## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", out.width = "100%", fig.asp = 0.5, dpi = 120 ) ## ----setup, message=FALSE, warning=FALSE-------------------------------------- # Load the clugenr library library(clugenr) # Load functions for plotting examples source("plot_examples_2d.R", local = knitr::knit_global()) # Keep examples reproducible in newer R versions RNGversion("3.6.0") ## ----------------------------------------------------------------------------- seed <- 123 ## ----------------------------------------------------------------------------- e001 <- clugen(2, 4, 200, c(1, 0), 0, c(10, 10), 10, 1.5, 0.5, seed = seed) e002 <- clugen(2, 4, 200, c(1, 1), 0, c(10, 10), 10, 1.5, 0.5, seed = seed) e003 <- clugen(2, 4, 200, c(0, 1), 0, c(10, 10), 10, 1.5, 0.5, seed = seed) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e001, t = "e001: direction = [1, 0]"), list(e = e002, t = "e002: direction = [1, 1]"), list(e = e003, t = "e003: direction = [0, 1]")) ## ----------------------------------------------------------------------------- seed <- 123 ## ----------------------------------------------------------------------------- # Custom angle_deltas function: arbitrarily rotate some clusters by 90 degrees angdel_90_fn <- function(nclu, astd) sample(c(0, pi / 2), nclu, replace = TRUE) ## ----------------------------------------------------------------------------- e004 <- clugen(2, 6, 500, c(1, 0), 0, c(10, 10), 10, 1.5, 0.5, seed = seed) e005 <- clugen(2, 6, 500, c(1, 0), pi / 8, c(10, 10), 10, 1.5, 0.5, seed = seed) e006 <- clugen(2, 6, 500, c(1, 0), 0, c(10, 10), 10, 1.5, 0.5, seed = seed, angle_deltas_fn = angdel_90_fn) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e004, t = "e004: angle_disp = 0"), list(e = e005, t = "e005: angle_disp = π/8"), list(e = e006, t = "e006: custom angle_deltas function")) ## ----------------------------------------------------------------------------- seed <- 321 ## ----------------------------------------------------------------------------- e007 <- clugen(2, 5, 800, c(1, 0), pi / 10, c(10, 10), 0, 0, 0.5, seed = seed, point_dist_fn = "n") e008 <- clugen(2, 5, 800, c(1, 0), pi / 10, c(10, 10), 10, 0, 0.5, seed = seed, point_dist_fn = "n") e009 <- clugen(2, 5, 800, c(1, 0), pi / 10, c(10, 10), 30, 0, 0.5, seed = seed, point_dist_fn = "n") ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e007, t = "e007: llength = 0"), list(e = e008, t = "e008: llength = 10"), list(e = e009, t = "e009: llength = 30")) ## ----------------------------------------------------------------------------- seed <- 765 ## ----------------------------------------------------------------------------- # Custom llengths function: line lengths grow for each new cluster llen_grow_fn <- function(nclu, llen, llenstd) { llen * 0:(nclu - 1) + rnorm(nclu, sd = llenstd) } ## ----------------------------------------------------------------------------- e010 <- clugen(2, 5, 800, c(1, 0), pi / 10, c(10, 10), 15, 0.0, 0.5, seed = seed, point_dist_fn = "n") e011 <- clugen(2, 5, 800, c(1, 0), pi / 10, c(10, 10), 15, 10.0, 0.5, seed = seed, point_dist_fn = "n") e012 <- clugen(2, 5, 800, c(1, 0), pi / 10, c(10, 10), 10, 0.1, 0.5, seed = seed, llengths_fn = llen_grow_fn, point_dist_fn = "n") ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e010, t = "e010: llength_disp = 0.0"), list(e = e011, t = "e011: llength_disp = 5.0"), list(e = e012, t = "e012: custom llengths function")) ## ----------------------------------------------------------------------------- seed <- 222 ## ----------------------------------------------------------------------------- e013 <- clugen(2, 8, 1000, c(1, 1), pi / 4, c(10, 10), 15, 2, 4, seed = seed) e014 <- clugen(2, 8, 1000, c(1, 1), pi / 4, c(30, 10), 15, 2, 4, seed = seed) e015 <- clugen(2, 8, 1000, c(1, 1), pi / 4, c(10, 30), 15, 2, 4, seed = seed) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e013, t = "e013: cluster_sep = [10, 10]"), list(e = e014, t = "e014: cluster_sep = [30, 10]"), list(e = e015, t = "e015: cluster_sep = [10, 