R/SEAtables.R
In benharden27/sea: Process and plot data from the Sea Education Association's archive
#######
# Make LATEX tables from SEA data
#######
#' Does the final table printing and saving after data has been edited
#'
#' Should only be called from one of the SEA table functions
#'
#' @param dfo data frame of data ready to be exported
#' @param caption caption of table.
#' @param SigF vector of significant figures for each column
#' @param secondRow List of entries for second row of table headings if needed
#' @param thirdRow List of entries for third row of table headings if needed
#' @param fileout name and location of the file to be exported
#' @export
#' @examples
#' printTable()
printTable <- function(dfo,caption="",SigF=NULL,secondRow=NULL,thirdRow=NULL,fileout="~/Desktop/tableOutput.tex") {
outTable<-xtable(dfo,caption = caption)
align(outTable) <- rep("c", ncol(dfo)+1)
if(!is.null(SigF)) {
digits(outTable) <- SigF
}
add.to.row <- list(pos = list(0), command = NULL)
if(!is.null(secondRow)) {
secondRowAdd <- paste0(paste(secondRow,collapse=' & ')," \\\\ \n")
} else {
secondRowAdd <- NULL
}
if(!is.null(thirdRow)) {
thirdRowAdd <- paste0(paste(thirdRow,collapse=' & ')," \\\\ \n")
} else {
thirdRowAdd <- NULL
}
command <- paste0(secondRowAdd,
thirdRowAdd,
"\\hline\n\\endfirsthead\n",
paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
secondRowAdd,
thirdRowAdd,
"\\hline\n\\endhead\n",
"\\hline\n",
"\\multicolumn{", ncol(dfo), "}{l}",
"{\\footnotesize Continued on next page}\n",
"\\endfoot\n",
"\\endlastfoot\n")
add.to.row$command <- command
a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
tabular.environment = "longtable",
floating=F,
include.rownames = FALSE,
caption.placement = 'top')
fileout <- gsub(" ","",fileout)
fileConn<-file(fileout)
writeLines(a, fileConn)
close(fileConn)
}
#' Creates station summary table
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableStatSum()
tableStatSum <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
dfa <- readSEAxls(filename,rplcsv = T)
df <- readSEAxls(filename,skip=1,rplcsv = T)
names(df) <- names(dfa)
names(df) <- gsub(' ','.',names(df))
xi <- sort(append(grep('Meter.Net',names(df)),grep('Meter.Net',names(df))+1))
df$Meter.Net <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('Secchi.Disk',names(df)),grep('Secchi.Disk',names(df))+1))
df$Secchi.Disk <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('Hydrocast',names(df)),grep('Hydrocast',names(df))+1))
df$Hydrocast <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi])&df[,xi]!='')+0)))),1,1)
xi <- sort(append(grep('Free.CTD',names(df)),grep('Free.CTD',names(df))+1))
df$Free.CTD <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('RBR',names(df)),grep('RBR',names(df))+1))
if(any(!is.na(df[,xi]))) {
# for (i in xi) {
# df[nchar(df[,i])==0,i] <- NA
# }
df$RBR <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
} else {
df$RBR <- rep('',nrow(df))
}
xi <- sort(append(grep('Shipek',names(df)),grep('Shipek',names(df))+1))
df$Shipek.Grab <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('Phyto',names(df)),grep('Phyto',names(df))+1))
df$Phyto.Net <- substr(gsub('[A-Z0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('Hydrophone',names(df)),grep('Hydrophone',names(df))+1))
df$hydrophone <- substr(gsub('[A-Z0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
Time <- df[,grep('Start',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
# Create Output data frame
dfo <- data.frame(Station = df$Station.Number,
Date = Date,
Time = Time,
Lon = df$LonDisplay,
Lat = df$LatDisplay,
NT = toupper(df$Neuston.Tow),
MN = toupper(df$Meter.Net),
PN = toupper(df$Phyto.Net),
HC = toupper(df$Hydrocast),
CTD = toupper(df$Free.CTD),
RBR = toupper(df$RBR),
SG = toupper(df$Shipek.Grab),
SD = toupper(df$Secchi.Disk),
HP = toupper(df$hydrophone),
SS = df$Surface.Station,
genLoc = df$General.Locale,
stringsAsFactors =F)
colnames(dfo) <- c('Station','Date','Time','Longitude','Latitude','NT','MN','PN','HC','CTD','RBR','SG','SD','HP','SS','General Locale')
dfo<- dfo[!sapply(dfo, function (k) all(k==''))]
caption <- paste0("\\label{stationSummary} Summary of oceanographic sampling stations for SEA Cruise ",cruiseID,". [",dim(dfo)[1]," Stations]")
fileout <- file.path(saveLoc,gsub(ext,'tex',file))
printTable(dfo,caption=caption,fileout=fileout)
}
#' Creates Hydrocast table
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableHydro()
tableHydro <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
df <- readSEAxls(filename,rplcsv = T)
names(df) <- gsub(' ','.',names(df))
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
Bottled <- as.character(round(as.numeric(df[,grep("Corr",names(df))])))
Bottled[is.na(Bottled)&df$Bottle!=13] <- 'DNF'
df$Bottle[grep('SS',df$Bottle)] <- "13"
Bottled[is.na(Bottled)&df$Bottle==13] <- '0'
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Bottle=df$Bottle,
Bottled = Bottled ,
NO3=df[grep("Nitrate.*uM",names(df))],
PO4=df[grep("PO4.*uM",names(df))],
pH=df[grep("pH",names(df))],
Chla=df[grep("Chl.*a.*ug",names(df))],
Temp=df[grep("Temp.*deg",names(df))],
Sal=df[grep("Salinity.*psu",names(df))],
stringsAsFactors =F)
colnames(dfo) <- c('Station','Date','Time','Bottle','Bottle Depth','NO3','PO4','pH','Chl-a','Temperature','Salinity')
secondRow <- c('','','(local)','','[m]','[uM]','[uM]','','[mg/L]','[degC]','')
SigF <- c(20,20,20,20,0,0,2,2,2,3,1,2)
emptyCols <- (sapply(dfo, function (k) all(k==''))|sapply(dfo, function (k) all(is.na(k))))
dfo<- dfo[!emptyCols]
secondRow <- secondRow[!emptyCols]
SigF <- SigF[!emptyCols]
caption = paste0("\\label{hydrowork} Hydrocast station data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(ext,'tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
#' Creates CTD summary table
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableCTD()
tableCTD <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
df <- readSEAxls(filename,rplcsv = T)
names(df) <- gsub(' ','.',names(df))
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Temp=df[grep("Temp",names(df))],
Sal=df[grep("Sal",names(df))],
Chla=df[grep("Fluor",names(df))],
dep=df[grep("Cast.*Depth",names(df))],
stringsAsFactors = F)
colnames(dfo) <- c('Station','Date','Time','Surf. Temperature','Surf. Salinity','Surf. Chl-a Fluoro','Cast Depth')
secondRow <- c('','','(local)','[degC]','','[Volts]','[m]')
SigF <- c(20,20,20,20,1,2,2,0)
caption <- paste0("\\label{ctdwork} CTD station data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(ext,'tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
#' Creates surface station summary table
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableSS()
tableSS <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
df <- readSEAxls(filename,rplcsv = T)
names(df) <- gsub(' ','.',names(df))
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
Nit <- as.numeric(df[,grep('NO3',names(df))[1]])
Phos <- as.numeric(df[,grep('PO4',names(df))[1]])
chla <- as.numeric(df[,grep('^(Chl.a)',names(df))[1]])
pH <- as.numeric(df[,grep('pH',names(df))[1]])
Alk <- as.numeric(df[,grep('^(?=.*Alk)(?!.*Carb).*$',names(df),perl=T)])
dfo = data.frame(Station=df$Station,
Date=Date,
Time=Time,
Lon=df$LonDisplay,
Lat=df$LatDisplay,
Temp=df[grep('Temp.*C',names(df))],
Sal=df[grep('Salinity',names(df))],
stringsAsFactors = F)
colnames(dfo) <- c('Station','Date','Time','Longitude','Latitude','Temperature','Salinity')
secondRow <- c('','','(local)','','','[degC]','')
possVar <- c('chla','Nit','Phos','pH','Alk')
nameVar <- c('Chl-a','NO3','PO4','pH','Total Alk.')
