rBatt

% ===============
% = Bookkeeping =
% ===============
% Equation 3: average respiration
R_{\mu} = \frac{\sum\limits_{i=1}^{n} \Delta DO_i - F_i}{n \Delta t}

NEP = \frac{NEP_t (\text{mg O}_2 \text{ L}^{\text{-}1} \Delta t)} {1}

rBatt

png(file="~/Desktop/figure.png", width=3.5, height=3.5, res=150, units="in") # open / setup device

par(
  mar=c(1.75, 1.75, 0.1, 0.1), # panel magin size in "line number" units
  mgp=c(1, 0.1, 0), # default is c(3,1,0); line number for axis label, tick label, axis
  tcl=-0.1, # size of tick marks as distance INTO figure (negative means pointing outward)
  cex=1, # character expansion factor; keep as 1; if you have a many-panel figure, they start changing the default!
  ps=8, # point size, which is the font size
  family="sans"

rBatt

# this is what 'test' looks like: 
# > test
#          s.reg year num      nameID     stratum    lon  lat btemp depth        N Nsite                      spp Z      u.a0          a1         a2
#       1:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83 Acantholithodes hispidus 0 -2.807526  0.60290095 -0.1560553
#       2:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83  Acantholumpenus mackayi 0 -4.294548  0.66363085 -0.1244255
#       3:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83       Actinauge verrilli 0 -2.763588  0.67887606 -0.1261046
#       4:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83            Admete regina 0 -3.658542  0.66688800 -0.1661476
#       5:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83         Aforia circinata 0 -9.954288  0.67970755 -0.1168343
#      ---

rBatt

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

rBatt

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))

rBatt

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

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

echo $PATH

cd
mkdir src

rBatt

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

rBatt

# 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, 

rBatt

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

rBatt

#' 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=","}