R/exinaceaLab.R

In stuartWagenius/echinaceaLab: useful functions for the Echinacea Project

#' @name exinaceaLab-paxage
#' @aliases exinaceaLab-paxage exinaceaLab
#' @title  exinaceaLab
#' @description Functions to help manage and visualize Echinacea Project datasets.
#' @details This package contains useful functions for the lab and in the field
#' see examples for how to use the functions
#' @author Stuart Wagenius
#' @examples
#' #####################################################################
#' ################# check scans and create upload csv #################
#' #####################################################################
#' \dontrun{
#' library(echinaceaLab)
#' library(plyr)
#' 
#' # this is the simple way of doing it ####
#' exps15 <- c("96_a", "99m", "99s", "inb1_a", "inb2_a", "2001", "inb2_b")
#' priority15 <- c(20, 30, 40, 50, 55, 60, 93)
#' expr <- data.frame(exps15, priority15)
#' 
#' writeUploadCSV("I:/Departments/Research/EchinaceaCG2015/cg2015scans",
#'                paste0("C:/Users/dhanson/Dropbox/CGData/165_count/count2015/",
#'                       "summer2016_prep/cg15ForSummer16.csv"), 2015, expr, "online")
#' 
#' 
#' # this is the longer, manual way of doing it ####
#' # check for missing scans ####
#' # create data frame with all scans found in "F:/cg2013scans" (on cgStorageA1)
#' loadScans("F:/cg2013scans")
#' # remove "extra" files, if present
#' scans <- scans[!(scans$filename %in% c("Thumbs.db", "itfiles.ini")),]
#' # folders that should be there but aren't
#' stillNeed <- setdiff(levels(hh.2013$batch), levels(scans$batch))
#' # folders that are there but shouldn't be
#' ignore <- setdiff(levels(scans$batch), levels(hh.2013$batch))

#' # check batch for all batches separately
#' batchecks <- aaply(levels(scans$batch), .margin = 1, .fun = check.batch, harvestFile=hh.2013)
#' batchecks <- cbind(batchecks, levels(scans$batch))
#' colnames(batchecks)[6] <- "batchName"
#' batchecks <- batchecks[,c(6,1,2,3,4,5)]
#' 
#' # rename writeTo to have date
#' writeTo <- "C:/Users/dhanson/Dropbox/CGData/155_scan/2013scanSummary.csv"
#' write.csv(batchecks, file = writeTo, row.names = F)
#' write.table(c("need experiments:", stillNeed, "\n"), file = writeTo, append = T,
#'             row.names = F, col.names = F);
#' write.table(c("ignore:", ignore, "\n"), file = writeTo, append = T,
#'             row.names = F, col.names = F);
#' write.table(c("file name:", writeTo, "\n"), file = writeTo, append = T,
#'             row.names = F, col.names = F)
#' # now look at your file and file and find everything that's missing 
#' 
#' 
#' # creating an assignment file for scans ####
#' # choose which experiments you'll be uploading and what their priorities will be
#' exps13 <- c("96_x", "inb1_b", "inb2_x", "M03", "qGen_b", "qGen_c", "qGen_x",
#'             "qGen2", "99s")
#' priority13 <- c(80, 79, 80, 90, 80, 85, 90, 60)
#' 
#' # do a quick double check to make sure everything is there 
#' loadScans(path = "F:/cg2013scans") 
#' scans <- scans[!(scans$filename %in% c("Thumbs.db", "itfiles.ini")),]
#' check.batch(batch = exps13, scansdf = scans, harvestFile = hh.2013)
#' 
#' # if there are no missing scans, create assignment csv and write to file
#' createCSV(scansdf = scans, harvYear = 2013, priority = 50)
#' # only take ones in the experiments we want to upload
#' out <- out[out$experiment %in% exps13,]
#' # change priorities to what you want
#' for (i in 1:length(exps13)) {
#'   out[out$experiment %in% exps13[i], "priority"] <- priority13[i]
#' }
#' out13 <- out # in case you're doing multiple years at once
#' 
#' # use this if you only want one person to count certain experiments
#' oneCt13 <- c("99s", "qGen2")
#' # get only one record per head for these experiments
#' out13[out13$experiment %in% oneCt13, "round"] <- 1
#' out13 <- out13[!duplicated(out13),]
#' # change this to decide who counts
#' out13[out13$user %in% "99s", "round"] <- "acouglin"
#' out13[out13$user %in% "qGen2", "round"] <- "lobenauf"
#' 
#' # write the file to a csv
#' write.csv(out13, 
#'           "C:/Users/dhanson/Dropbox/CGData/165_count/count2015/scanAssignments2013.csv",
#'           row.names = FALSE)
#' }
#' 
#' 
#' ####################################################################
#' ######################### check count data #########################
#' ####################################################################
#' \dontrun{
#' library(echinaceaLab)
#' # check count data
#' polaph3 <- read.csv("C:/Users/dhanson/Dropbox/CGData/165_count/count2015/checkCounts/polLon_aphids_2014.csv")
#' source("C:/Users/dhanson/Dropbox/CGData/165_count/count2014/manageCountData.R")
#' 
#' # checking for large numbers
#' big <- polaph3[polaph3$letno %in% polaph3[polaph3$count > 300, "letno"],]
#' big <- big[order(big$letno),c("letno", "count", "notes")]
#' 
#' qman <- manageCountData(polaph3)
#' library(plyr)
#' sortqman <- function(probs) {
#'   probs[order(probs$letno),]
#' }
#' qman2 <- llply(qman, .fun = sortqman)
#' 
#' probnos <- qman$checkNotes$letno
#' probnos <- probnos[!duplicated(probnos)]
#' probnos <- sort(probnos)
#' checkem <- polaph3[polaph3$letno %in% probnos,]
#' checkem <- checkem[order(checkem$letno, checkem$notes), ]
#' }
#' 
#' 
#' ####################################################################
#' ########################### add gps data ###########################
#' ####################################################################
#' 
#' \dontrun{
#' library(echinaceaLab)
#' # use the gps protocol to copy files from the gps to
#' # the geospatialDataBackup folder for the summer and then convert those files
#' # from .tsj to .xml files on HAL using topcon link
#' # if done on a computer besides Hal, you'll likely have to change "Echinacea" to something else
#' folderXML <- "C:/Users/Echinacea/Dropbox/geospatialDataBackup2015/convertedXML2015/"
#' folderRD <- "C:/Users/Echinacea/Dropbox/geospatialDataBackup2015/convertedRDataFiles2015/"
#' (fileNames <- dir(folderXML)) # make sure your files are there
#' 
#' # copy and paste this for every new job
#' # use the name format of the original job (from the GPS unit) for convertXMLtoRdata
#' convertXMLtoRdata("JOB_YYYYMMDD_MACHINE.xml")
#' (fileNames <- dir(folderRD))
#' (rdataNames <- makeGPSFileName(newFiles))
#' # use the name format from make GPS file name for the next two functions
#' errorCheckRData(folderRD, "aYYYYMMDD_job_MACHINE")
#' addToSurv.csv("aYYYYMMDD_job_MACHINE")
#' }
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