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library("data.table")
load("clean.neus.RData")

s2c <- function (x, type = "list") 
{
    as.call(lapply(c(type, x), as.symbol))
}
colsuwant <- c("depth","btemp","stemp","bsalin","ssalin")
jho_cneus <- clean.neus[spp=="Paralichthys dentatus", structure(lapply(eval(s2c(colsuwant)),meanna, na.rm=TRUE),.Names=colsuwant),by=c("reg","datetime","year","stratum","lon","lat","haulid","season","station","spp","common")]
setkey(jho_cneus, datetime, year, stratum, station)

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# ============
# = Packages =
# ============
# to do everything in this script, make sure the following packages are installed
# install.packages(c("rgenoud", "strucchange"))


# =============
# = Functions =

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#' Read JHo
#' 
#' Read in a file formatted like Jennifer's data sets
#' 
#' @param file a character indicating the file name (and possibly path)
#' @param n_nrows integer indicating number of rows for each matrix
#' @param n_matrices integer indicating number of matrices in the file
#' @param n_comment integer indicating the number of comment lines preceding each matrix of data; should include blank lines
#' @param n_top_comment integer indicating the number of comment lines that are unique to the start of the file; default is 0 lines
#' @param ... arguments to be passed to \code{scan}, such as \code{what=numeric()} and \code{sep=","}

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#' Read JHo
#' 
#' Read in a file formatted like Jennifer's data sets
#' 
#' @param file a character indicating the file name (and possibly path)
#' @param n_nrows integer indicating number of rows for each matrix
#' @param n_matrices integer indicating number of matrices in the file
#' @param n_comment integer indicating the number of comment lines preceding each matrix of data; should include blank lines
#' @param n_top_comment integer indicating the number of comment lines that are unique to the start of the file; default is 0 lines
#' @param ... arguments to be passed to \code{scan}, such as \code{what=numeric()} and \code{sep=","}

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df <- data.frame(x = rnorm(20, mean=20, sd = 10))
threshold <- 25
replace_val <- 0

df[,"x2"] <- df[,"x"] # make them the same to start
df[df[,"x"] >= threshold, "x2"] <- replace_val # replace values at or above threshold with replacement value

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# for Eva (foreva eva)

eg <- structure(c(608416320, 608416320, 608416320, 608416320, 608416320, 
608416320, 608416320, 608416320, 608416320, 608416320, 608416320, 
608416320, 608416320, 608416320, 608416320, 608416320, 608416320, 
608416320, 608416320, 608416320, 608416320, 608416320, 608416320, 
608416320, 608416320, 608416320, 608416320, 608416320, 608416320, 
608416320, 608416320, 608416320, 608416320, 608416320, 608416320, 
608416320, 608416320, 608416320, 608416320, 608416320, 608416320, 
608416320, 608416320, 608416320, 608416320, 608416320, 608416320, 

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## All R files that are used must be listed here:
packages:
  - data.table
  - LaF
  - bit64
  - stringr
  - stringi
  - PBSmapping
  - devtools

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export PATH=$HOME/bin:$PATH
source ~/.bashrc

export PATH=$PATH:/usr/include
source ~/.bashrc

echo $PATH

cd
mkdir src

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plot(crop(subset(soda.annMax, 5:51), extent(c(-76, -65, 36, 46))), maxnl=200, bigplot=bgplt, smallplot=smplt, axis.args=axargs, col=tim.colors(), zlim=range(values(crop(subset(soda.annMax, 5:51), extent(c(-76, -65, 36, 46)))),na.rm=T))

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zCol <- function(nCols, Z){
	cols <- colorRampPalette(c("#000099", "#00FEFF", "#45FE4F", "#FCFF00", "#FF9400", "#FF3100"))(nCols)
	colVec_ind <- cut(Z, breaks=nCols)
	colVec <- cols[colVec_ind]
}

# Example
X <- rnorm(1E3)
Y <- rnorm(1E3)
Z <- X*Y