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#' Description: Code using deSolve for some simple ecological ODE models
#' There are 3 examples, one is a simple LV Pred-Prey example with plots
#' The next is a Macarthur-Wilson model with plots of both the species curve and the equlibrium points
#' The last plot is a quick crack at putting stochasticity into the model by adding oscillations in I with t.
#' LV code is modified from a blog post here: http://assemblingnetwork.wordpress.com/2013/01/31/two-species-predator-prey-systems-with-r/
#' Other additions are my own
#' 
#' Author: Edmund Hart
#' Date: 3/28/2013
#' E-mail: edmund.m.hart@gmail.com

alfcrisci

##' Function readDFile
##' 
##' Function readDFile
##' @param pathname       the pathname of the directory containing the data to import
##' @return outData       Output is a matrix of ion counts with rows as scantime and 
##' columns as mass, and the respective values as labels
##' @export
readDFile<-function(pathname){
  
  filename<-file.path(pathname,'DATA.MS')

alfcrisci

# dependencies on fedora23:
# gdal-devel geos-devel proj-devel proj-nad proj-epsg

library(htmlwidgets)
library(raster)
library(leaflet)

# PATHS TO INPUT / OUTPUT FILES
projectPath = "/home/kreis/git/geotiff/"
#imgPath = paste(projectPath,"data/cea.tif", sep = "")

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# Here are a few methods for getting text from PDF files. Do read through 
# the instructions carefully! NOte that this code is written for Windows 7,
# slight adjustments may be needed for other OSs

# Tell R what folder contains your 1000s of PDFs
dest <- "G:/somehere/with/many/PDFs"

# make a vector of PDF file names
myfiles <- list.files(path = dest, pattern = "pdf",  full.names = TRUE)

alfcrisci

library(SPARQL)
library(ggplot2)
library(rworldmap)

wdqs <- "https://query.wikidata.org/bigdata/namespace/wdq/sparql"
query = "PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX v: <http://www.wikidata.org/prop/statement/>

alfcrisci

# Libraries
library(RMySQL)

# Connect to server
conn <- dbConnect(MySQL(), user="ab428", password="", 
                  dbname="event_data", host="")

country <- "Turkey"
start.date <- "2013-05-15"
end.date <- "2013-06-15"

alfcrisci

# Copyright (c) 2013, Andrea Grandi and individual contributors.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, 
# are permitted provided that the following conditions are met:
#
#       1) Redistributions of source code must retain the above copyright notice, 
# 	   this list of conditions and the following disclaimer.
#
# 	2) Redistributions in binary form must reproduce the above copyright notice, 

alfcrisci

ols <- lm(Temp ~ Solar.R,
  data = airquality)

summary(ols)

str(ols)

plot(Temp ~ Solar.R,
  data = airquality)
abline(ols)

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library(leaflet)

## OSM

leaflet() %>%
  setView(-97.3606922, 32.7084083, zoom = 16) %>%
  addTiles()

## OSM black-and-white

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#### Temporal Interpolation ####################################################
# Perform cell-wise linear interpolation between multiple raster layers, and 
# extrapolation beyond the upper limit of input data. Output is saved in .tif 
# format.
#
# Arguments
# s: a rasterStack containing the time slices to be interpolated 
#
# xin: a numeric vector that indicates the times associated with layers in s (in
# the same order as the layers of s - see names(s))