unitVar <- c('[mg/L]','[uM]','[uM]','','[Meq/L]')
sigFig<-c(3,3,3,3,3)
usedVar <- usedSig <- usedUnit <-NULL
initCol <- colnames(dfo)
initSig <- c(20,20,20,20,20,20,1,2)
for (i in 1:length(possVar)) {
if(length(which(!is.na(get(possVar[i]))))>0) {
dfo <- cbind(dfo,get(possVar[i]))
usedVar <- append(usedVar,nameVar[i])
usedSig <- append(usedSig,sigFig[i])
usedUnit <- append(usedUnit,unitVar[i])
}
}
SigF <- append(initSig,usedSig)
colnames(dfo) <- append(initCol,usedVar)
fileout <- file.path(saveLoc,gsub(ext,'tex',file))
caption = paste0("\\label{surfsamp} Surface station data for SEA Cruise ",cruiseID)
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
#' Creates Neuston tow summary table
#'
#' Creates two tables - one for overview and the second for nekton data
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableNeuston)
tableNeuston <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
ship <- str_extract(file,"[CS]")
if(ship=="C"){
skip = 1
} else {
skip = 0
}
df <- readSEAxls(filename,skip=skip,rplcsv = T)
names(df) <- gsub(' ','.',names(df))
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
Moon <- df[,grep("Moon",names(df))]
if(mean(Moon,na.rm=T)<1) {Moon<-Moon*100}
# OVERVIEW DATA
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Moon=Moon,
Temp=as.numeric(df[,grep("Temp",names(df))]),
Sal=as.numeric(df[,grep("Salinity",names(df))]),
Chla=as.numeric(df[,grep("Fluor",names(df))]),
TowA=as.numeric(df[,grep("Tow.*Distance",names(df))]),
BioV=as.numeric(df[,grep("Zoo.*Biomass",names(df))]),
Den=as.numeric(df[,grep("Density",names(df))])*1000,
stringsAsFactors = F)
colnames(dfo) <- c('Station','Date','Time','Moon Phase','Temperature','Salinity','Chl-a','Tow Area','Zooplankton','Zooplankton')
secondRow <-c('','','(local)','[\\% full]','[degC]','','Fluoroesence','[$m^2$]','Biovolume','Density')
thirdRow <- c('','','','','','','[Volts]','','[mL]','[$uL/m^2$]')
SigF <- c(20,20,20,20,0,1,2,2,0,1,2)
caption <- paste0("\\label{neuston1} Neuston tow hydrographic data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(paste0(".",ext),'_1.tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,thirdRow=thirdRow,fileout=fileout)
# NEKTON
dfo <- data.frame(Station=df$Station,
Phyl=as.numeric(df[,grep("Phyll.*#",names(df))]),
Lept=as.numeric(df[,grep("Lepto.*#",names(df))]),
Halo=as.numeric(df[,grep("Halob.*#",names(df))]),
Myct=as.numeric(df[,grep("Mycto.*#",names(df))]),
Plas1=as.numeric(df[,grep("Plastic.*pellets",names(df))]),
Plas2=as.numeric(df[,grep("Plastic.*pieces",names(df))]),
Tar=as.numeric(df[,grep("Tar",names(df))]),
Nekt=as.numeric(df[,grep("Total.*Nekton.*ml",names(df))]),
Gel=as.numeric(df[,grep("Gelat.*ml",names(df))]),
stringsAsFactors = F)
colnames(dfo) <- c('Station','Phyl','Lept','Halo','Myct','Plastic Pellets','Plastic Pieces','Tar','Nekton > 2cm','Gelatinous > 2cm')
secondRow <- c('','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[mL]','[mL]')
SigF <- c(20,20,0,0,0,0,0,0,0,1,1)
caption <- paste0("\\label{neuston2} Neuston tow biological data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(paste0(".",ext),'_2.tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
#' Creates 100 count data summary table
#'
#' Creates table in two parts due to length of dataset
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' table100Count()
table100Count <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
df <- readSEAxls(filename,rplcsv = T,sheet=2)
if(sum(is.na(df[1,]))==ncol(df)) {
df <- df[2:nrow(df),]
}
# df <- readSEAxls(filename,rplcsv = T,sheet=2,skip=1)
# names(df) <- gsub(' ','.',names(dfn)[1:dim(df)[2]])
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Cnid=as.numeric(df[,grep("Medu",names(df))]),
Siph=as.numeric(df[,grep("Sipho",names(df))]),
Cten=as.numeric(df[,grep("Cteno",names(df))]),
Pter=as.numeric(df[,grep("Ptero",names(df))]),
Nud=as.numeric(df[,grep("Nudib",names(df))]),
Other=as.numeric(df[,grep("Other.*Snail",names(df))]),
Poly=as.numeric(df[,grep("Polycheate",names(df))]),
Chaet=as.numeric(df[,grep("Chaet",names(df))]),
Cop=as.numeric(df[,grep("Copep",names(df))]),
Gam=as.numeric(df[,grep("Gamma",names(df))]),
Hyp=as.numeric(df[,grep("Hyper",names(df))]),
Crab=as.numeric(df[,grep("Zoea",names(df))]) + as.numeric(df[,grep("Megal",names(df))]),
stringsAsFactors = F)
secondRow <- rep('',ncol(dfo))
secondRow[3]<-'[local]'
secondRow[9]<-'Snail'
secondRow[ncol(dfo)] <- 'Larv.'
