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# load libraries
library(sp) # for meuse
library(sf) # for sf objects
library(ggmap) # for base maps
library(ggplot2) # for mapping

# import dataset, check structure
data(meuse)
str(meuse)

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#import relevant packages
library(gstat)
library(sp)
library(nlme)

#create simulated data, lat and lon from uniformly distributed variable, exp1 and exp2 from random normal
set.seed(2)
samp.sz<-400
lat<-runif(samp.sz,-4,4)
lon<-runif(samp.sz,-4,4)

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mc.int.ex<-function(x.range=c(-3,3),int=c(-1.96,1.96),n=10000,plot=T,
  plot.pts=T,plot.poly=T,cols=list('black','green','blue'),round.val=2,val=F){
	
	require(scales)
	
	#create data for model fit
	x.fit<-seq(x.range[1],x.range[2],length=n)
	y.fit<-dnorm(x.fit)
	dat.fit<-data.frame(x.fit,y.fit)
	

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#credit http://stackoverflow.com/questions/13649473/add-a-common-legend-for-combined-ggplots

require(ggplot2)
require(reshape)
require(gridExtra)

p.dat<-data.frame(step=row.names(grp.dat),grp.dat,stringsAsFactors=F)
p.dat<-melt(p.dat,id='step')
p.dat$step<-as.numeric(p.dat$step)

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#' Format a text file for mothur
#'
#' @param fl chr string for input file
#' @param rev_cmp logical if file needs reverse complemeNT
#' @param savefl logical if output file is saved, otherwise the output is returned in the console
moth_form <- function(fl, rev_cmp = FALSE, savefl = TRUE, flnm = 'myfile.txt'){

  # import file
  dat <- read.table(fl, sep = '\t')
  

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plotFlowConc <- function(eList, month = c(1:12), years = NULL, col_vec = c('red', 'green', 'blue'), ylabel = NULL, xlabel = NULL, alpha = 1, size = 1,  allflo = FALSE, ncol = NULL, grids = TRUE, scales = NULL, interp = 4, pretty = TRUE, use_bw = TRUE, fac_nms = NULL, ymin = 0){
  
  localDaily <- getDaily(eList)
  localINFO <- getInfo(eList)
  localsurfaces <- getSurfaces(eList)
  
  # plot title
  toplab <- with(eList$INFO, paste(shortName, paramShortName, sep = ', '))

  # flow, date info for interpolation surface

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plot.qual<-function(x,x.locs=c(0.01,0.99),y.locs=c(0,1),steps=NULL,sp.names=NULL,dt.tx=T,rsc=T,
	ln.st=NULL,rs.ln=c(3,15),ln.cl='RdYlGn',alpha=0.7,leg=T,rnks=FALSE,...){

	require(RColorBrewer)
	require(scales)
	
	if(length(x.locs) != 2 | length(y.locs) != 2) 
		stop('x and y dimensions must be two-element vectors')
	
	if(x.locs[1]<0 | x.locs[2]>1 | y.locs[1]<0 | y.locs[2]>1) 

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# PPOTM:  Practical-Programming Of The Month (2016 January)

# iMAINloop:  Continue asking users "what file to load" until they type a zero.
iMAINloop <- 0;
while (iMAINloop < 1 ) {
  
  # Below creates a list of all files (in the current working directory) of pattern *.csv
  # Note that you can set  path="xxxx" to look in a different folder area
  filenames <- list.files(pattern = ".csv")

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lek.fun<-function(mod.in,var.sens=NULL,resp.name=NULL,exp.in=NULL,steps=100,split.vals=seq(0,1,by=0.2),val.out=F){
  
  require(ggplot2)
  require(reshape)
  
  ##
  #sort out exp and resp names based on object type of call to mod.in
  #get matrix for exp vars
  
  #for nnet

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plot.area<-function(x,col=NULL,horiz=F,prop=T,stp.ln=T,grp.ln=T,axs.cex=1,axs.lab=T,lab.cex=1,
                    names=c('Group','Step','Value'),...){
  
  #sort out color fector  
  if(!is.null(col)){
    if(sum(col %in% colors()) != length(col)) stop('col vector must be in "colors()"')
    col<-colorRampPalette(col)(ncol(x))
  }
  else col<-colorRampPalette(c('lightblue','green'))(ncol(x))