I would like to set the working directory of my scripts to the parent directory of the file.
My folder structure is projet/code/test.R
In the script 'test.R', I wrote:
getwd()
setwd(dirname(getwd()))
print(getwd())
However, the working directory will depend on where I source the script in the Terminal.
In the Terminal, I launched the script from the folders 'project' and 'project/code' and got the following results:
~/Documents/project: Rscript code/test.R
~/Documents/project
~/Documents
~/Documents/project/code: Rscript test.R
~/Documents/project/code
~/Documents/project
I would like a way of finding the directory in which the file is located.
My session info is here:
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin16.5.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2 dplyr_0.7.2
loaded via a namespace (and not attached):
[1] Biobase_2.36.2 jsonlite_1.5
[3] bit64_0.9-7 splines_3.4.0
[5] Formula_1.2-2 assertthat_0.2.0
[7] stats4_3.4.0 latticeExtra_0.6-28
[9] blob_1.1.0 GenomeInfoDbData_0.99.0
[11] yaml_2.1.14 RSQLite_2.0
[13] backports_1.1.0 lattice_0.20-35
[15] glue_1.1.1 digest_0.6.12
[17] GenomicRanges_1.28.4 RColorBrewer_1.1-2
[19] XVector_0.16.0 checkmate_1.8.3
[21] colorspace_1.3-2 htmltools_0.3.6
[23] Matrix_1.2-10 plyr_1.8.4
[25] DESeq2_1.16.1 XML_3.98-1.9
[27] pkgconfig_2.0.1 pheatmap_1.0.8
[29] genefilter_1.58.1 zlibbioc_1.22.0
[31] purrr_0.2.3 xtable_1.8-2
[33] scales_0.4.1 BiocParallel_1.10.1
[35] htmlTable_1.9 tibble_1.3.3
[37] annotate_1.54.0 IRanges_2.10.2
[39] ggplot2_2.2.1 SummarizedExperiment_1.6.3
[41] nnet_7.3-12 BiocGenerics_0.22.0
[43] lazyeval_0.2.0 survival_2.41-3
[45] magrittr_1.5 evaluate_0.10.1
[47] memoise_1.1.0 foreign_0.8-69
[49] tools_3.4.0 data.table_1.10.4
[51] matrixStats_0.52.2 stringr_1.2.0
[53] S4Vectors_0.14.3 munsell_0.4.3
[55] locfit_1.5-9.1 cluster_2.0.6
[57] DelayedArray_0.2.7 AnnotationDbi_1.38.2
[59] compiler_3.4.0 GenomeInfoDb_1.12.2
[61] rlang_0.1.2 grid_3.4.0
[63] RCurl_1.95-4.8 rstudioapi_0.6
[65] htmlwidgets_0.9 rmarkdown_1.6
[67] bitops_1.0-6 base64enc_0.1-3
[69] labeling_0.3 gtable_0.2.0
[71] DBI_0.7 R6_2.2.2
[73] gridExtra_2.2.1 knitr_1.17
[75] bit_1.1-12 rprojroot_1.2
[77] bindr_0.1 Hmisc_4.0-3
[79] stringi_1.1.5 parallel_3.4.0
[81] Rcpp_0.12.12 geneplotter_1.54.0
[83] rpart_4.1-11 acepack_1.4.1
Thanks.
Best, C.