SigF <- rep(0,ncol(dfo)+1)
caption <-paste0("\\label{100count1} Zooplankton 100 count data for SEA Cruise ",cruiseID," (part 1). Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(paste0(".",ext),'_100Count_1.tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
### SECOND PART
Other <- as.numeric(rowSums(df[,grep("^Other$|^Other[_]+",names(df))],na.rm=T))
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Shr=as.numeric(df[,grep("Shrimp",names(df))]),
Lob=as.numeric(df[,grep("Lobster",names(df))]),
Mys=as.numeric(df[,grep("Mysid",names(df))]),
Euph=as.numeric(df[,grep("Euph",names(df))]),
Stom=as.numeric(df[,grep("Stoma",names(df))]),
Ostr=as.numeric(df[,grep("Ostra",names(df))]),
Iso=as.numeric(df[,grep("Isopo",names(df))]),
Salp=as.numeric(df[,grep("Salp",names(df))]),
Fish=as.numeric(df[,grep("Fish.*Larva",names(df))]),
Fishe=as.numeric(df[,grep("Fish.*Eggs",names(df))]),
Other=Other,
Shan=as.numeric(df[,grep("Shannon",names(df))]),
stringsAsFactors = F)
cn <- colnames(dfo)
cn[grep('Fishe',cn)] <- 'Fish'
cn[grep('Shan',cn)] <- 'Shannon-Weiner'
colnames(dfo) <- cn
secondRow <- rep('',ncol(dfo))
secondRow[c(4,5,8,12)]<-'Larv.'
secondRow[13] <- 'Eggs'
secondRow[ncol(dfo)] <- 'Diversity Index'
secondRow[3] <- '[local]'
SigF <- rep(0,ncol(dfo)+1)
SigF[ncol(dfo)+1] <- 2
caption <- paste0("\\label{100count2} Zooplankton 100 count data for SEA Cruise ",cruiseID," (part 2). Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(paste0(".",ext),'_100Count_2.tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
# FIXME: Everything after this needs reworking.
#
#
#
# ## METER NET
# filename <- paste0(cruiseID,'_meterwork.xlsm')
# system(paste('xlsx2csv',file.path(shipfold,filename),'-s 1 >',file.path(outfold,gsub('.xlsm','_1.csv',filename)),sep=' '))
# system(paste('xlsx2csv',file.path(shipfold,filename),'-s 2 >',file.path(outfold,gsub('.xlsm','_2.csv',filename)),sep=' '))
#
#
#
#
# # METER NET OVERVIEW
# df <- read.csv(file.path(outfold,gsub('.xlsm','_1.csv',filename)),stringsAsFactors = F)
# nrows <- which(nchar(as.character(df$Station))==0)[1]-1
# df <- df[1:nrows,]
# df$Date <- gsub('\\[\\$-409\\]','',df$Date)
#
# Time <- df$Time
# Time[!grepl(':',Time)] <- paste0('00:',gsub(' ','0',format(round(as.numeric(Time[!grepl(':',Time)])*1440),width=2)))
#
#
# dfo <- data.frame(Station=df$Station,
# Date=df$Date,
# Time=Time,
# Temp=df$Temp..oC.,
# Sal=df$Salinity..psu.,
# Chla=df$Fluoro..chl.a.,
# Towd=df$Tow.depth..m.,
# TowD=df$Tow.Length..m.,
# TowV=df$Tow.Volume..m3.,
# BioV=df$Zoop.Biomass..ml.,
# Den=as.numeric(df$Zpl.Density..ml.m3.)*1000)
#
# colnames(dfo) <- c('Station','Date','Time','Temperature','Salinity','Chl-a','Tow','Tow','Tow','Zooplankton','Zooplankton')
# secondRow <-c('','','(local)','[degC]','','Fluoroesence','Depth','Length','Volume','Biovolume','Density')
# thirdRow <- c('','','','','','[Volts]','[m]','[m]','[$m^3]','[mL]','[$uL/m^3$]')
# SigF <- c(20,20,20,20,1,2,2,0,0,1,1,2)
# outTable<-xtable(dfo,caption = paste0("\\label{meter1} 1-meter and 2-meter net tow hydrographic data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}"))
# align(outTable) <- rep("c", ncol(dfo)+1)
# digits(outTable) <- SigF
#
# add.to.row <- list(pos = list(0), command = NULL)
# command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# paste0(paste(thirdRow,collapse=' & ')," \\\\ \n"),
# "\\hline\\n\\endfirsthead\n",
# paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
# paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# paste0(paste(thirdRow,collapse=' & ')," \\\\ \n"),
# "\\hline\n\\endhead\n",
# "\\hline\n",
# "\\multicolumn{", ncol(dfo), "}{l}",
# "{\\footnotesize Continued on next page}\n",
# "\\endfoot\n",
# "\\endlastfoot\n")
# # command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# # paste0(paste(thirdRow,collapse=' & ')," \\\\ \n"),
# # "\\hline\n\\endhead\n",
# # "\\hline\n",
# # "\\multicolumn{", ncol(dfo), "}{l}",
# # "{\\footnotesize Continued on next page}\n",
# # "\\endfoot\n",
# # "\\endlastfoot\n")
# add.to.row$command <- command
#
# a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
# tabular.environment = "longtable",
# floating=F,
# include.rownames = FALSE,
# caption.placement = 'top')
#
# fileout <- gsub(paste0(cruiseID,'_'),'',gsub('.xlsm','_1.tex',filename))
# fileConn<-file(file.path(tablefold,fileout))
# writeLines(a, fileConn)
# close(fileConn)
#
#
#
#
# # NEKTON
#
# dfo <- data.frame(Station=df$Station,
# Phyl=df$Phyllosoma..,
# Lept=df$Leptocephali..,
# Halo=df$Halobates..,
# Myct=df$Myctophids..,
# Plas1=df$Plastic.pellets,
# Plas2=df$Plastic.pieces,
# Tar=df$Tar,
# Nekt=df$Total.Nekton.ml,
# Gel=df$Geltanious.ml)
#
# colnames(dfo) <- c('Station','Phyl','Lept','Halo','Myct','Plastic Pellets','Plastic Pieces','Tar','Nekton > 2cm','Gelatinous > 2cm')
# secondRow <- c('','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[mL]','[mL]')
# SigF <- c(20,20,0,0,0,0,0,0,0,1,1)
#
# outTable<-xtable(dfo,caption = paste0("\\label{meter2} 1-meter and 2-meter net tow biological data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}"))
# align(outTable) <- rep("c", ncol(dfo)+1)
# digits(outTable) <- SigF
#
# add.to.row <- list(pos = list(0), command = NULL)
# command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\\n\\endfirsthead\n",
# paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
# paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\n\\endhead\n",
# "\\hline\n",
# "\\multicolumn{", ncol(dfo), "}{l}",
# "{\\footnotesize