Jarrett Byrnes jebyrnes
jebyrnes
/ addZeroes.R
Last active
August 29, 2015 13:56
A demonstration of how to add rows with zeroes using melt and dcast. There are other ways, but this is pretty simple.
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| ################################ | |
| # Problem: You have a ragged | |
| # data frame where species that have not | |
| # been seen as a site simply don't have a | |
| # line in your data frame. You have a long | |
| # data frame, but you want a long data frame | |
| # where missing species have proper zeroes | |
| # | |
| # Solution: a combination of dcast and melt | |
| # from the reshape2 package |
jebyrnes
/ germany_biodepth_zissou.R
Created
March 31, 2014 21:25
A multifunctionality analysis using the threshold effect for Biodepth in Germany using the Zissou color scheme from Karthik's wesanderson package for color palates.
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| library(multifunc) | |
| library(wesanderson) | |
| data(all_biodepth) | |
| allVars<-qw(biomassY3, root3, N.g.m2, light3, N.Soil, wood3, cotton3) | |
| germany<-subset(all_biodepth, all_biodepth$location=="Germany") | |
| vars<-whichVars(germany, allVars) | |
| #re-normalize N.Soil so that everything is on the same sign-scale (e.g. the maximum level of a function is the "best" function) |
jebyrnes
/ new_multifunc.R
Created
September 2, 2014 21:34
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| library(multifunc) | |
| data(all_biodepth) | |
| allVars<-qw(biomassY3, root3, N.g.m2, light3, N.Soil, wood3, cotton3) | |
| germany<-subset(all_biodepth, all_biodepth$location=="Germany") | |
| vars<-whichVars(germany, allVars) | |
| #re-normalize N.Soil so that everything is on the same sign-scale (e.g. the maximum level of a function is the "best" function) | |
| germany$N.Soil<- -1*germany$N.Soil +max(germany$N.Soil, na.rm=TRUE) |
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| \documentclass{article} | |
| \begin{document} | |
| <<echo=FALSE>>= | |
| activityDF <- structure(list(julian_day = 1:365, food = c(92.6182247978374, | |
| 199.361820535986, 128.619308542186, 131.048504694701, 44.6344539529983, | |
| 139.02542881751, 118.815437972886, 85.5963235153311, 73.9459098960665, | |
| 85.6671795660157, 195.954639346317, 192.942941724749, 193.341526021202, | |
| 142.419581610027, 130.23002915561, 232.843857188757, 105.14817987285, | |
| 131.58751463704, 123.30056211349, 150.447279408636, 138.40775613945, |
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| #just create a range of values | |
| grdVals <- function(x, bound=0.01) seq(range(x)[1]-bound, range(x)[2]+bound, length.out=50) | |
| #instantiate a new persp object for a scatterplot | |
| makeScatterBox <- function(x,y,z, bound=0, ...){ | |
| x <- grdVals(x, bound=bound) | |
| y <- grdVals(y, bound=bound) | |
| z <- grdVals(z, bound=bound) | |
| z <- matrix(rep(z, 50), nrow=50) |
jebyrnes
/ leafletMapWithLegend.R
Last active
August 29, 2015 14:19
A demo of leaflet using a color legend
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| #devtools::install_github("rstudio/leaflet", ref="feature/color-legend") | |
| library(leaflet) | |
| library(RColorBrewer) | |
| set.seed(100) | |
| pdf <- data.frame(Latitude = runif(100, -90,90), Longitude = runif(100, -180,180)) | |
| #make a property with colors | |
| pdf$Study <- rep(1:10,10) | |
| #need to create a pal using colorbin |
jebyrnes
/ projects.csv
Created
November 13, 2011 00:23
Code to scrape RocketHub's xml feeds for the #SciFund projects, add it to a log file, then plot it. Run the data scrape without appending the first time to generate a log file.
We can make this file beautiful and searchable if this error is corrected: Unclosed quoted field in line 9.
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| "ID","Title","Name","Project.Link","Goal" | |
| 1,"Why is this Dolphin's Fin on Backwards!?","Matthew S. Leslie","http://www.rockethub.com/projects/3754-why-is-this-dolphin-s-fin-on-backwards","5000" | |
| 2,"Tracking the migration of the Atlantic Puffin","Robin Freeman","http://www.rockethub.com/projects/3818-tracking-the-migration-of-the-atlantic-puffin","5000" | |
| 3,"Cancer? Yeast has the answers","Marisa Alonso-N??ez","http://www.rockethub.com/projects/3753-cancer-yeast-has-the-answers","2500" | |
| 4,"Athlete's Foot in Worms?","Rebecca Rashid Achterman","http://www.rockethub.com/projects/3703-athlete-s-foot-in-worms","1000" | |
| 5,"Support Zombie Research!","Kelly Weinersmith","http://www.rockethub.com/projects/3737-support-zombie-research","3500" | |
| 6,"Doctor Zen and the Amazon Crayfish","Zen Faulkes","http://www.rockethub.com/projects/3695-doctor-zen-and-the-amazon-crayfish","1000" | |
| 7,"C-Cilia in Motion!!","Aditya Rao","http://www.rockethub.com/projects/3792-c-cilia-in-motion","5000" | |
| 8,"Force of Duck: Measuring explosive erection"," |
jebyrnes
/ allPredPrey.r
Created
December 7, 2011 23:06
Simulations of all predators and prey applying the p(eaten) formula for a probabilistic approach to food webs
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| ###############FUNCTIONS | |
| #If you find the 0 predators remaining formulation more intuitive | |
| pEaten2<-function(Sp.max, E, prey.vec) { | |
| 1-mean(dhyper(0,prey.vec, Sp.max-prey.vec, Sp.max-E)) | |
| } | |
| #vectorize it | |
| pEaten2<-Vectorize(pEaten2, vectorize.args="E") | |
| #generate all permutations of prey being eaten |
jebyrnes
/ iworkfortheinternet.R
Created
December 14, 2011 01:26
— forked from sckott/iworkfortheinternet.R
Code for searching Twitter using the twitteR #rstats package.
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| require(plyr); require(stringr); require(ggplot2); require(lubridate); require(twitteR) | |
| ##need to figure out why there are two datout objects and not just 1... | |
| twitterPlot<-function(myString, n=1500, since=NULL, until=NULL){ | |
| since2<-as.character(strptime(since, '%Y-%m-%d')+2*24*60*60) | |
| until2<-as.character(strptime(until, '%Y-%m-%d')+2*24*60*60) | |
| datout_1 <- searchTwitter(myString, n = n, since=since, until=until) | |
| datout_2 <- searchTwitter(myString, n = n, since=since2, until=until2) |
jebyrnes
/ goal_success_scifund.R
Created
February 28, 2012 23:16
Analysis code for looking at the relationship between project goal and % success from #SciFund. Note, I did it with my own private data set that has a lot of merged fields in it, but you can run this analysis or something like it with Zen's data at http:
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| source("./sciFundFunctions.r") | |
| library(gridExtra) | |
| ################################################# | |
| #######HISTOGRAMS | |
| ################################################# | |
| #total raised histogram distribution | |
| raised<-qplot(total, data=projects) + | |
| theme_bw(base_size=16) + | |
| xlab("\nTotal Raised") + |
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