Reproducibility #37
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Reproducibility #37
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vladpetyuk
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Jun 8, 2023
vladpetyuk
reviewed
Jun 8, 2023
Ben-Drucker
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Ben-Drucker
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Aug 7, 2023
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| res <- parLapply(cl = multiproc_cl, X = 1:K, fun = fn) | ||
| # stopCluster(multiproc_cl) # replaced with on.exit() | ||
| # | ||
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Ben-Drucker
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Aug 7, 2023
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| y=dSet[!i,response]) | ||
| y=dSet[!i,response], seed = seed) |
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pass seed to downstream FUN
Ben-Drucker
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Aug 7, 2023
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| linters: linters_with_defaults(cyclocomp_linter = NULL, commented_code_linter = NULL, object_name_linter = NULL, line_length_linter = line_length_linter(length = 90L)) | ||
| encoding: "UTF-8" |
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Boilerplate static analysis setup
Ben-Drucker
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Aug 7, 2023
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| sel.alg=c("varSelRF","Boruta","top"), ...){ | ||
| sel.alg=c("varSelRF","Boruta","top"), cores=NULL, | ||
| seed=0, ...){ |
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Provided cores and seed options
Ben-Drucker
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Aug 7, 2023
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| Boruta = function(x,y) select_features_Boruta(x,y,...), | ||
| Boruta = function(x,y, ...) select_features_Boruta(x,y,...), |
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Enables seed to be passed to select_features_Boruta.
Ben-Drucker
commented
Aug 7, 2023
| top = select_features_top) | ||
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| # do K-fold split here | ||
| if(is.null(K)) | ||
| K <- nrow(dSet) | ||
| num_rep <- ceiling(nrow(dSet)/K) | ||
| set.seed(seed) |
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Set seed to determine cv_idx.
Ben-Drucker
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Aug 7, 2023
R/rf_modeling.R
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| RNGkind("L'Ecuyer-CMRG") | ||
| set.seed(i) | ||
| seed <- i |
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Set random number generator kind and random seed in worker function by its index (i).
Ben-Drucker
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Aug 7, 2023
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| clusterEvalQ(multiproc_cl, invisible(suppressWarnings({ | ||
| Sys.setenv(`_R_S3_METHOD_REGISTRATION_NOTE_OVERWRITES_` = "false") | ||
| suppressWarnings(suppressPackageStartupMessages({ | ||
| library("MSnID") | ||
| library("Biobase") | ||
| })) | ||
| }))) |
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Enable quiet evaluation of library loads
Ben-Drucker
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Aug 7, 2023
R/rf_modeling.R
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| if(is.null(cores)){ | ||
| cores <- max(1, detectCores() - 1) | ||
| } | ||
| stopifnot(1 <= cores) | ||
| if(cores > detectCores()){ | ||
| msg <- sub("\n", "", "The number of specified processes is greater than | ||
| the number of cores available on this computer. | ||
| This may lead to high computational overhead.") | ||
| warning(msg) | ||
| } | ||
| multiproc_cl <- makeCluster(cores, outfile = "") |
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Automatic # of cores determination
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To try out, use remotes::install_github("PNNL-Comp-Mass-Spec/MSnSet.utils", ref = "ben-reproducibility", force = TRUE) |
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