rossibarra

REU Site Proposal: Ecology, evolution, and equity of environmental change 
 
outline 
Overview 
Nature of student activities 
Proposals should address the approach to undergraduate research training being taken and should provide detailed descriptions of examples of research projects that students will pursue. So that reviewers can evaluate intellectual merit, this discussion should indicate the significance of the research area and, when appropriate, the underlying theoretical framework, hypotheses, research questions, etc. Undergraduate research experiences have their greatest impact in situations that lead the students from a relatively dependent status to as independent a status as their competence warrants. Proposals must present plans that will ensure the development of student-faculty interaction and student-student communication. Development of collegial relationships and interactions is an important part of the project. 
The research environment 
This subsection should describe the history and charac

rossibarra

library(tidyverse)
x<-read.table("~/Desktop/ogut.map")

# OK we're missing bits on  ends
group_by(x,V1) %>% 
  summarize(end=max(V3),start=min(V3))

#spline to get them
pos.starts<-rep(0,10)
pos.ends<-c(307041717,244442276,235667834,246994605,223902240,174033170,182381542,181122637,159769782,150982314)

rossibarra

library(tidyverse)
library(cowplot)
Ne=25000
mu=1E-8
win_size=20000
theta=win_size*4*mu*Ne
before<-as.numeric(sapply(1:20, function(i) 
  system(paste("~/src/msdir/ms 10 1000 -t", 4*theta, "-r", 4*theta, "1000 | ~/src/msdir/sample_stats | cut -f 2 | ~/src/msdir/stats | cut -f 1")
         ,intern=T)))

rossibarra

#find outliers for some cutoff
probs<-lapply(1:5, function(pop) pbinom(dh_freq[[pop]],size=sample_size,prob=filtered_pop_ancestral[[pop]]))

outliers<-lapply(1:5, function(pop) probs[[pop]]<cutoff)


#find shared loci. calculate their mean freq.

shared=outliers[[1]]+outliers[[2]]+outliers[[3]]+outliers[[4]]+outliers[[5]]

rossibarra

#
# This is the server logic of a Shiny web application. You can run the 
# application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
# 
#    http://shiny.rstudio.com/
#

library(shiny)

rossibarra

Line	Gsize	Rep
Ki3	6.01	1
 Ky21	5.63	1
 NC358	5.88	1
 B73	5.46	1
 CML247	6.05	1
 CML52	6.13	1
 P39	5.5	1
 H95	5.8	1
 A188	5.63	1

rossibarra

rossibarra

---
title: "Identifying sweeps with reduced representation sequencing"
output: 
  html_document: default
bibliography: biblio.bib
---

## Setup

To run this, you will need the R packages ``gsl``, ``cowplot``, ``tidyverse``, and ``viridis`` installed, as well as the software [ms](http://home.uchicago.edu/rhudson1/source/mksamples.html) installed. The original R markdown code can be found on [github](https://gist.github.com/rossibarra/be44cc3b3796f45840d942ad11c01ba1#file-tag_probs).

rossibarra

fullid	AcID	Pop	Ind	genomesize	leaf3.0	leaf3.1	leaf3.2	leaf3.3	dailyavg3	leaf4.0	leaf4.1	leaf4.2	leaf4.3	dailyavg4	dailyavgall	stom_cell1	stom_cell2	stom_cell3	stom_cell4	stom_cell5	stom_cell6	stom_cell7	stom_cell8	stom_cell9	stom_cell10	stom_cell11	stom_cell12	stom_cell13	stom_cell14	stom_cell15	stom_cell16	stom_cell17	stom_cell18	stom_cell19	stom_cell20	stom_cell21	stom_cell22	stom_cell23	stom_cell24	stom_cell25	stom_cell26	stom_cell27	stom_cell28	stom_cell29	stom_cell30	stom_cell31	stom_cell32	stom_cell33	stom_cell34	stom_cell35	stom_cell36	stom_cell37	stom_cell38	stom_cell39	stom_cell40	stom_cell41	stom_cell42	stom_cell43	stom_cell44	stom_cell45	stom_cell46	stom_cell47	stom_cell48	stom_cell49	stom_cell50	stom_cell51	stom_cell52	stom_cell53	stom_cell54	stom_cell55	stom_cell56	stom_cell57	stom_cell58	stom_cell59	stom_cell60	stom_cell61	mid_cell1	mid_cell2	mid_cell3	mid_cell4	mid_cell5	mid_cell6	mid_cell7	mid_cell8	mid_cell9	mid_cell10	mid_cell11	mid_cell12	mid_cell13	mid_cell14	mid_cell15	mid_cell16	mid_cel

rossibarra

f	Freq
0	240519
1	15155
2	8763
3	6083
4	4801
5	3999
6	3652
7	3225
8	3005