## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", out.width = "100%", fig.asp = 0.4, fig.width = 8.766 ) ## ----setup, message=FALSE, warning=FALSE-------------------------------------- library(clugenr) # The clugenr library options(rgl.useNULL = TRUE) # Create RGL plots in systems without displays (CI) library(rgl) setupKnitr(autoprint = TRUE) # Render RGL plots directly on generated page # Load helper functions for plotting examples source("plot_examples_3d.R", local = knitr::knit_global()) # Keep examples reproducible in newer R versions RNGversion("3.6.0") ## ----------------------------------------------------------------------------- seed <- 456 ## ----------------------------------------------------------------------------- e064 <- clugen(3, 4, 300, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 0.0, seed = seed) e065 <- clugen(3, 4, 300, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 1.0, seed = seed) e066 <- clugen(3, 4, 300, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 3.0, seed = seed) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e064, t = "e064: lateral_disp = 0"), list(e = e065, t = "e065: lateral_disp = 1"), list(e = e066, t = "e066: lateral_disp = 3")) ## ----------------------------------------------------------------------------- e067 <- clugen(3, 4, 300, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 0.0, seed = seed, proj_dist_fn = "unif") e068 <- clugen(3, 4, 300, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 1.0, seed = seed, proj_dist_fn = "unif") e069 <- clugen(3, 4, 300, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 3.0, seed = seed, proj_dist_fn = "unif") ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e067, t = "e067: lateral_disp = 0"), list(e = e068, t = "e068: lateral_disp = 1"), list(e = e069, t = "e069: 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 ## ----------------------------------------------------------------------------- e070 <- clugen(3, 4, 400, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 0.0, seed = seed, proj_dist_fn = proj_beta) e071 <- clugen(3, 4, 400, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 1.0, seed = seed, proj_dist_fn = proj_beta) e072 <- clugen(3, 4, 400, c(1, 0, 0), pi / 2, c(20, 20, 20), 13, 2, 3.0, seed = seed, proj_dist_fn = proj_beta) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e070, t = "e070: lateral_disp = 0"), list(e = e071, t = "e071: lateral_disp = 1"), list(e = e072, t = "e072: 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 ## ----------------------------------------------------------------------------- e073 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed) e074 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed, proj_dist_fn = "unif") e075 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed, proj_dist_fn = proj_beta) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e073, t = "e073: proj_dist_fn = 'norm' (default)"), list(e = e074, t = "e074: proj_dist_fn = 'unif'"), list(e = e075, t = "e075: custom proj_dist_fn (Beta dist.)")) ## ----------------------------------------------------------------------------- e076 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed, point_dist_fn = "n") e077 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed, point_dist_fn = "n", proj_dist_fn = "unif") e078 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed, point_dist_fn = "n", proj_dist_fn = proj_beta) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e076, t = "e076: proj_dist_fn = 'norm' (default)"), list(e = e077, t = "e077: proj_dist_fn = 'unif'"), list(e = e078, t = "e078: 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) } ## ----------------------------------------------------------------------------- e079 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed, point_dist_fn = clupoints_n_1_exp) e080 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed, point_dist_fn = clupoints_n_1_exp, proj_dist_fn = "unif") e081 <- clugen(3, 5, 400, c(1, 0, 0), pi / 3, c(20, 20, 20), 22, 3, 2, seed = seed, point_dist_fn = clupoints_n_1_exp, proj_dist_fn = proj_beta) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e079, t = "e079: proj_dist_fn = 'norm' (default)"), list(e = e080, t = "e080: proj_dist_fn = 'unif'"), list(e = e081, t = "e081: 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[3], csep[1], -csep[2], -csep[3], -csep[1], csep[2], csep[3], csep[1], csep[2], csep[3]), nrow = nclu, byrow = TRUE) } # Custom clusizes_fn (e083): 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 (e084): clusters all have the same size, no correction for # total points clusizes_equal <- function(nclu, npts, ae) npts %/% nclu * rep.int(1, nclu) ## ----------------------------------------------------------------------------- e082 <- clugen(3, 4, 400, c(1, 1, 1), pi, c(20, 20, 20), 0, 0, 5, seed = seed, point_dist_fn = "n", clucenters_fn = centers_fixed) e083 <- clugen(3, 4, 400, c(1, 1, 1), pi, c(20, 20, 20), 0, 0, 5, seed = seed, clusizes_fn = clusizes_unif, point_dist_fn = "n", clucenters_fn = centers_fixed) e084 <- clugen(3, 4, 400, c(1, 1, 1), pi, c(20, 20, 20), 0, 0, 5, seed = seed, clusizes_fn = clusizes_equal, point_dist_fn = "n", clucenters_fn = centers_fixed) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e082, t = "e082: normal dist. (default)"), list(e = e083, t = "e083: unif. dist. (custom)"), list(e = e084, t = "e084: equal size (custom)"))