noamross

library(dplyr)
library(tidyr)
library(ggplot2)
library(gridExtra)

df = data_frame(a = rnorm(100, mean=1), b=rnorm(100, mean=2),  c=rnorm(100, mean=0)) %>% 
  gather("var", "value", a,b,c)

ggplot(df, aes(x=value)) +
  geom_density(fill="black", col="white", lwd=1) +

noamross

library(rstanarm)
library(tidyverse)
library(viridis)

gtemp <- read.delim("http://www.metoffice.gov.uk/hadobs/hadcrut4/data/current/time_series/HadCRUT.4.5.0.0.annual_ns_avg.txt",
                    sep="", header = FALSE) %>%
  select(1,2) %>%
  set_names(c("Year", "Temperature"))

st_mod2 <- stan_gamm4(Temperature ~ s(Year), data = gtemp)

noamross

library(tidyverse)
library(igraph)
library(ggraph)
library(gganimate)
library(ggforce)

#File at https://dl.dropbox.com/s/hxmsut19lelgw33/epinetwork.rds
episim <- readRDS("epinetwork.rds") # Saved is the simulation data and an adjacency matrix for the network
# Create an undirected graph from this matrix
ign <- graph_from_adjacency_matrix(episim$network > 0, "undirected")

noamross

# I believe I found a bug in R's quartz() device, specifically it's
# GECap method (the C routine called by dev.capture).  The following
# yields the two images in the comment below.  This occurs whether working
# from the terminal or RStudio.  This works fine with Cairo devices that
# support raster capture.

quartz()
plot(1,1)
aa <- dev.capture()
dev.size("px")

noamross

bias_matrix <- as.matrix(bias_raster)  # Bias measure
num_matrix <- as.matrix(number_raster) # Number of samples measure
# Boolean matrix for signficant bias
bias_mat2 <- ifelse((bias_matrix > bias_funs$upper(num_matrix)) | bias_matrix < bias_funs$lower(num_matrix), 1, NA) 

 # Convert bias boolean to shapes. This is a list of shapes, each shape being an NX2 matrix of points. 
  bias_shapes <- fasteraster::raster2vector(bias_mat2) %>% 
  # Remove shapes that are actually just points or lines (<= 3 defining points)
  {Filter(function(x) nrow(x) > 3, .) } %>%  
  # Convert matrix coords to lat/long for each shape

noamross

library(rtweet) #rtweet API creds should already be set up
library(stringi)
library(dplyr)

friends = get_friends(user="noamross")
followers = get_followers("noamross")
tweeps_id = distinct(bind_rows(friends, followers))
tweeps_info = lookup_users(tweeps_id$user_id)

# A regex for a visit to Durham

noamross

Position Title: Research Scientist

https://www.ecohealthalliance.org/career/research-scientist

POSITION SUMMARY

EcoHealth Alliance seeks a creative and analytically-minded research scientist with strong quantitative skills to support our Modeling and Analytics team. The research scientist will work closely with our team of scientists and staff on multiple projects related to disease emergence, antimicrobial resistance, land-use change, and conservation. The research scientist will work as part of the USAID supported PREDICT project as well as other federally-funded research. Responsibilities of the research scientist include performing statistical analyses, assembling and curating data sets, performing literature reviews, and writing scientific publications and government reports. The candidate must be self-motivated, proactive, and willing and able to help design new research projects that fit with the mission and direction of EcoHealth Alliance. The candidate must be

noamross

JOB ADVERTISMENT: Disease Ecologist

https://www.ecohealthalliance.org/career/disease-ecologist

EcoHealth Alliance seeks a Disease Ecologist with strong quantitative skills for a six-month, full-time position. The Disease Ecologist will work with our team of scientists and staff on a research project modeling the risk of import and spread of foot-and-mouth disease in the cattle and swine sectors in the USA. Responsibilities of the Disease Ecologist include developing and performing simulations, performing statistical analyses, assembling and curating data sets, performing literature reviews and writing reports. The candidate must have strong epidemiological and computational skills, including experience with stochastic simulation, spatial analyses, and network models. The candidate must have strong writing skills and the ability to work independently.

PRIMARY RESPONSIBILITIES

noamross

#!/bin/bash

# Usage: mkproj [projectname]
# projectname defaults to name of current directory

template="Version: 1.0

RestoreWorkspace: No
SaveWorkspace: No
AlwaysSaveHistory: Yes

noamross

# TODO (maybe)
# - Vectorize on URLs
# - Allow for downloading whole directory contents if path is a directory
#     -  Make a recursive = TRUE argument for this case
# - Error messages/input checking

#' Gets a file from a github repo, using the Data API blob endpoint
#'
#' This avoids the 1MB limit of the content API and uses [gh::gh] to deal with
#' authorization and such.  See https://developer.github.com/v3/git/blobs/