View distance-sampling.stan
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data { | |
int<lower=1> n_site; | |
int<lower=1> n_distance_bins; | |
vector[n_distance_bins + 1] bin_breakpoints; | |
array[n_site, n_distance_bins] int y; | |
array[n_site] int n_obs; | |
} | |
transformed data { | |
real max_distance = max(bin_breakpoints); |
View plot-test-times.R
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library(forcats) | |
library(ggplot2) | |
library(testthat) | |
path <- testthat_example("success") | |
l <- test_file(path, reporter = "list") | |
l %>% | |
as.data.frame() %>% | |
ggplot(aes(y = fct_reorder(test, real), x = real)) + |
View minimal-wildfire-brms.R
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library(tidyverse) | |
library(sf) | |
library(here) | |
library(brms) | |
library(lubridate) | |
library(reshape2) | |
# Get ecoregion data ------------------------------------------------------ | |
download.file("ftp://newftp.epa.gov/EPADataCommons/ORD/Ecoregions/us/us_eco_l4.zip", | |
destfile = "ecoregions.zip") |
View dist.R
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# Distance sampling model with data augmentation. | |
# Based on section 8.3.1 of the Applied Hierarchical Modeling book by Royle and Kery | |
library(rstan) | |
B <- 50 | |
# note that I'm dividing by 10 and adding 1e-6 to put this on a manageable | |
# scale and prevent values == 0 | |
d_obs <- c(71.93, 26.05, 58.47, 92.35, 163.83, 84.52, 163.83, 157.33, |
View zoib.ipynb
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View linear-interp-spectra.R
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library(tidyverse) | |
library(reshape2) | |
library(pbapply) | |
n_samples <- 100 | |
n_wavelength <- 400 | |
wavelengths <- matrix(nrow = n_samples, ncol = n_wavelength) | |
reflectances <- matrix(nrow = n_samples, ncol = n_wavelength) | |
for (i in 1:n_samples) { |
View lme4-predict-new-ranef-levels.R
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library(lme4) | |
# adapted from ?predict.merMod | |
gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 |herd), | |
cbpp, | |
binomial) | |
# add some new levels to herd, which is a random effect | |
newdata <- with(cbpp, | |
expand.grid(period=unique(period), |
View multiscale-occupancy.R
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library(rstan) | |
options(mc.cores = parallel::detectCores()) | |
rstan_options(auto_write = TRUE) | |
psi <- .2 | |
theta <- .3 | |
p <- .5 | |
nsite <- 100 | |
ntime <- 4 |
View sgd-intro.ipynb
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View timing-overlay-vs-clip_shp.ipynb
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