marcosci
/ quantomPlot.R
Last active
October 20, 2015 21:20
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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) | |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Specify remote worker | |
| login <- tweak(remote, workers = "SERVER IP", user = 'USERNAME') | |
| # Specify future topology | |
| ## login node -> { multiple cores } | |
| plan(list( | |
| login, | |
| multiprocess | |
| )) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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)
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(NLMR) | |
| library(sf) | |
| library(purrr) | |
| library(rcartocolor) | |
| library(gganimate) | |
| library(classInt) | |
| landscape <- NLMR::nlm_fbm(50, 100, fract_dim = 1.2) | |
| breaks <- landscape %>% |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| future_results <- list.files("/home/uni08/msciain/.future", pattern = glob2rx("*1.rds"), recursive = T, full.names = TRUE) %>% map_dfr(readRDS) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ## 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", |
OlderNewer