emhart

#' @description Rescale a vector of numbers to an arbitrary range.
#' @param minVal The minimum value in the range to rescale your numbers to
#' @param maxVal The maximum value on the range to rescale your numbers to
#' @param vec The vector you want to rescale
#' @example /dontrun{
#' orig <- runif(10,1,30)
#' rescaled <- arb_rescale(2,5,orig)
#' cbind(orig,rescaled)
#' }
arb_rescale <- function(minVal,maxVal, vec){

emhart

## Installation
install.packages("devtools")
library(devtools)
devtools::install_github("ropensci/reol")
library("Reol")

res <- DownloadSearchedTaxa(c("Diceros bicornis","Anolis carolinensis", "Anolis garmani"), to.file=FALSE, exact=TRUE)
## Get IUCN status
GetIUCNStat(res)
### Extract the full page information.

emhart

library(devtools)
install_github("ropensci/mdextract",dependencies = TRUE)
library(spocc)
saltest <- occ("Ambystoma maculatum",from="inat")
saltest <- occ2df(saltest)
## See a bounding box
scov <- coverage_extract(saltest,spatial=list(type="box",lat = "latitude", lon = "longitude",elevation = FALSE))
plot(scov)

### Now let's try poly

emhart

library(MASS)
library(lars)
library(lavaan)

####Code to wrap lasso and extra CV...
### Taken from: http://www4.stat.ncsu.edu/~boos/var.select/lasso.dr1.txt

lasso.dr1<-function(x,y,kfold=5,rep=10,plot=T,grid=seq(from=0,to=1,length=100)){
  # wrapper for lasso in lars, with modifications to cv.lars
  require(lars)

emhart

# sapply gone terribly terribly wrong, or used perfectly, I can't tell.
# Use:
# input: a vector of words, and I want to know are any of the words in input are in the vector out
# out: a vector of words that I want to check against, a master list of words 
# I then want to return an index of TRUE/FALSE to determine if a word is in in the master list

input <- c("Lorem","ipsum","testing")
out <- c("Loremipsum","qwerty","keyboard","dvorak")

dindex <- sapply(input, function(x,y){ind <- grep(x,y);ifelse(length(ind) > 0, for(i in ind){ifelse(x == y[i],return(TRUE),return(FALSE))},return(FALSE))},y=out)

emhart

emhart

emhart

library("sp")
library("maptools")

options(stringsAsFactors=F)
coords <- read.csv("~/Downloads/latlongcoord.csv")
biome<-readShapeSpatial("~/Downloads/official/wwf_terr_ecos.shp")

### Load subset of data just as a quick test

spobj <- SpatialPoints(as.matrix(coords[1:100,c('decimalLongitude','decimalLatitude')]))

emhart

knnCont <- function(X, y, k = 4){
  
  y <- y[order(X)]
  X <- sort(X)
  x.out <- vector()
  y.out <- vector()
  for(x in 1:(length(X)-(k-1))){
    
    x.out <- c(x.out,mean(X[x:(x+(k-1))]))
    y.out <- c(y.out,mean(y[x:(x+(k-1))]))

emhart

library(sp)
library(raster)

### Data source: http://nadp.sws.uiuc.edu/ntn/annualmapsByYear.aspx#2012
### Sites provided by sarah
# Load up our data
depF<-'NO3_dep_2012.tif' 
concF<-'NO3_conc_2012.tif' 
sites <- read.csv("neonsites.csv")
unprojDep <- raster(depF)