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| Original file line number | Diff line number | Diff line change |
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@@ -4,3 +4,6 @@ template: | |
| prefix: nf-core | ||
| skip: | ||
| - igenomes | ||
| lint: | ||
| files_exist: | ||
| - conf/igenomes.config | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,44 @@ | ||
| #!/usr/bin/env Rscript | ||
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| args = commandArgs(trailingOnly=TRUE) | ||
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| if (length(args) < 3) { | ||
| stop("\nthis program needs at least 3 inputs\n1: output filename\n2-*: input files", call.=FALSE) | ||
| } | ||
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| fout <- args[1] | ||
| finp <- args[2:length(args)] | ||
| nf <- length(finp) | ||
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| require(raster) | ||
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| img <- brick(finp[1]) | ||
| nc <- ncell(img) | ||
| nb <- nbands(img) | ||
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| sum <- matrix(0, nc, nb) | ||
| num <- matrix(0, nc, nb) | ||
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| for (i in 1:nf){ | ||
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| data <- brick(finp[i])[] | ||
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| num <- num + !is.na(data) | ||
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| data[is.na(data)] <- 0 | ||
| sum <- sum + data | ||
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| } | ||
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| mean <- sum/num | ||
| img[] <- mean | ||
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| writeRaster(img, filename = fout, format = "GTiff", datatype = "INT2S", | ||
| options = c("INTERLEAVE=BAND", "COMPRESS=LZW", "PREDICTOR=2", | ||
| "NUM_THREADS=ALL_CPUS", "BIGTIFF=YES", | ||
| sprintf("BLOCKXSIZE=%s", img@file@blockcols[1]), | ||
| sprintf("BLOCKYSIZE=%s", img@file@blockrows[1]))) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,38 @@ | ||
| #!/usr/bin/env Rscript | ||
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| args = commandArgs(trailingOnly=TRUE) | ||
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| if (length(args) < 3) { | ||
| stop("\nthis program needs at least 3 inputs\n1: output filename\n2-*: input files", call.=FALSE) | ||
| } | ||
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| fout <- args[1] | ||
| finp <- args[2:length(args)] | ||
| nf <- length(finp) | ||
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| require(raster) | ||
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| img <- raster(finp[1]) | ||
| nc <- ncell(img) | ||
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| last <- rep(1, nc) | ||
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| for (i in 1:nf){ | ||
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| data <- raster(finp[i])[] | ||
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| last[!is.na(data)] <- data[!is.na(data)] | ||
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| } | ||
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| img[] <- last | ||
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| writeRaster(img, filename = fout, format = "GTiff", datatype = "INT2S", | ||
| options = c("INTERLEAVE=BAND", "COMPRESS=LZW", "PREDICTOR=2", | ||
| "NUM_THREADS=ALL_CPUS", "BIGTIFF=YES", | ||
| sprintf("BLOCKXSIZE=%s", img@file@blockcols[1]), | ||
| sprintf("BLOCKYSIZE=%s", img@file@blockrows[1]))) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,143 @@ | ||
| #!/usr/bin/env Rscript | ||
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| args = commandArgs(trailingOnly=TRUE) | ||
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| if (length(args) != 7) { | ||
| stop("\ngive input directory (mosaic) as 1st arg\ngive reference rasters (*.tif) as 2nd-7th args in order: | ||
| woody cover change, woody cover year of change, | ||
| herbaceous cover change, herbaceous cover year of change, | ||
| peak change, peak year of change, ", call.=FALSE) | ||
| } | ||
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| dinp <- args[1] | ||
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| # load package | ||
| require(terra) | ||
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| # LOAD REFERENCE | ||
| ####################################################################### | ||
| woody_cover_changes_ref <- rast(args[2]) | ||
| woody_cover_year_of_change_ref <- rast(args[3]) | ||
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| herbaceous_cover_changes_ref <- rast(args[4]) | ||
| herbaceous_cover_year_of_change_ref <- rast(args[5]) | ||
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| peak_changes_ref <- rast(args[6]) | ||
| peak_year_of_change_ref <- rast(args[7]) | ||
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| # WOODY COVER CHANGE (VALUE OF BASE LEVEL) | ||
| ####################################################################### | ||