Continued on next page}\n",
# "\\endfoot\n",
# "\\endlastfoot\n")
# # command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# # "\\hline\n\\endhead\n",
# # "\\hline\n",
# # "\\multicolumn{", ncol(dfo), "}{l}",
# # "{\\footnotesize Continued on next page}\n",
# # "\\endfoot\n",
# # "\\endlastfoot\n")
# add.to.row$command <- command
#
# a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
# tabular.environment = "longtable",
# floating=F,
# include.rownames = FALSE,
# caption.placement = 'top')
#
# fileout <- gsub(paste0(cruiseID,'_'),'',gsub('.xlsm','_2.tex',filename))
# fileConn<-file(file.path(tablefold,fileout))
# writeLines(a, fileConn)
# close(fileConn)
#
#
# ## PHYTONETS
#
# filename <- paste0(cruiseID,'_phytowork.xlsm')
# if(file.exists(filename)) {
# system(paste('xlsx2csv',file.path(shipfold,filename),file.path(outfold,gsub('.xlsm','.csv',filename)),sep=' '))
# df <- read.csv(file.path(outfold,gsub('.xlsm','.csv',filename)),stringsAsFactors = F)
# lasti <- which(df$Date=='')[1]-1
# df <- df[1:lasti,]
# df$Date <- gsub('\\[\\$-409\\]','',df$Date)
# Time <- df$Time
# Time[!grepl(':',Time)] <- paste0('00:',gsub(' ','0',format(round(as.numeric(Time[!grepl(':',Time)])*1440),width=2)))
#
#
# dfo <- data.frame(Station=df$Station,
# Date=df$Date,
# Time=Time,
# Temp=df$Temp..oC.,
# Sal = df$Salinity..psu.,
# Chla=df$Fluoro..raw.,
# dia=df$X..Diatoms*100,
# din=df$X..Dinoflagellates*100,
# oth=df$X..Other*100)
#
# colnames(dfo) <- c('Station','Date','Time','Temperature','Salinity','Chl-a Fluoroesence','Diatom','Dinoflagellate','Other')
# secondRow <- c('','','(local)','[degC]','','[Volts]','[\\%]','[\\%]','[\\%]')
# SigF <- c(20,20,20,20,1,2,2,0,0,0)
#
# outTable<-xtable(dfo,caption = paste0("\\label{phytowork} Phytoplankton net data for ",cruiseID,". Locations as in Table \\ref{stationSummary}"))
# align(outTable) <- rep("c", ncol(dfo)+1)
# digits(outTable) <- SigF
#
# add.to.row <- list(pos = list(0), command = NULL)
# command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\\n\\endfirsthead\n",
# paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
# paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\n\\endhead\n",
# "\\hline\n",
# "\\multicolumn{", ncol(dfo), "}{l}",
# "{\\footnotesize Continued on next page}\n",
# "\\endfoot\n",
# "\\endlastfoot\n")
# # command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# # "\\hline\n\\endhead\n",
# # "\\hline\n",
# # "\\multicolumn{", ncol(dfo), "}{l}",
# # "{\\footnotesize Continued on next page}\n",
# # "\\endfoot\n",
# # "\\endlastfoot\n")
# add.to.row$command <- command
#
# a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
# tabular.environment = "longtable",
# floating=F,
# include.rownames = FALSE,
# caption.placement = 'top')
#
# fileout <- gsub(paste0(cruiseID,'_'),'',gsub('.xlsm','.tex',filename))
# fileConn<-file(file.path(tablefold,fileout))
# writeLines(a, fileConn)
# close(fileConn)
#
# }
#
# ## SHIPEK
#
# filename <- paste0(cruiseID,'_shipekwork.xlsm')
#
# if(file.exists(filename)) {
# system(paste('xlsx2csv',file.path(shipfold,filename),file.path(outfold,gsub('.xlsm','.csv',filename)),sep=' '))
# df <- read.csv(file.path(outfold,gsub('.xlsm','.csv',filename)),stringsAsFactors = F)
# lasti <- which(df$Date=='')[1]-1
# df <- df[1:lasti,]
# df$Date <- gsub('\\[\\$-409\\]','',df$Date)
#
# Time <- df$Time
# Time[!grepl(':',Time)] <- paste0('00:',gsub(' ','0',format(round(as.numeric(Time[!grepl(':',Time)])*1440),width=2)))
#
#
# dfo <- data.frame(Station=df$Station,
# Date=df$Date,
# Time=Time,
# Temp=df$Temp..oC.,
# Sal = df$Sal..psu.,
# Chla=df$Fluoro...chl.a.,
# dep=df$Bottom.Depth..m.,
# comm=df$Comments)
#
# colnames(dfo) <- c('Station','Date','Time','Temperature','Salinity','Chl-a Fluoro','Depth','Comments')
# secondRow <- c('','','(local)','[degC]','','[Volts]','[m]','')
# SigF <- c(20,20,20,20,1,2,2,0,0)
#
# outTable<-xtable(dfo,caption = paste0("\\label{shipek} Shipek grab data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}"))
# align(outTable) <- rep("c", ncol(dfo)+1)
# digits(outTable) <- SigF
#
# add.to.row <- list(pos = list(0), command = NULL)
# command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\\n\\endfirsthead\n",
# paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
# paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\n\\endhead\n",
# "\\hline\n",
# "\\multicolumn{", ncol(dfo), "}{l}",
# "{\\footnotesize Continued on next page}\n",
# "\\endfoot\n",
# "\\endlastfoot\n")
# # command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# # "\\hline\n\\endhead\n",
# # "\\hline\n",
# # "\\multicolumn{", ncol(dfo), "}{l}",
# # "{\\footnotesize Continued on next page}\n",
# # "\\endfoot\n",
# # "\\endlastfoot\n")
# add.to.row$command <- command
#
# a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
# tabular.environment = "longtable",
# floating=F,
# include.rownames = FALSE,
# caption.placement = 'top')
#
# fileout <- gsub(paste0(cruiseID,'_'),'',gsub('.xlsm','.tex',filename))
# fileConn<-file(file.path(tablefold,fileout))
# writeLines(a, fileConn)
# close(fileConn)
# }
benharden27/sea documentation built on May 14, 2019, 4:18 p.m.
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#######
# Make LATEX tables from SEA data
#######
#' Does the final table printing and saving after data has been edited
#'
#' Should only be called from one of the SEA table functions
#'
#' @param dfo data frame of data ready to be exported
#' @param caption caption of table.
