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trawlData yml
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| ## All R files that are used must be listed here: | |
| packages: | |
| - data.table | |
| - LaF | |
| - bit64 | |
| - stringr | |
| - stringi | |
| - PBSmapping | |
| - devtools | |
| sources: | |
| ## - R/clean.columns.R | |
| ## - R/clean.format.R | |
| ## - R/clean.names.R | |
| ## - R/clean.tax.R | |
| ## - R/clean.trimCol.R | |
| ## - R/clean.trimRow.R | |
| ## - R/formatStrat.R | |
| ## - R/formatValue.R | |
| ## - R/helperFile.R | |
| ## - R/helperMisc.R | |
| ## - R/helperStat.R | |
| ## - R/read.trawl.R | |
| ## - R/tax.getCmmn.R | |
| ## - R/tax.getSpp.R | |
| ## - R/tax.getTax.R | |
| - R/ | |
| - man-roxygen/ | |
| - pkgBuild/R/makeData.R | |
| - pkgBuild/R/update_spp.key.R | |
| - pkgBuild/R/update_rawData.R | |
| - pkgBuild/R/update_cleanData.R | |
| - pkgBuild/R/createSppKey.R | |
| # - pkgBuild/R/update_trimData.R | |
| ## Most of a remakefile will be targets. They can be listed in any | |
| ## order; whatever makes most sense. Files can be split up and | |
| ## included into the main file if you need to impose more structure. | |
| targets: | |
| ## 'all' is a special target that will be used as the default | |
| ## target by 'remake'. It doesn't actually make anything but | |
| ## "depends" on other targets. | |
| all: | |
| depends: | |
| # - spp | |
| # - raw_data | |
| - clean_data | |
| # - data_scripts | |
| ## - trim_data | |
| # command: check() | |
| # ====================== | |
| # = Update Species Key = | |
| # ====================== | |
| spp: | |
| depends: | |
| - data/spp.key.RData | |
| - helper_scripts | |
| # - inst/extdata/taxonomy/spp.key.csv | |
| command: | |
| - update_spp.key() | |
| inst/extdata/taxonomy/spp.key.csv: | |
| depends: | |
| - raw_data | |
| command: update_spp.key(check_raw=TRUE) | |
| data/spp.key.RData: | |
| command: update_spp.key("inst/extdata/taxonomy/spp.key.csv") | |
| # ============================ | |
| # = Scripts that affect data = | |
| # ============================ | |
| # data_scripts: | |
| # depends: | |
| # - raw_scripts | |
| # - clean_scripts | |
| # - helper_scripts | |
| # command: | |
| # - document() | |
| raw_scripts: | |
| depends: | |
| - R/read.trawl.R | |
| - helper_scripts | |
| command: | |
| # - document() | |
| clean_scripts: | |
| depends: | |
| - R/clean.names.R | |
| - R/clean.format.R | |
| - R/clean.columns.R | |
| - R/clean.tax.R | |
| - R/clean.trimRow.R | |
| - helper_scripts | |
| command: | |
| # - document() | |
| helper_scripts: | |
| depends: | |
| - R/helperFile.R | |
| - R/helperMisc.R | |
| - R/helperStat.R | |
| command: | |
| # - document() | |
| # inst/extdata/taxonomy/spp.key.csv: | |
| # command: update_spp.key("data/spp.key.RData") | |
| # =========================== | |
| # = Update Raw .RData Files = | |
| # =========================== | |
| raw_data: | |
| depends: | |
| - data/raw.ai.RData | |
| - data/raw.ebs.RData | |
| - data/raw.gmex.RData | |
| - data/raw.goa.RData | |
| - data/raw.neus.RData | |
| - data/raw.newf.RData | |
| - data/raw.sa.RData | |
| - data/raw.sgulf.RData | |
| - data/raw.shelf.RData | |
| - data/raw.wcann.RData | |
| - data/raw.wctri.RData | |
| - raw_scripts | |
| command: | |
| - document() | |
| data/raw.ai.RData: | |
| command: update_rawData("inst/extdata/ai.zip") | |
| depends: | |
| - raw_scripts | |
| data/raw.ebs.RData: | |
| command: update_rawData("inst/extdata/ebs.zip") | |
| depends: | |
| - raw_scripts | |
| data/raw.gmex.RData: | |
| command: update_rawData("inst/extdata/gmex.zip") | |
| depends: | |
| - raw_scripts | |
| data/raw.goa.RData: | |
| command: update_rawData("inst/extdata/goa.zip") | |
| depends: | |
| - raw_scripts | |
| neus_raw_files: | |
| command: c("inst/extdata/neus/neus-bigelow_fall_calibration.csv", "inst/extdata/neus/neus-bigelow_spring_calibration.csv", "inst/extdata/neus/neus-neusStrata.csv", "inst/extdata/neus/neus-station.RData", "inst/extdata/neus/neus-SurvDat.RData", "inst/extdata/neus/neus-SVSPP.RData") | |
| data/raw.neus.RData: | |
| command: update_rawData(neus_raw_files) | |
| depends: | |
| - raw_scripts | |
| data/raw.newf.RData: | |
| command: update_rawData("inst/extdata/newf.zip") | |
| depends: | |
| - raw_scripts | |
| data/raw.sa.RData: | |
| command: update_rawData("inst/extdata/sa.zip") | |
| depends: | |
| - raw_scripts | |
| data/raw.sgulf.RData: | |
| command: update_rawData("inst/extdata/sgulf.zip") | |
| depends: | |
| - raw_scripts | |
| data/raw.shelf.RData: | |
| command: update_rawData("inst/extdata/shelf.zip") | |
| depends: | |
| - raw_scripts | |
| data/raw.wcann.RData: | |
| command: update_rawData("inst/extdata/wcann.zip") | |
| depends: | |
| - raw_scripts | |
| data/raw.wctri.RData: | |
| command: update_rawData("inst/extdata/wctri.zip") | |
| depends: | |
| - raw_scripts | |
| # ============================= | |
| # = Update Clean .RData Files = | |
| # ============================= | |
| # clean_input: | |
| # depends: | |
| # - clean_scripts | |
| # - spp | |
| clean_data: | |
| depends: | |
| - data/clean.ai.RData | |
| - data/clean.ebs.RData | |
| - data/clean.gmex.RData | |
| - data/clean.goa.RData | |
| - data/clean.neus.RData | |
| - data/clean.newf.RData | |
| - data/clean.sa.RData | |
| - data/clean.sgulf.RData | |
| - data/clean.shelf.RData | |
| - data/clean.wcann.RData | |
| - data/clean.wctri.RData | |
| command: | |
| - document() | |
| data/clean.ai.RData: | |
| command: update_cleanData("data/raw.ai.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.ebs.RData: | |
| command: update_cleanData("data/raw.ebs.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.gmex.RData: | |
| command: update_cleanData("data/raw.gmex.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.goa.RData: | |
| command: update_cleanData("data/raw.goa.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.neus.RData: | |
| command: update_cleanData("data/raw.neus.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.newf.RData: | |
| command: update_cleanData("data/raw.newf.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.sa.RData: | |
| command: update_cleanData("data/raw.sa.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.sgulf.RData: | |
| command: update_cleanData("data/raw.sgulf.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.shelf.RData: | |
| command: update_cleanData("data/raw.shelf.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.wcann.RData: | |
| command: update_cleanData("data/raw.wcann.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
| data/clean.wctri.RData: | |
| command: update_cleanData("data/raw.wctri.RData") | |
| depends: | |
| # - clean_input | |
| # - data/spp.key.RData | |
| - clean_scripts | |
| - spp | |
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