oliviergimenez

### Title: Back to basics: High quality plots using base R graphics
###	An interactive tutorial for the Davis R Users Group meeting on April 24, 2015
###
### Date created: 20150418
### Last updated: 20150423
###
### Author: Michael Koontz
### Email: [email protected]
###	Twitter: @michaeljkoontz
###

oliviergimenez

# Implements Lasso for logistic regression, both classical/bayesian ways

## 1. SIMULATION

# for reproducibility
set.seed(666)

# sample size
n <- 100

oliviergimenez

# we seek to test whether two parameters, say theta1 and theta2, are diff from each other, using a z-test
# we assume we have an estimate of the thetaj's (mle1 and mle2) and associated standard errors (se1 and se2)
# we write a function that calculate the z-statistic and return the p-value (both-sided test)

# function
ztest <- function(mle1, mle2, se1, se2){
  stat <- (mle1 - mle2)/sqrt(se1^2+se2^2)
  pvalue <- ifelse(stat > 0, 2 * pnorm(stat, lower.tail = FALSE), 2 * pnorm(stat, lower.tail = TRUE))
  return(data.frame("z-score" = stat, "p-value" = pvalue))
}

oliviergimenez

# Cook, J. D., D. M. Williams, W. F. Porter, and S. A. Christensen. 2022. 
# Improved predictions and forecasts of chronic wasting disease occurrence 
# using multiple mechanism dynamic occupancy modelling. 
# Journal of Wildlife Management.

# Simulation and multi-mechanism dynamic occupancy model code

#load necessary libraries
library(raster)
library(mvtnorm)

oliviergimenez

# from Cole Monnahan https://github.com/colemonnahan/fcwhales
convert_to_df <- function(fit, name = NULL){
  fit <- as.mcmc(fit)
  post <- data.frame(do.call(rbind, fit))
  new <- gsub('[.]$', '', names(post))
  new <- gsub('[.]','_', new)
  names(post) <- new
  if(!is.null(name)) post$model <- name
  return(post)
}

oliviergimenez

##--- Finite-mixture capture-recapture models
##--- O. Gimenez & D. Turek, December 2019 & October 2020

##--- Check out our paper
##--- Turek, D., C. Wehrhahn, Gimenez O. (2021). Bayesian Non-Parametric Detection Heterogeneity in Ecological Models. 
##--- Environmental and Ecological Statistics 28: 355-381.
##--- PDF available here: https://arxiv.org/abs/2007.10163

##--- More on heterogeneity in capture-recapture models in
##--- https://onlinelibrary.wiley.com/doi/abs/10.1111/oik.04532

oliviergimenez

# we get same AIC when fitting Rota model with no interaction 
# vs fitting MacKenzie model to species separatately

library(unmarked)
library(mipfp)
?occuMulti

# simulate 2 species data
# https://github.com/oliviergimenez/2speciesoccupancy

oliviergimenez

Keybase proof

I hereby claim:

• I am oliviergimenez on github.
• I am oliviergimenez (https://keybase.io/oliviergimenez) on keybase.
• I have a public key ASB-o-5D4dk5Z6DU4-8VoO-wp5QG9xYe5qDlKeahp3FveAo

To claim this, I am signing this object:

oliviergimenez

# some R code to mimic animated gifs created by Etienne Jacob 
# @etiennejcb
# https://bleuje.github.io/tutorials/

## load required packages
library(tidyverse)
theme_set(theme_void(base_size = 14))
library(gganimate)

##-- first tutorial https://bleuje.github.io/tutorial1/

oliviergimenez

# https://zhuhao.org/post/tips-on-designing-a-hex-sticker-for-rstats-packages/
# https://github.com/GuangchuangYu/hexSticker/

library(tidyverse)
library(hexSticker)
library(png)
library(grid)

theme_set(theme_minimal())
df <- 4