Revisions on Prosecutors Fallacy

• Email Alan re: Prosecutor’s fallacy manuscript. Schedule meeting.

• Proof corrections for rfishbase manuscript. Done.

• Fallacy simulations: calibration range for May model: expect small fraction of runs to transition by chance from stable state.

Here we’re getting a bit less than 2% chance transitions in 5000 steps.

>   sn <- 
+   sapply(1:1000, function(rep){
  +     x <- vector(mode="double", length=n)
  +     x[1] <- 8 # positive equilibrium
  +     z <- rlnorm(n, 0, .1)
  +     r = .75; k = 10; a=1.55; H=1; Q = 3
  +     for(t in 1:n){
    +       x[t+1] = z[t] *  x[t] * exp(r * (1 - x[t] / k) - a * x[t] ^ (Q - 1) / (x[t] ^ Q + H ^ Q)) 
    +     }
    +     x
    +   })
> crashed <- which(sn[n,] < 2)
>   length(crashed)/1000
[1] 0.017
> 
> n
[1] 5000

• Fallacy simulation analysis running on farm using May model. See fallacy.Rmd, prosecutor branch
  

• rerun using different point to indicate transition. Tracking runs on Issue 5

• add figure plotting b and d curves, or at least b-d curve. Likewise for May model.

Misc

• Exploring twitteR finding publications under discussion

• Migrated labnotebook plugins to separate repository

• Updated vimrc to preview pandoc:

map \md : call PreviewMarkdown()<CR>
func! PreviewMarkdown()
exec "w"
exec "! pandoc -s % -o .temp.html"
exec "! google-chrome .temp.html"
endfunc

Should add css templates from my notebook or github.
Could also parse with github’s own API instead of pandoc, e.g. with ruby:

#!/usr/bin/env ruby

# Example usage 
# ./render_gfm.rb input.md > output.html
# 

require 'octokit'
puts Octokit.markdown(File.read(ARGV.first))

• twitteR authentication keys configured in .Rprofile