GBif2.Rmd

---
title: "GBIF2"
author: "BradMcFall"
date: "October 1, 2018"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}


library(rgbif)
library(tidyverse)

Eluc<-occ_search(scientificName = "Eurycea lucifuga", limit = 400)
 Elong<-occ_search(scientificName = "Eurycea longicauda", limit =400)
 Espel<-occ_search(scientificName = "Eurycea spelaea", limit =400)
 Ety<-occ_search(scientificName = "Eurycea tynerensis", limit = 400)
 Emult<-occ_search(scientificName = "Eurycea multiplicata", limit =400)

```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}

Argia_translata<-occ_search(scientificName = "Argia translata", limit = 400)
 Argia_bipunctulata<-occ_search(scientificName = "Argia bipunctula", limit =400)
 Gomphus_ozarkensis<-occ_search(scientificName = "Gomphus ozarkensis", limit=400)
 Gomphus_quadricolor<-occ_search(scientificName = "Gomphus quadricolor", limit=400)
 

```



```{r}
Elucdff<-as.tibble(Eluc$data)
Elongdff<-as.tibble(Elong$data)
Etydf<-as_tibble(Ety$data)
Emultdf<-as_tibble(Emult$data)
Espeldf<-as_tibble(Espel$data)
Argtran<-as.tibble(Argia_translata$data)
Gooz<-as.tibble(Gomphus_ozarkensis$data)
Goqu<-as.tibble(Gomphus_quadricolor$data)

```

```{r}

Elongluc<-merge(Elucdff,Elongdff, all=TRUE)
EtdfEspe<-merge(Etydf,Espeldf, all = TRUE)
ElonlucGo<-merge(Elongluc,Gozqu, all=TRUE)
ElonlucArgtr<-merge(Elongluc,Argtran, all=TRUE)
EtdfEsdpmult<-merge(Emultdf,EtdfEspe,all=TRUE)

GozArgtr<-merge(Gooz,Argtran, all=TRUE)
Gozqu<-merge(Gooz,Goqu, all=TRUE)

EGA<-merge(GozArgtr,EtdfEspe, all=TRUE)

SalOz<-merge(EtdfEsdpmult, Gooz, all=TRUE)

```



```{r}
ElonlucArgtr%>%
  ggplot( aes(x=decimalLongitude, y=decimalLatitude, color=name))+
   geom_point()+
   geom_density2d()+
  coord_cartesian(ylim = c(25,45))

Gozqu%>%
  ggplot( aes(x=decimalLongitude, y=decimalLatitude, color=name))+
   geom_point()+
   geom_density2d()+
  coord_cartesian(ylim = c(25,45))


ElonlucGo%>%
  ggplot( aes(x=decimalLongitude, y=decimalLatitude, color=name))+
   geom_point()+
   geom_density2d()+
  coord_cartesian(ylim = c(32,45),xlim=c(-105,-60))



```


```{r}


SalOz%>%
  ggplot( aes(x=decimalLongitude, y=decimalLatitude, color=name))+
   geom_point()+
   geom_density2d()+
  coord_cartesian(ylim = c(32,40),xlim=c(-97,-90))


```


```{r}

 library(ks)
 set.seed(8192)
 samp <- 200
 mus <- rbind(c(-2,2), c(0,0), c(2,-2))
 Sigmas <- rbind(diag(2), matrix(c(0.8, -0.72, -0.72, 0.8), nrow=2), diag(2))
 cwt <- 3/11
 props <- c((1-cwt)/2, cwt, (1-cwt)/2)
 x <- rmvnorm.mixt(n=samp, mus=mus, Sigmas=Sigmas, props=props)
 Hpi1 <- Hpi(x=x)
Hpi2 <- Hpi.diag(x=x)
fhat.pi1 <- kde(x=x, H=Hpi1)
fhat.pi2 <- kde(x=x, H=Hpi2)
 plot(fhat.pi1)
 plot(fhat.pi2)

Cay<-tibble(Lat=c(x[,2]),
       Long=c(x[,1])
       
       )

ggplot(Cay,aes(x=Lat,y=Long))+
  geom_density2d()


```