infotroph

# Testing a soft-left-censored Stan model:
# Values above some minimum are detected normally, 
# values less than minimum go detected with some probability > 0.

set.seed(2345767)
library(rstan)
rstan_options(auto_write = TRUE)
options(mc.cores = 7)

sim_mu = 3

infotroph

library(ggplot2)
library(dplyr)
library(zoo) # for rollmean()

d_mean = (diamonds 
	%>% mutate(price=round(price, -2))
	%>% group_by(price)
	%>% mutate(mean_x = mean(x)))

d_roll = (diamonds

infotroph

set.seed(254469)
n=100
xlo=0
xhi=20
loc_logis=5
scale_logis=3


x = runif(n, xlo, xhi)
p_detect = plogis(x, location=loc_logis, scale=scale_logis)

infotroph

sim_mixdist = function(
		n_tubes=1,
		depths=1:3,
		intercept=1, 			# E[y] at depth=0 (log scale)
		b_depth=-1, 		# slope for depth (log scale)
		sig_tube=1, 			# sd for N(0) tube offsets (log scale)
		detect_loc=1,			# intercept for detection logistic. (scale... same as mu?)
		detect_scale=1, 		# slope for detection logistic. (scale?)
		sigma=1){ 			# residual (log scale)
	

infotroph

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

> packageVersion("ggplot2")
[1] ‘1.0.1’
> library(ggplotTicks)
Error in library(ggplotTicks) : there is no package called ‘ggplotTicks’
> library(devtools)

infotroph

# Sample data: 2x2 manipulation, replicated 4x, multiple responses measured repeatedly over time.
# The response variables aren't related: y_also doesn't come "after" y_1 in any meaningful sense.
df = expand.grid(
	day=1:3, 
	replicate=1:4, 
	t1=c("ctrl", "more"), 
	t2=c("ambient", "manipulated"))
df$y_1 = rnorm(48)
df$y_other = runif(48)
df$y_also = rlnorm(48)

infotroph

strs = c("nomatch", "Odum 1969", "2001FACE_3b", "1800", "sdfghj1928qwer")
strs_yrs = gsub(".*((19|20)[0-9]{2}).*", "\\1", strs)
strs_yrs
# [1] "nomatch" "1969"    "2001"    "1800"    "1928"   
# Oops, strings with no year (or year from wrong century) are returned unchanged! Let's remove them separately:
strs_haveyr = grepl("(19|20)[0-9]{2}", strs)
strs_yrs[!strs_haveyr] = ""
strs_yrs
# [1] ""     "1969" "2001" ""     "1928"

infotroph

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  base     

infotroph

anycolors = function(n)rgb(runif(n), runif(n), runif(n))

color_grid = function(x, y, nx=10, ny=nx){
  g = expand.grid(
    x=seq(min(x), max(x), by=diff(range(x))/nx),
    y=seq(min(y), max(y), by=diff(range(y))/ny))
  g$color = anycolors(nrow(g))
  g
}

infotroph

library(ggplot2)
library(dplyr)
library(lubridate)

dates = c(
	seq(from=as.Date("2014-10-01"), to=as.Date("2015-05-30"), by="days"),
	seq(from=as.Date("2015-10-01"), to=as.Date("2016-05-30"), by="days"))
Tmin = rnorm(length(dates), mean=10*sin((yday(dates) - 90)/365*2*pi))
Tmax = Tmin + rnorm(length(dates), mean=5)