.file"]
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# Verify that output spreadsheets are identical within rounding error
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# (relaxed tolerance to 1e-6 to make the test pass on Windows 7 with R 3.2.0)
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stopifnot(all.equal(new.output.table,old.output.table,tolerance=1e-6))
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# Clean up
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unlink(OUTPUT.DIR, recursive=T)
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