Marco Sciaini marcosci

💭

in progress ...

geo | r | viz | data

marcosci / quantomPlot.R

Last active October 20, 2015 21:20

	# Function to create a plot for the spatstat class ‘fv’, combined with 'Quantum Plots' from:
	# Esser, D. S., Leveau, J. H. J., Meyer, K. M., & Wiegand, K. (2014). Spatial scales of interactions among bacteria and between bacteria and the leaf surface. FEMS Microbiology Ecology, 91(3), fiu034. http://doi.org/10.1093/femsec/fiu034
	# The colored bands highlight the spatial scales at which the summary statistics deviate from the simulation envelopes.

	quantumPlot <- function(x,colour=c("#d73027", "#ffffbf", "#91bfdb")){

	# load Packages
	require(ggplot2)
	require(ggthemes)

marcosci / gist:a020333a37d40e432725850734c36039

Last active November 21, 2017 17:33

sliding_box.R

	library(raster)

	nlm_raster <- nlm_gaussianfield(100, 100, 5)

	setGeneric(
	"splitRaster",
	function(r, nx = 1, ny = 1, buffer = c(0, 0), path = file.path(getwd(), names(r)), cl) {
	standardGeneric("splitRaster")
	})

marcosci / gist:8d01f06adfeba47b55115da425e4147c

Created December 8, 2017 15:14

	# create landscapes
	set.seed(5)

	percolation_landscape <- nlm_percolation(100,100,0.4, resolution = 10)
	random_landscape <- nlm_random(100,100, resolution = 10)
	distagrad_landscape <- nlm_distancegradient(100, 100, origin = c(10,15,10,15), resolution = 10)
	edgegradient_landscape <- nlm_edgegradient(100,100, 90, resolution = 10)
	planar_landscape <- nlm_planargradient(100,100, resolution = 10)
	randomRecCluster_landscape <- nlm_randomrectangularcluster(100, 100, minL = 8, maxL = 16, rescale = FALSE, resolution = 10)
	randomElement_landscape <- nlm_randomelement(100,100, n = 90, resolution = 10)

marcosci / test.R

Created March 16, 2018 08:59

velox problem

	ncol <- 100
	nrow <- 100
	germs <- 50

	# bounding box placing germs and clipping ----
	bounding_box <- sf::st_sfc(sf::st_polygon(list(rbind(c(0, 0),
	c(ncol, 0),
	c(ncol, nrow),
	c(0, nrow),
	c(0, 0)))))

marcosci / remote_future.R

Created June 5, 2018 08:33

how to setup a remote connection with future in R

	# Specify remote worker
	login <- tweak(remote, workers = "SERVER IP", user = 'USERNAME')

	# Specify future topology
	## login node -> { multiple cores }
	plan(list(
	login,
	multiprocess
	))

marcosci / gist:993a3f5ed0c32889d17c80a0d858c85b

Created July 1, 2018 14:04

groupseminar

	---
	title: "???? <html><div style='float:left'></div><hr color='#EB811B' size=1px width=796px></html>"
	author: "Marco Sciaini"
	date: "`r Sys.Date()`"
	output:
	xaringan::moon_reader:
	css: [default, metropolis, metropolis-fonts]
	nature:
	beforeInit: "macros.js"
	highlightStyle: github

marcosci / clumpy

Created July 9, 2018 15:02

clumpiness metric from fragstats

	landscape_padded <- pad_raster(landscape)
	# landscape_padded <- landscape

	adjacent_cells <- raster::adjacent(
	landscape_padded,
	cells = seq_len(raster::ncell(landscape_padded)),
	directions = 4,
	pairs = TRUE
	)

marcosci / buffer_anim.R

Created September 25, 2018 10:03

animation to illustrate sample_lsm (sample landscape metrics in buffers around points of interest)

	library(NLMR)
	library(sf)
	library(purrr)
	library(rcartocolor)
	library(gganimate)
	library(classInt)

	landscape <- NLMR::nlm_fbm(50, 100, fract_dim = 1.2)

	breaks <- landscape %>%

marcosci / recover_future.R

Created October 10, 2018 04:30

read results from .future

future_results  <-  list.files("/home/uni08/msciain/.future", pattern = glob2rx("*1.rds"), recursive = T, full.names = TRUE) %>% map_dfr(readRDS)

marcosci / nlrx_links_team

Created January 11, 2019 21:51

nlrx Team Assembly

	## Step1: Create a nl obejct:
	nl <- nl(nlversion = "6.0.4",
	nlpath = "/home/marco/nlrx_usecase/1_Helper/NetLogo 6.0.4/",
	modelpath = "/home/marco/nlrx_usecase/1_Helper/NetLogo 6.0.4/app/models/Sample Models/Networks/Team Assembly.nlogo",
	jvmmem = 1024)

	## Step2: Add Experiment

	# Inspect the model available model parameters:
	nl@experiment <- experiment(expname = "links_team",