jebyrnes’s gists

jebyrnes / coastline_crop.R

Last active January 12, 2018 20:16

crop out coasts with R

jebyrnes / error.R

Created February 4, 2018 23:46

odd gdal error running polygonizer

	Traceback (most recent call last):
	File "/usr/local/bin/gdal_polygonize.py", line 36, in <module>
	import gdal, ogr, osr
	File "/Library/Frameworks/GDAL.framework/Versions/1.11/Python/2.7/site-packages/gdal.py", line 2, in <module>
	from osgeo.gdal import deprecation_warn
	File "/Library/Frameworks/GDAL.framework/Versions/1.11/Python/2.7/site-packages/osgeo/__init__.py", line 21, in <module>
	_gdal = swig_import_helper()
	File "/Library/Frameworks/GDAL.framework/Versions/1.11/Python/2.7/site-packages/osgeo/__init__.py", line 17, in swig_import_helper
	_mod = imp.load_module('_gdal', fp, pathname, description)
	ImportError: dlopen(/Library/Frameworks/GDAL.framework/Versions/1.11/Python/2.7/site-packages/osgeo/_gdal.so, 2): Symbol not found: _GTIFAllocDefn

jebyrnes / plot_poly_fits.R

Created May 16, 2018 00:38

plot predictions of a model with an interaction and a poly term

	library(tidyverse)
	library(ggplot2)
	library(visreg)

	#some fake data
	set.seed(35)
	my_data <- data.frame(x1 = runif(100,-50,50), x2 = runif(100, -50, 50)) %>%
	mutate(y = rnorm(100, 0.001x2(x1 - x1^2), 100))

	#let's see that data

jebyrnes / nesting_models.R

Created May 17, 2018 19:23

Using gapminder to show how tidyr and broom and dplyr can fit a lot of models all at once.

jebyrnes / discrete_grrrowth.R

Created October 2, 2018 03:58

How to use purrr::iwalk to do discrete time logistic growth models.

	#'----------------
	#' Discrete time logistic growth model
	#' Using purrr and iwalk
	#'----------------


	library(purrr)

	r <- 3.95237783423
	n0 <- 0.3

jebyrnes / ocean_lambert.R

Created October 2, 2018 04:20

	library(sf)
	library(rnaturalearth)
	library(rnaturalearthdata)
	library(ggplot2)


	oceans <- ne_download(type = "ocean", category = "physical", returnclass="sf")
	ocean_antarctic <- st_transform(oceans, 2154)
	ggplot(ocean_antarctic) +
	geom_sf(fill = "lightblue", color=NA)

jebyrnes / glm_profile.R

Last active April 22, 2019 21:20

Take a glm and creates a deviance profile, as MASS::profile only returns a transformed version of the deviance.

	library(ggplot2)

	#A glm from the glm helpfile
	counts <- c(18,17,15,20,10,20,25,13,12)
	outcome <- gl(3,1,9)
	treatment <- gl(3,3)
	print(d.AD <- data.frame(treatment, outcome, counts))
	glm.D93 <- glm(counts ~ outcome + treatment, family = poisson())

	#The old way...

jebyrnes / sst_lambert.R

Created October 6, 2018 03:10

SST change in the lambert projection

	library(raster)
	#devtools::install_github("jebyrnes/hadsstr")
	library(hadsstr) #from jebyrnes/hadsstr
	library(ggplot2)
	library(sf)
	library(rnaturalearth)

	#get the world in the lambert projection
	countries_50_sf <- ne_download(scale = 50, category = 'cultural', type = 'countries', returnclass="sf")
	countries_lambert <- st_transform(oceans, 2154)

jebyrnes / bayesian_posthoc.R

Last active February 10, 2023 20:29

Posthoc contrasts with emmeans, tidybayes, and brms

	library(tidyverse)
	library(emmeans)
	library(brms)
	library(tidybayes)

	warp.brms <- brm(breaks ~ wool * tension, data = warpbreaks)

	#get the adjusted means
	warp_em <- emmeans (warp.brms, ~ tension \| wool)
	warp_em

jebyrnes / data.r

Created November 3, 2018 03:07

	brainGene <- structure(list(group = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
	1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
	2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
	3L, 3L, 3L, 3L, 3L, 3L), .Label = c("control", "schizo", "bipolar"
	), class = "factor"), PLP1.expression = c(-0.02, -0.27, -0.11,
	0.09, 0.25, -0.02, 0.48, -0.24, 0.06, 0.07, -0.3, -0.18, 0.04,
	-0.16, 0.25, -0.1, -0.31, -0.05, 0.11, -0.38, 0.23, -0.23, -0.28,
	-0.36, -0.22, -0.4, -0.19, -0.34, -0.29, -0.12, -0.34, -0.39,

Jarrett Byrnes jebyrnes