Commit f96cd20c authored by Eric Coissac's avatar Eric Coissac

Initial commit...

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.RData
.Ruserdata
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---
title: "Untitled"
author: "Aurlie & Eric"
date: "27/03/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(ade4)
library(vegan)
```
```{r}
euk = read.csv("australia.euk.reads.plot.csv",head=TRUE,row.names = 1)
bac = read.csv("australia.bac.reads.plot.csv",head=TRUE,row.names = 1)
env = read.csv("biogegraphy_and_environment.csv",head=TRUE,row.names = 1)
```
```{r}
env=env[,lapply(env,class)=="numeric"]
euk=euk[rownames(env),]
bac=bac[rownames(env),]
```
```{r}
env = sweep(env,MARGIN = 2,colMeans(env),'-')
env = sweep(env,MARGIN = 2,apply(env,2,sd),'/')
```
```{r eval=FALSE, include=FALSE}
euk=sqrt(euk)
euk = sweep(euk,MARGIN = 2,colMeans(euk),'-')
euk = sweep(euk,MARGIN = 2,apply(euk,2,sd),'/')
```
```{r eval=FALSE, include=FALSE}
bac=sqrt(bac)
bac = sweep(bac,MARGIN = 2,colMeans(bac),'-')
bac = sweep(bac,MARGIN = 2,apply(bac,2,sd),'/')
```
```{r}
euk.dist=quasieuclid(vegdist(euk,method = "jaccard"))
euk.pco =dudi.pco(euk.dist,full = TRUE)
euk.pco.li = euk.pco$li
dim(euk.pco.li)
plot(euk.pco.li[,1:2],cex=0)
text(euk.pco.li[,1:2],labels = rownames(euk.pco.li),cex=0.6)
```
```{r}
bac.dist=quasieuclid(vegdist(bac,method = "jaccard"))
bac.pco =dudi.pco(bac.dist,full = TRUE)
bac.pco.li = bac.pco$li
dim(bac.pco.li)
plot(bac.pco.li[,1:2],cex=0)
text(bac.pco.li[,1:2],labels = rownames(bac.pco.li),cex=0.6)
```
```{r}
euk.sct = sum(euk.pco.li**2)
bac.sct = sum(bac.pco.li**2)
```
```{r}
x = procrustes(euk.pco.li,bac.pco.li,scale = TRUE)
```
```{r}
y = procrustes(bac.pco.li,euk.pco.li,scale = TRUE)
```
```{r}
SCR.E.B = sum((euk.pco.li-x$Yrot)^2)
SCT.E = sum((euk.pco.li- colMeans(euk.pco.li))^2)
SCR.E.B/SCT.E
```
```{r}
SCR.B.E = sum((bac.pco.li-y$Yrot)^2)
SCT.B = sum((bac.pco.li- colMeans(bac.pco.li))^2)
SCR.B.E/SCT.B
```
```{r}
x = procrustes(sweep(euk.pco.li,2,colMeans(euk.pco.li),"-"),
sweep(bac.pco.li,2,colMeans(bac.pco.li),"-"),scale = TRUE)
y = procrustes(sweep(bac.pco.li,2,colMeans(bac.pco.li),"-"),
sweep(euk.pco.li,2,colMeans(euk.pco.li),"-"),scale = TRUE)
x$scale
1/y$scale
```
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