#' @param SigF vector of significant figures for each column
#' @param secondRow List of entries for second row of table headings if needed
#' @param thirdRow List of entries for third row of table headings if needed
#' @param fileout name and location of the file to be exported
#' @export
#' @examples
#' printTable()
printTable <- function(dfo,caption="",SigF=NULL,secondRow=NULL,thirdRow=NULL,fileout="~/Desktop/tableOutput.tex") {
outTable<-xtable(dfo,caption = caption)
align(outTable) <- rep("c", ncol(dfo)+1)
if(!is.null(SigF)) {
digits(outTable) <- SigF
}
add.to.row <- list(pos = list(0), command = NULL)
if(!is.null(secondRow)) {
secondRowAdd <- paste0(paste(secondRow,collapse=' & ')," \\\\ \n")
} else {
secondRowAdd <- NULL
}
if(!is.null(thirdRow)) {
thirdRowAdd <- paste0(paste(thirdRow,collapse=' & ')," \\\\ \n")
} else {
thirdRowAdd <- NULL
}
command <- paste0(secondRowAdd,
thirdRowAdd,
"\\hline\n\\endfirsthead\n",
paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
secondRowAdd,
thirdRowAdd,
"\\hline\n\\endhead\n",
"\\hline\n",
"\\multicolumn{", ncol(dfo), "}{l}",
"{\\footnotesize Continued on next page}\n",
"\\endfoot\n",
"\\endlastfoot\n")
add.to.row$command <- command
a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
tabular.environment = "longtable",
floating=F,
include.rownames = FALSE,
caption.placement = 'top')
fileout <- gsub(" ","",fileout)
fileConn<-file(fileout)
writeLines(a, fileConn)
close(fileConn)
}
#' Creates station summary table
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableStatSum()
tableStatSum <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
dfa <- readSEAxls(filename,rplcsv = T)
df <- readSEAxls(filename,skip=1,rplcsv = T)
names(df) <- names(dfa)
names(df) <- gsub(' ','.',names(df))
xi <- sort(append(grep('Meter.Net',names(df)),grep('Meter.Net',names(df))+1))
df$Meter.Net <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('Secchi.Disk',names(df)),grep('Secchi.Disk',names(df))+1))
df$Secchi.Disk <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('Hydrocast',names(df)),grep('Hydrocast',names(df))+1))
df$Hydrocast <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi])&df[,xi]!='')+0)))),1,1)
xi <- sort(append(grep('Free.CTD',names(df)),grep('Free.CTD',names(df))+1))
df$Free.CTD <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('RBR',names(df)),grep('RBR',names(df))+1))
if(any(!is.na(df[,xi]))) {
# for (i in xi) {
# df[nchar(df[,i])==0,i] <- NA
# }
df$RBR <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
} else {
df$RBR <- rep('',nrow(df))
}
xi <- sort(append(grep('Shipek',names(df)),grep('Shipek',names(df))+1))
df$Shipek.Grab <- substr(gsub('[0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('Phyto',names(df)),grep('Phyto',names(df))+1))
df$Phyto.Net <- substr(gsub('[A-Z0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
xi <- sort(append(grep('Hydrophone',names(df)),grep('Hydrophone',names(df))+1))
df$hydrophone <- substr(gsub('[A-Z0-9]','X',gsub('0','',as.character(rowSums((!is.na(df[,xi]))+0)))),1,1)
Time <- df[,grep('Start',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
# Create Output data frame
dfo <- data.frame(Station = df$Station.Number,
Date = Date,
Time = Time,
Lon = df$LonDisplay,
Lat = df$LatDisplay,
NT = toupper(df$Neuston.Tow),
MN = toupper(df$Meter.Net),
PN = toupper(df$Phyto.Net),
HC = toupper(df$Hydrocast),
CTD = toupper(df$Free.CTD),
RBR = toupper(df$RBR),
SG = toupper(df$Shipek.Grab),
SD = toupper(df$Secchi.Disk),
HP = toupper(df$hydrophone),
SS = df$Surface.Station,
genLoc = df$General.Locale,
stringsAsFactors =F)
colnames(dfo) <- c('Station','Date','Time','Longitude','Latitude','NT','MN','PN','HC','CTD','RBR','SG','SD','HP','SS','General Locale')
dfo<- dfo[!sapply(dfo, function (k) all(k==''))]
caption <- paste0("\\label{stationSummary} Summary of oceanographic sampling stations for SEA Cruise ",cruiseID,". [",dim(dfo)[1]," Stations]")
fileout <- file.path(saveLoc,gsub(ext,'tex',file))
printTable(dfo,caption=caption,fileout=fileout)
}
#' Creates Hydrocast table
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableHydro()
tableHydro <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
df <- readSEAxls(filename,rplcsv = T)
names(df) <- gsub(' ','.',names(df))
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
Bottled <- as.character(round(as.numeric(df[,grep("Corr",names(df))])))
Bottled[is.na(Bottled)&df$Bottle!=13] <- 'DNF'
df$Bottle[grep('SS',df$Bottle)] <- "13"
Bottled[is.na(Bottled)&df$Bottle==13] <- '0'
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Bottle=df$Bottle,
Bottled = Bottled ,
NO3=df[grep("Nitrate.*uM",names(df))],
PO4=df[grep("PO4.*uM",names(df))],
pH=df[grep("pH",names(df))],
Chla=df[grep("Chl.*a.*ug",names(df))],
Temp=df[grep("Temp.*deg",names(df))],
Sal=df[grep("Salinity.*psu",names(df))],
stringsAsFactors =F)
colnames(dfo) <- c('Station','Date','Time','Bottle','Bottle Depth','NO3','PO4','pH','Chl-a','Temperature','Salinity')
secondRow <- c('','','(local)','','[m]','[uM]','[uM]','','[mg/L]','[degC]','')
SigF <- c(20,20,20,20,0,0,2,2,2,3,1,2)
emptyCols <- (sapply(dfo, function (k) all(k==''))|sapply(dfo, function (k) all(is.na(k))))
dfo<- dfo[!emptyCols]
secondRow <- secondRow[!emptyCols]
SigF <- SigF[!emptyCols]
caption = paste0("\\label{hydrowork} Hydrocast station data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(ext,'tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
#' Creates CTD summary table
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableCTD()
tableCTD <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
df <- readSEAxls(filename,rplcsv = T)
names(df) <- gsub(' ','.',names(df))
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Temp=df[grep("Temp",names(df))],
Sal=df[grep("Sal",names(df))],
Chla=df[grep("Fluor",names(df))],
dep=df[grep("Cast.*Depth",names(df))],
stringsAsFactors = F)
colnames(dfo) <- c('Station','Date','Time','Surf. Temperature','Surf. Salinity','Surf. Chl-a Fluoro','Cast Depth')
secondRow <- c('','','(local)','[degC]','','[Volts]','[m]')
SigF <- c(20,20,20,20,1,2,2,0)
caption <- paste0("\\label{ctdwork} CTD station data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(ext,'tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
#' Creates surface station summary table
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableSS()
tableSS <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
df <- readSEAxls(filename,rplcsv = T)
names(df) <- gsub(' ','.',names(df))
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
Nit <- as.numeric(df[,grep('NO3',names(df))[1]])
Phos <- as.numeric(df[,grep('PO4',names(df))[1]])
chla <- as.numeric(df[,grep('^(Chl.a)',names(df))[1]])
pH <- as.numeric(df[,grep('pH',names(df))[1]])
Alk <- as.numeric(df[,grep('^(?=.*Alk)(?!.*Carb).*$',names(df),perl=T)])
dfo = data.frame(Station=df$Station,
Date=Date,
Time=Time,
Lon=df$LonDisplay,
Lat=df$LatDisplay,
Temp=df[grep('Temp.*C',names(df))],
Sal=df[grep('Salinity',names(df))],
stringsAsFactors = F)
colnames(dfo) <- c('Station','Date','Time','Longitude','Latitude','Temperature','Salinity')
secondRow <- c('','','(local)','','','[degC]','')
possVar <- c('chla','Nit','Phos','pH','Alk')
nameVar <- c('Chl-a','NO3','PO4','pH','Total Alk.')