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| fname <- dir(dinp, ".*HL_TSA_LNDLG_SMA_VBL-CAO.vrt$", full.names=TRUE) | ||
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| woody_cover_rast <- rast(fname) | ||
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| woody_cover_changes <- woody_cover_rast$CHANGE | ||
| woody_cover_year_of_change <- woody_cover_rast["YEAR-OF-CHANGE"] | ||
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| # HERBACEOUS COVER CHANGE (VALUE OF SEASONAL APLITUDE) | ||
| ####################################################################### | ||
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| fname <- dir(dinp, ".*HL_TSA_LNDLG_SMA_VSA-CAO.vrt$", full.names=TRUE) | ||
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| herbaceous_cover_rast <- rast(fname) | ||
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| herbaceous_cover_changes <- herbaceous_cover_rast$CHANGE | ||
| herbaceous_cover_year_of_change <- herbaceous_cover_rast["YEAR-OF-CHANGE"] | ||
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| # VALUE OF PEAK SEASON | ||
| ####################################################################### | ||
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| fname <- dir(dinp, ".*HL_TSA_LNDLG_SMA_VPS-CAO.vrt$", full.names=TRUE) | ||
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| peak_rast <- rast(fname) | ||
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| peak_changes <- peak_rast$CHANGE | ||
| peak_year_of_change <- peak_rast["YEAR-OF-CHANGE"] | ||
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| # FOR REFERENCE: SAVE RASTERS | ||
| ####################################################################### | ||
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| #writeRaster(woody_cover_changes, "woody_cover_chg_ref.tif") | ||
| #writeRaster(woody_cover_year_of_change, "woody_cover_yoc_ref.tif") | ||
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| #writeRaster(herbaceous_cover_changes, "herbaceous_cover_chg_ref.tif") | ||
| #writeRaster(herbaceous_cover_year_of_change, "herbaceous_cover_yoc_ref.tif") | ||
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| #writeRaster(peak_changes, "peak_chg_ref.tif") | ||
| #writeRaster(peak_year_of_change, "peak_yoc_ref.tif") | ||
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| # COMPARE TESTRUN WITH REFERENCE EXECUTION | ||
| ####################################################################### | ||
| failure <- FALSE | ||
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| woody_cover_changes_result <- all.equal(woody_cover_changes, woody_cover_changes_ref) | ||
| if (is.character(woody_cover_changes_result)) { | ||
| print(paste0("Error: ", woody_cover_changes_result, " for woody cover changes.")) | ||
| failure <- TRUE | ||
| } else { | ||
| print("Woody cover change check passed.") | ||
| } | ||
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| woody_cover_year_of_change_result <- all.equal(woody_cover_year_of_change, woody_cover_year_of_change_ref) | ||
| if (is.character(woody_cover_year_of_change_result)) { | ||
| print(paste0("Error: ", woody_cover_year_of_change_result, " for woody cover year of change.")) | ||
| failure <- TRUE | ||
| } else { | ||
| print("Woody cover year of change check passed.") | ||
| } | ||
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| herbaceous_cover_changes_result <- all.equal(herbaceous_cover_changes, herbaceous_cover_changes_ref) | ||
| if (is.character(herbaceous_cover_changes_result)) { | ||
| print(paste0("Error: ",herbaceous_cover_changes_result, " for herbaceous cover changes.")) | ||
| failure <- TRUE | ||
| } else { | ||
| print("Herbaceous cover change check passed.") | ||
| } | ||
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| herbaceous_cover_year_of_change_result <- all.equal(herbaceous_cover_year_of_change, herbaceous_cover_year_of_change_ref) | ||
| if (is.character(herbaceous_cover_year_of_change_result)) { | ||
| print(paste0("Error: ", herbaceous_cover_year_of_change_result, " for herbaceous cover year of change.")) | ||
| failure <- TRUE | ||
| } else { | ||
| print("Herbaceous cover year of change check passed.") | ||
| } | ||
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| peak_changes_result <- all.equal(peak_changes, peak_changes_ref) | ||
| if (is.character(peak_changes_result)) { | ||
| print(paste0("Error: ", peak_changes_result, " for peak changes.")) | ||
| failure <- TRUE | ||
| } else { | ||
| print("Peak change check passed.") | ||
| } | ||
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| peak_year_of_change_result <- all.equal(peak_year_of_change, peak_year_of_change_ref) | ||
| if (is.character(peak_year_of_change_result)) { | ||
| print(paste0("Error: ", peak_year_of_change_result, " for peak year of change.")) | ||
| failure <- TRUE | ||
| } else { | ||
| print("Peak year of change check passed.") | ||
| } | ||
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| if (failure) { | ||
| stop("Some test failed.") | ||
| } else { | ||
| print("All checks passed.") | ||
| } |
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