pkgBuild/remake.R

In rBatt/trawlData: Read and Clean Data from Bottom Trawl Surveys

setwd("~/Documents/School&Work/pinskyPost/trawlData")

library('devtools')
library('data.table')
library("remake")
library(LaF)
library(bit64)
library(stringr)
library(stringi)
library(PBSmapping)

source("R//add_grid.R")
source("R//check_strat.R")
source("R//clean.columns.R")
source("R//clean.format.R")
source("R//clean.names.R")
source("R//clean.tax.R")
source("R//clean.trimCol.R")
source("R//clean.trimRow.R")
source("R//datasets.R")
source("R//declareColumns.R")
source("R//formatStrat.R")
source("R//formatValue.R")
source("R//helperFile.R")
source("R//helperMisc.R")
source("R//helperStat.R")
source("R//mpick.R")
source("R//pick.R")
source("R//plot_check.R")
source("R//read.trawl.R")
source("R//sppImg.R")
source("R//tax.getCmmn.R")
source("R//tax.getSpp.R")
source("R//tax.getTax.R")
source("R//tax.getTL.R")
source("R//trawlAgg.R")
source("R//trawlCast.R")
source("R//trawlData-package.R")
source("R//trawlTrim.R")
source("man-roxygen//areaswept.R")
source("man-roxygen//BGSCODE.R")
source("man-roxygen//BGSID.R")
source("man-roxygen//btemp.R")
source("man-roxygen//clean_seeAlso_template.R")
source("man-roxygen//cnt.R")
source("man-roxygen//cntcpue.R")
source("man-roxygen//common.R")
source("man-roxygen//cruise.R")
source("man-roxygen//date.R")
source("man-roxygen//datetime.R")
source("man-roxygen//depth.R")
source("man-roxygen//depth2.R")
source("man-roxygen//DepthIntervalm.R")
source("man-roxygen//duration.R")
source("man-roxygen//gearsize.R")
source("man-roxygen//geartype.R")
source("man-roxygen//genus.R")
source("man-roxygen//haul.R")
source("man-roxygen//haulid.R")
source("man-roxygen//helperStatTemplate.R")
source("man-roxygen//lat.deg.R")
source("man-roxygen//lat.min.R")
source("man-roxygen//lat.R")
source("man-roxygen//lon.deg.R")
source("man-roxygen//lon.min.R")
source("man-roxygen//lon.R")
source("man-roxygen//meshsize.R")
source("man-roxygen//NPFMCArea.R")
source("man-roxygen//OldStratumCode.R")
source("man-roxygen//SID.R")
source("man-roxygen//species.R")
source("man-roxygen//spp.R")
source("man-roxygen//station.R")
source("man-roxygen//stemp.R")
source("man-roxygen//stratum.R")
source("man-roxygen//stratumarea.R")
source("man-roxygen//stratumarea2.R")
source("man-roxygen//StratumCode.R")
source("man-roxygen//Subarea.R")
source("man-roxygen//time.R")
source("man-roxygen//timezone.R")
source("man-roxygen//towspeed.R")
source("man-roxygen//vessel.R")
source("man-roxygen//weight.R")
source("man-roxygen//wtcpue.R")
source("man-roxygen//X_reg.R")
source("man-roxygen//year.R")
source("pkgBuild/R/makeData.R")
source("pkgBuild/R/update_spp.key.R")
source("pkgBuild/R/update_rawData.R")
source("pkgBuild/R/update_cleanData.R")
source("pkgBuild/R/createSppKey.R")
dir.create("inst/extdata/taxonomy", FALSE, TRUE)
dir.create("data", FALSE, TRUE)
update_rawData("inst/extdata/ai.zip")
update_rawData("inst/extdata/ebs.zip")
update_rawData("inst/extdata/gmex.zip")
update_rawData("inst/extdata/goa.zip")
neus_raw_files <- 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")
update_rawData(neus_raw_files)
update_rawData("inst/extdata/newf.zip")
update_rawData("inst/extdata/sa.zip")
update_rawData("inst/extdata/sgulf.zip")
update_rawData("inst/extdata/shelf.zip")
update_rawData("inst/extdata/wcann.zip")
update_rawData("inst/extdata/wctri.zip")
raw_data <- document()
update_spp.key(check_raw = TRUE)
update_spp.key("inst/extdata/taxonomy/spp.key.csv")
spp <- update_spp.key()
update_cleanData("data/raw.ai.RData")
update_cleanData("data/raw.ebs.RData")
update_cleanData("data/raw.gmex.RData")
update_cleanData("data/raw.goa.RData")
update_cleanData("data/raw.neus.RData")
update_cleanData("data/raw.newf.RData")
update_cleanData("data/raw.sa.RData")
update_cleanData("data/raw.sgulf.RData")
update_cleanData("data/raw.shelf.RData")
update_cleanData("data/raw.wcann.RData")
update_cleanData("data/raw.wctri.RData")
all <- document()