unitVar <- c('[mg/L]','[uM]','[uM]','','[Meq/L]')
sigFig<-c(3,3,3,3,3)
usedVar <- usedSig <- usedUnit <-NULL
initCol <- colnames(dfo)
initSig <- c(20,20,20,20,20,20,1,2)
for (i in 1:length(possVar)) {
if(length(which(!is.na(get(possVar[i]))))>0) {
dfo <- cbind(dfo,get(possVar[i]))
usedVar <- append(usedVar,nameVar[i])
usedSig <- append(usedSig,sigFig[i])
usedUnit <- append(usedUnit,unitVar[i])
}
}
SigF <- append(initSig,usedSig)
colnames(dfo) <- append(initCol,usedVar)
fileout <- file.path(saveLoc,gsub(ext,'tex',file))
caption = paste0("\\label{surfsamp} Surface station data for SEA Cruise ",cruiseID)
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
#' Creates Neuston tow summary table
#'
#' Creates two tables - one for overview and the second for nekton data
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' tableNeuston)
tableNeuston <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
ship <- str_extract(file,"[CS]")
if(ship=="C"){
skip = 1
} else {
skip = 0
}
df <- readSEAxls(filename,skip=skip,rplcsv = T)
names(df) <- gsub(' ','.',names(df))
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
Moon <- df[,grep("Moon",names(df))]
if(mean(Moon,na.rm=T)<1) {Moon<-Moon*100}
# OVERVIEW DATA
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Moon=Moon,
Temp=as.numeric(df[,grep("Temp",names(df))]),
Sal=as.numeric(df[,grep("Salinity",names(df))]),
Chla=as.numeric(df[,grep("Fluor",names(df))]),
TowA=as.numeric(df[,grep("Tow.*Distance",names(df))]),
BioV=as.numeric(df[,grep("Zoo.*Biomass",names(df))]),
Den=as.numeric(df[,grep("Density",names(df))])*1000,
stringsAsFactors = F)
colnames(dfo) <- c('Station','Date','Time','Moon Phase','Temperature','Salinity','Chl-a','Tow Area','Zooplankton','Zooplankton')
secondRow <-c('','','(local)','[\\% full]','[degC]','','Fluoroesence','[$m^2$]','Biovolume','Density')
thirdRow <- c('','','','','','','[Volts]','','[mL]','[$uL/m^2$]')
SigF <- c(20,20,20,20,0,1,2,2,0,1,2)
caption <- paste0("\\label{neuston1} Neuston tow hydrographic data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(paste0(".",ext),'_1.tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,thirdRow=thirdRow,fileout=fileout)
# NEKTON
dfo <- data.frame(Station=df$Station,
Phyl=as.numeric(df[,grep("Phyll.*#",names(df))]),
Lept=as.numeric(df[,grep("Lepto.*#",names(df))]),
Halo=as.numeric(df[,grep("Halob.*#",names(df))]),
Myct=as.numeric(df[,grep("Mycto.*#",names(df))]),
Plas1=as.numeric(df[,grep("Plastic.*pellets",names(df))]),
Plas2=as.numeric(df[,grep("Plastic.*pieces",names(df))]),
Tar=as.numeric(df[,grep("Tar",names(df))]),
Nekt=as.numeric(df[,grep("Total.*Nekton.*ml",names(df))]),
Gel=as.numeric(df[,grep("Gelat.*ml",names(df))]),
stringsAsFactors = F)
colnames(dfo) <- c('Station','Phyl','Lept','Halo','Myct','Plastic Pellets','Plastic Pieces','Tar','Nekton > 2cm','Gelatinous > 2cm')
secondRow <- c('','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[mL]','[mL]')
SigF <- c(20,20,0,0,0,0,0,0,0,1,1)
caption <- paste0("\\label{neuston2} Neuston tow biological data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(paste0(".",ext),'_2.tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
#' Creates 100 count data summary table
#'
#' Creates table in two parts due to length of dataset
#'
#' @param filename Path of the file to be read in
#' @param saveLoc Folder to save the output
#' @export
#' @examples
#' table100Count()
table100Count <- function(filename,saveLoc = "~/Desktop") {
file <- tail(strsplit(filename,'/')[[1]],1)
ext <- tools::file_ext(file)
df <- readSEAxls(filename,rplcsv = T,sheet=2)
if(sum(is.na(df[1,]))==ncol(df)) {
df <- df[2:nrow(df),]
}
# df <- readSEAxls(filename,rplcsv = T,sheet=2,skip=1)
# names(df) <- gsub(' ','.',names(dfn)[1:dim(df)[2]])
Time <- df[,grep('Time',names(df))[1]]
Time <- format(Time,format="%H:%M")
Date <- format(df$Date,format="%Y-%m-%d")
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Cnid=as.numeric(df[,grep("Medu",names(df))]),
Siph=as.numeric(df[,grep("Sipho",names(df))]),
Cten=as.numeric(df[,grep("Cteno",names(df))]),
Pter=as.numeric(df[,grep("Ptero",names(df))]),
Nud=as.numeric(df[,grep("Nudib",names(df))]),
Other=as.numeric(df[,grep("Other.*Snail",names(df))]),
Poly=as.numeric(df[,grep("Polycheate",names(df))]),
Chaet=as.numeric(df[,grep("Chaet",names(df))]),
Cop=as.numeric(df[,grep("Copep",names(df))]),
Gam=as.numeric(df[,grep("Gamma",names(df))]),
Hyp=as.numeric(df[,grep("Hyper",names(df))]),
Crab=as.numeric(df[,grep("Zoea",names(df))]) + as.numeric(df[,grep("Megal",names(df))]),
stringsAsFactors = F)
secondRow <- rep('',ncol(dfo))
secondRow[3]<-'[local]'
secondRow[9]<-'Snail'
secondRow[ncol(dfo)] <- 'Larv.'