30]")) ## ----------------------------------------------------------------------------- seed <- 222 ## ----------------------------------------------------------------------------- # Custom clucenters function: places clusters in a diagonal centers_diag <- function(nclu, csep, coff) { matrix(1, nrow = nclu, ncol = length(csep)) * (1:nclu * max(csep)) + rep(coff, each = nclu) } ## ----------------------------------------------------------------------------- e016 <- clugen(2, 8, 1000, c(1, 1), pi / 4, c(10, 10), 10, 2, 2.5, seed = seed) e017 <- clugen(2, 8, 1000, c(1, 1), pi / 4, c(10, 10), 10, 2, 2.5, seed = seed, cluster_offset = c(20, -20)) e018 <- clugen(2, 8, 1000, c(1, 1), pi / 4, c(10, 10), 10, 2, 2.5, seed = seed, cluster_offset = c(-50, -50), clucenters_fn = centers_diag) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e016, t = "e016: default"), list(e = e017, t = "e017: cluster_offset = [20, -20]"), list(e = e018, t = "e018: custom clucenters function")) ## ----------------------------------------------------------------------------- seed <- 234 ## ----------------------------------------------------------------------------- e019 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 0.0, seed = seed) e020 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 1.0, seed = seed) e021 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 3.0, seed = seed) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e019, t = "e019: lateral_disp = 0"), list(e = e020, t = "e020: lateral_disp = 1"), list(e = e021, t = "e021: lateral_disp = 3")) ## ----------------------------------------------------------------------------- e022 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 0.0, seed = seed, proj_dist_fn = "unif") e023 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 1.0, seed = seed, proj_dist_fn = "unif") e024 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 3.0, seed = seed, proj_dist_fn = "unif") ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e022, t = "e022: lateral_disp = 0"), list(e = e023, t = "e023: lateral_disp = 1"), list(e = e024, t = "e024: lateral_disp = 3")) ## ----------------------------------------------------------------------------- # Custom proj_dist_fn: point projections placed using the Beta distribution proj_beta <- function(len, n) len * rbeta(n, 0.1, 0.1) - len / 2 ## ----------------------------------------------------------------------------- e025 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 0.0, seed = seed, proj_dist_fn = proj_beta) e026 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 1.0, seed = seed, proj_dist_fn = proj_beta) e027 <- clugen(2, 4, 1000, c(1, 0), pi / 2, c(20, 20), 13, 2, 3.0, seed = seed, proj_dist_fn = proj_beta) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e025, t = "e025: lateral_disp = 0"), list(e = e026, t = "e026: lateral_disp = 1"), list(e = e027, t = "e027: lateral_disp = 3")) ## ----------------------------------------------------------------------------- seed <- 12321 ## ----------------------------------------------------------------------------- # Custom proj_dist_fn: point projections placed using the Beta distribution proj_beta <- function(len, n) len * rbeta(n, 0.1, 0.1) - len / 2 ## ----------------------------------------------------------------------------- e028 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed) e029 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed, proj_dist_fn = "unif") e030 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed, proj_dist_fn = proj_beta) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e028, t = "e028: proj_dist_fn = 'norm' (default)"), list(e = e029, t = "e029: proj_dist_fn = 'unif'"), list(e = e030, t = "e030: custom proj_dist_fn (Beta dist.)")) ## ----------------------------------------------------------------------------- e031 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed, point_dist_fn = "n") e032 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed, point_dist_fn = "n", proj_dist_fn = "unif") e033 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed, point_dist_fn = "n", proj_dist_fn = proj_beta) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e031, t = "e031: proj_dist_fn = 'norm' (default)"), list(e = e032, t = "e032: proj_dist_fn = 'unif'"), list(e = e033, t = "e033: custom proj_dist_fn (Beta dist.)")) ## ----------------------------------------------------------------------------- # Custom point_dist_fn: final points placed using the Exponential distribution clupoints_n_1_exp <- function(projs, lat_std, len, clu_dir, clu_ctr) { dist_exp <- function(npts, lstd) lstd * rexp(npts, rate = 2 / lstd) clupoints_n_1_template(projs, lat_std, clu_dir, dist_exp) } ## ----------------------------------------------------------------------------- e034 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed, point_dist_fn = clupoints_n_1_exp) e035 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed, point_dist_fn = clupoints_n_1_exp, proj_dist_fn = "unif") e036 <- clugen(2, 5, 1500, c(1, 0), pi / 4, c(20, 20), 14, 2, 2.0, seed = seed, point_dist_fn = clupoints_n_1_exp, proj_dist_fn = proj_beta) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e034, t = "e034: proj_dist_fn = 'norm' (default)"), list(e = e035, t = "e035: proj_dist_fn = 'unif'"), list(e = e036, t = "e036: custom proj_dist_fn (Beta dist.)")) ## ----------------------------------------------------------------------------- seed <- 87 ## ----------------------------------------------------------------------------- # Custom clucenters_fn (all): yields fixed positions for the clusters centers_fixed <- function(nclu, csep, coff) { matrix(c(-csep[1], -csep[2], csep[1], -csep[2], -csep[1], csep[2], csep[1], csep[2]), nrow = nclu, byrow = TRUE) } # Custom clusizes_fn (e038): cluster sizes determined via the uniform distribution, # no correction for total points clusizes_unif <- function(nclu, npts, ae) sample(2 * npts / nclu, nclu, replace = TRUE) # Custom clusizes_fn (e039): clusters all have the same size, no correction for # total points clusizes_equal <- function(nclu, npts, ae) npts %/% nclu * rep.int(1, nclu) ## ----------------------------------------------------------------------------- e037 <- clugen(2, 4, 1500, c(1, 1), pi, c(20, 20), 0, 0, 5, seed = seed, clucenters_fn = centers_fixed, point_dist_fn = "n") e038 <- clugen(2, 4, 1500, c(1, 1), pi, c(20, 20), 0, 0, 5, seed = seed, clucenters_fn = centers_fixed, clusizes_fn = clusizes_unif, point_dist_fn = "n") e039 <- clugen(2, 4, 1500, c(1, 1), pi, c(20, 20), 0, 0, 5, seed = seed, clucenters_fn = centers_fixed, clusizes_fn = clusizes_equal, point_dist_fn = "n") ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e037, t = "e037: normal dist. (default)"), list(e = e038, t = "e038: unif. dist. (custom)"), list(e = e039, t = "e039: equal size (custom)")) ## ----------------------------------------------------------------------------- seed <- 9876 ## ----------------------------------------------------------------------------- e040 <- clugen(2, 4, 1000, c(-1, 1), 0, c(0, 0), 0, 0, 0.2, seed = seed, proj_dist_fn = "unif", point_dist_fn = "n", clusizes_fn = c(50, 200, 500, 2000), llengths_fn = c(0, 2, 4, 6), clucenters_fn = matrix(c(-5, -5, -2.5, -2.5, 0, 0, 2.5, 2.5), nrow = 4, byrow = TRUE)) e041 <- clugen(2, 5, 1000, matrix(c(1, 1, 1, 0, 1, 0, 0, 1, 0, 1), nrow = 5, byrow = TRUE), 0, c(0, 0), 0, 0, 0.2, seed = seed, proj_dist_fn = "unif", point_dist_fn = "n", clusizes_fn = c(200, 500, 500, 500, 500), llengths_fn = c(0, 5, 5, 5, 5), clucenters_fn = matrix(c(0, 0, 0, 5, 0, -5, 5, 0, -5, 0), nrow = 5, byrow = TRUE)) e042 <- clugen(2, 5, 1000, matrix(c(0, 1, 0.25, 0.75, 0.5, 0.5, 0.75, 0.25, 1, 0), nrow = 5, byrow = TRUE), 0, c(0, 0), 5, 0, 0.2, seed = seed, proj_dist_fn = "unif", point_dist_fn = "n", clusizes_fn = c(500, 500, 500, 500, 500), clucenters_fn = matrix(c(-5, 0, -3, -0.3, -1, -0.8, 1, -1.6, 3, -2.5), nrow = 5, byrow = TRUE)) ## ----------------------------------------------------------------------------- plot_examples_2d(list(e = e040, t = "e040: direct params 1"), list(e = e041, t = "e041: direct params 2"), list(e = e042, t = "e042: direct params 3"))