Commit 7c7578ca authored by Georges Kunstler's avatar Georges Kunstler
Browse files

summarise dat now working with a simple test

parent fd75b8ad
......@@ -42,9 +42,9 @@ $(D2)/TRY/data.TRY.std.rds:
#-------------------------------------------------------
GLOBAL: $(D3)/Done.txt
$(D3)/Done.txt: scripts/process.data/remove.out.R $(D3)/Done.t.txt
Rscript $<
$(D3)/Done.txt: scripts/process.data/remove.out.R scripts/process.data/summarise.data.R $(D3)/Done.t.txt
Rscript $<
Rscript scripts/process.data/summarise.data.R
$(D3)/Done.t.txt: scripts/process.data/merge.all.processed.data.R
Rscript $<
......
......@@ -32,7 +32,8 @@ for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; d
qsub trait.workshop/glmerspeciesS1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.2,model.files.glmer.Tf.3), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/glmerspeciesS2${trait}.sh
qsub trait.workshop/glmerspeciesS2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS2${trait}" -q opt32G -j oe
qsub trait.workshop/glmerspeciesS2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS
2${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.4,model.files.glmer.Tf.5), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/glmerspeciesS3${trait}.sh
......
......@@ -19,14 +19,13 @@ system.time( data.summarise <- fun.compute.all.var.cluster( data.all ) )
## test
test.data.all <- table(data.all$biomes, data.all$set) == 0
test.data.summarise <- table(data.summarise1$biomes, data.summarise1$set) == 0
test.data.summarise <- table(data.summarise$biomes, data.summarise$set) == 0
if(!identical(test.data.summarise, test.data.all)) stop('error in summarise data')
if(!identical(test.data.summarise[, colnames(test.data.all)], test.data.all)) stop('error in summarise data')
saveRDS(data.summarise, 'output/data.summarise.rds')
saveRDS(data.summarise, 'output/data.summarise.rds')
unique(data.all$sp.name[data.all$biomes == 'Temperate grassland desert'])
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