SigF <- rep(0,ncol(dfo)+1)
caption <-paste0("\\label{100count1} Zooplankton 100 count data for SEA Cruise ",cruiseID," (part 1). Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(paste0(".",ext),'_100Count_1.tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
### SECOND PART
Other <- as.numeric(rowSums(df[,grep("^Other$|^Other[_]+",names(df))],na.rm=T))
dfo <- data.frame(Station=df$Station,
Date=Date,
Time=Time,
Shr=as.numeric(df[,grep("Shrimp",names(df))]),
Lob=as.numeric(df[,grep("Lobster",names(df))]),
Mys=as.numeric(df[,grep("Mysid",names(df))]),
Euph=as.numeric(df[,grep("Euph",names(df))]),
Stom=as.numeric(df[,grep("Stoma",names(df))]),
Ostr=as.numeric(df[,grep("Ostra",names(df))]),
Iso=as.numeric(df[,grep("Isopo",names(df))]),
Salp=as.numeric(df[,grep("Salp",names(df))]),
Fish=as.numeric(df[,grep("Fish.*Larva",names(df))]),
Fishe=as.numeric(df[,grep("Fish.*Eggs",names(df))]),
Other=Other,
Shan=as.numeric(df[,grep("Shannon",names(df))]),
stringsAsFactors = F)
cn <- colnames(dfo)
cn[grep('Fishe',cn)] <- 'Fish'
cn[grep('Shan',cn)] <- 'Shannon-Weiner'
colnames(dfo) <- cn
secondRow <- rep('',ncol(dfo))
secondRow[c(4,5,8,12)]<-'Larv.'
secondRow[13] <- 'Eggs'
secondRow[ncol(dfo)] <- 'Diversity Index'
secondRow[3] <- '[local]'
SigF <- rep(0,ncol(dfo)+1)
SigF[ncol(dfo)+1] <- 2
caption <- paste0("\\label{100count2} Zooplankton 100 count data for SEA Cruise ",cruiseID," (part 2). Locations as in Table \\ref{stationSummary}")
fileout <- file.path(saveLoc,gsub(paste0(".",ext),'_100Count_2.tex',file))
printTable(dfo,caption=caption,SigF=SigF,secondRow=secondRow,fileout=fileout)
}
# FIXME: Everything after this needs reworking.
#
#
#
# ## METER NET
# filename <- paste0(cruiseID,'_meterwork.xlsm')
# system(paste('xlsx2csv',file.path(shipfold,filename),'-s 1 >',file.path(outfold,gsub('.xlsm','_1.csv',filename)),sep=' '))
# system(paste('xlsx2csv',file.path(shipfold,filename),'-s 2 >',file.path(outfold,gsub('.xlsm','_2.csv',filename)),sep=' '))
#
#
#
#
# # METER NET OVERVIEW
# df <- read.csv(file.path(outfold,gsub('.xlsm','_1.csv',filename)),stringsAsFactors = F)
# nrows <- which(nchar(as.character(df$Station))==0)[1]-1
# df <- df[1:nrows,]
# df$Date <- gsub('\\[\\$-409\\]','',df$Date)
#
# Time <- df$Time
# Time[!grepl(':',Time)] <- paste0('00:',gsub(' ','0',format(round(as.numeric(Time[!grepl(':',Time)])*1440),width=2)))
#
#
# dfo <- data.frame(Station=df$Station,
# Date=df$Date,
# Time=Time,
# Temp=df$Temp..oC.,
# Sal=df$Salinity..psu.,
# Chla=df$Fluoro..chl.a.,
# Towd=df$Tow.depth..m.,
# TowD=df$Tow.Length..m.,
# TowV=df$Tow.Volume..m3.,
# BioV=df$Zoop.Biomass..ml.,
# Den=as.numeric(df$Zpl.Density..ml.m3.)*1000)
#
# colnames(dfo) <- c('Station','Date','Time','Temperature','Salinity','Chl-a','Tow','Tow','Tow','Zooplankton','Zooplankton')
# secondRow <-c('','','(local)','[degC]','','Fluoroesence','Depth','Length','Volume','Biovolume','Density')
# thirdRow <- c('','','','','','[Volts]','[m]','[m]','[$m^3]','[mL]','[$uL/m^3$]')
# SigF <- c(20,20,20,20,1,2,2,0,0,1,1,2)
# outTable<-xtable(dfo,caption = paste0("\\label{meter1} 1-meter and 2-meter net tow hydrographic data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}"))
# align(outTable) <- rep("c", ncol(dfo)+1)
# digits(outTable) <- SigF
#
# add.to.row <- list(pos = list(0), command = NULL)
# command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# paste0(paste(thirdRow,collapse=' & ')," \\\\ \n"),
# "\\hline\\n\\endfirsthead\n",
# paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
# paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# paste0(paste(thirdRow,collapse=' & ')," \\\\ \n"),
# "\\hline\n\\endhead\n",
# "\\hline\n",
# "\\multicolumn{", ncol(dfo), "}{l}",
# "{\\footnotesize Continued on next page}\n",
# "\\endfoot\n",
# "\\endlastfoot\n")
# # command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# # paste0(paste(thirdRow,collapse=' & ')," \\\\ \n"),
# # "\\hline\n\\endhead\n",
# # "\\hline\n",
# # "\\multicolumn{", ncol(dfo), "}{l}",
# # "{\\footnotesize Continued on next page}\n",
# # "\\endfoot\n",
# # "\\endlastfoot\n")
# add.to.row$command <- command
#
# a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
# tabular.environment = "longtable",
# floating=F,
# include.rownames = FALSE,
# caption.placement = 'top')
#
# fileout <- gsub(paste0(cruiseID,'_'),'',gsub('.xlsm','_1.tex',filename))
# fileConn<-file(file.path(tablefold,fileout))
# writeLines(a, fileConn)
# close(fileConn)
#
#
#
#
# # NEKTON
#
# dfo <- data.frame(Station=df$Station,
# Phyl=df$Phyllosoma..,
# Lept=df$Leptocephali..,
# Halo=df$Halobates..,
# Myct=df$Myctophids..,
# Plas1=df$Plastic.pellets,
# Plas2=df$Plastic.pieces,
# Tar=df$Tar,
# Nekt=df$Total.Nekton.ml,
# Gel=df$Geltanious.ml)
#
# colnames(dfo) <- c('Station','Phyl','Lept','Halo','Myct','Plastic Pellets','Plastic Pieces','Tar','Nekton > 2cm','Gelatinous > 2cm')
# secondRow <- c('','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[\\#]','[mL]','[mL]')
# SigF <- c(20,20,0,0,0,0,0,0,0,1,1)
#
# outTable<-xtable(dfo,caption = paste0("\\label{meter2} 1-meter and 2-meter net tow biological data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}"))
# align(outTable) <- rep("c", ncol(dfo)+1)
# digits(outTable) <- SigF
#
# add.to.row <- list(pos = list(0), command = NULL)
# command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\\n\\endfirsthead\n",
# paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
# paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\n\\endhead\n",
# "\\hline\n",
# "\\multicolumn{", ncol(dfo), "}{l}",
# "{\\footnotesize Continued on next page}\n",
# "\\endfoot\n",
# "\\endlastfoot\n")
# # command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# # "\\hline\n\\endhead\n",
# # "\\hline\n",
# # "\\multicolumn{", ncol(dfo), "}{l}",
# # "{\\footnotesize Continued on next page}\n",
# # "\\endfoot\n",
# # "\\endlastfoot\n")
# add.to.row$command <- command
#
# a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
# tabular.environment = "longtable",
# floating=F,
# include.rownames = FALSE,
# caption.placement = 'top')
#
# fileout <- gsub(paste0(cruiseID,'_'),'',gsub('.xlsm','_2.tex',filename))
# fileConn<-file(file.path(tablefold,fileout))
# writeLines(a, fileConn)
# close(fileConn)
#
#
# ## PHYTONETS
#
# filename <- paste0(cruiseID,'_phytowork.xlsm')
# if(file.exists(filename)) {
# system(paste('xlsx2csv',file.path(shipfold,filename),file.path(outfold,gsub('.xlsm','.csv',filename)),sep=' '))
# df <- read.csv(file.path(outfold,gsub('.xlsm','.csv',filename)),stringsAsFactors = F)
# lasti <- which(df$Date=='')[1]-1
# df <- df[1:lasti,]
# df$Date <- gsub('\\[\\$-409\\]','',df$Date)
# Time <- df$Time
# Time[!grepl(':',Time)] <- paste0('00:',gsub(' ','0',format(round(as.numeric(Time[!grepl(':',Time)])*1440),width=2)))
#
#
# dfo <- data.frame(Station=df$Station,
# Date=df$Date,
# Time=Time,
# Temp=df$Temp..oC.,
# Sal = df$Salinity..psu.,
# Chla=df$Fluoro..raw.,
# dia=df$X..Diatoms*100,
# din=df$X..Dinoflagellates*100,
# oth=df$X..Other*100)
#
# colnames(dfo) <- c('Station','Date','Time','Temperature','Salinity','Chl-a Fluoroesence','Diatom','Dinoflagellate','Other')
# secondRow <- c('','','(local)','[degC]','','[Volts]','[\\%]','[\\%]','[\\%]')
# SigF <- c(20,20,20,20,1,2,2,0,0,0)
#
# outTable<-xtable(dfo,caption = paste0("\\label{phytowork} Phytoplankton net data for ",cruiseID,". Locations as in Table \\ref{stationSummary}"))
# align(outTable) <- rep("c", ncol(dfo)+1)
# digits(outTable) <- SigF
#
# add.to.row <- list(pos = list(0), command = NULL)
# command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\\n\\endfirsthead\n",
# paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
# paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\n\\endhead\n",
# "\\hline\n",
# "\\multicolumn{", ncol(dfo), "}{l}",
# "{\\footnotesize Continued on next page}\n",
# "\\endfoot\n",
# "\\endlastfoot\n")
# # command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# # "\\hline\n\\endhead\n",
# # "\\hline\n",
# # "\\multicolumn{", ncol(dfo), "}{l}",
# # "{\\footnotesize Continued on next page}\n",
# # "\\endfoot\n",
# # "\\endlastfoot\n")
# add.to.row$command <- command
#
# a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
# tabular.environment = "longtable",
# floating=F,
# include.rownames = FALSE,
# caption.placement = 'top')
#
# fileout <- gsub(paste0(cruiseID,'_'),'',gsub('.xlsm','.tex',filename))
# fileConn<-file(file.path(tablefold,fileout))
# writeLines(a, fileConn)
# close(fileConn)
#
# }
#
# ## SHIPEK
#
# filename <- paste0(cruiseID,'_shipekwork.xlsm')
#
# if(file.exists(filename)) {
# system(paste('xlsx2csv',file.path(shipfold,filename),file.path(outfold,gsub('.xlsm','.csv',filename)),sep=' '))
# df <- read.csv(file.path(outfold,gsub('.xlsm','.csv',filename)),stringsAsFactors = F)
# lasti <- which(df$Date=='')[1]-1
# df <- df[1:lasti,]
# df$Date <- gsub('\\[\\$-409\\]','',df$Date)
#
# Time <- df$Time
# Time[!grepl(':',Time)] <- paste0('00:',gsub(' ','0',format(round(as.numeric(Time[!grepl(':',Time)])*1440),width=2)))
#
#
# dfo <- data.frame(Station=df$Station,
# Date=df$Date,
# Time=Time,
# Temp=df$Temp..oC.,
# Sal = df$Sal..psu.,
# Chla=df$Fluoro...chl.a.,
# dep=df$Bottom.Depth..m.,
# comm=df$Comments)
#
# colnames(dfo) <- c('Station','Date','Time','Temperature','Salinity','Chl-a Fluoro','Depth','Comments')
# secondRow <- c('','','(local)','[degC]','','[Volts]','[m]','')
# SigF <- c(20,20,20,20,1,2,2,0,0)
#
# outTable<-xtable(dfo,caption = paste0("\\label{shipek} Shipek grab data for SEA Cruise ",cruiseID,". Locations as in Table \\ref{stationSummary}"))
# align(outTable) <- rep("c", ncol(dfo)+1)
# digits(outTable) <- SigF
#
# add.to.row <- list(pos = list(0), command = NULL)
# command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\\n\\endfirsthead\n",
# paste0(paste(colnames(dfo),collapse=' & ')," \\\\ \n"),
# paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# "\\hline\n\\endhead\n",
# "\\hline\n",
# "\\multicolumn{", ncol(dfo), "}{l}",
# "{\\footnotesize Continued on next page}\n",
# "\\endfoot\n",
# "\\endlastfoot\n")
# # command <- paste0(paste0(paste(secondRow,collapse=' & ')," \\\\ \n"),
# # "\\hline\n\\endhead\n",
# # "\\hline\n",
# # "\\multicolumn{", ncol(dfo), "}{l}",
# # "{\\footnotesize Continued on next page}\n",
# # "\\endfoot\n",
# # "\\endlastfoot\n")
# add.to.row$command <- command
#
# a<-print(outTable, hline.after=c(0), add.to.row = add.to.row,
# tabular.environment = "longtable",
# floating=F,
# include.rownames = FALSE,
# caption.placement = 'top')
#
# fileout <- gsub(paste0(cruiseID,'_'),'',gsub('.xlsm','.tex',filename))
# fileConn<-file(file.path(tablefold,fileout))
# writeLines(a, fileConn)
# close(fileConn)
# }
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