## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 16, fig.height = 8, fig.retina = NULL, out.width = "100%" ) ## ----include = FALSE---------------------------------------------------------- if (Sys.getenv("RGL_USE_NULL") == "" && !interactive()) { Sys.setenv(RGL_USE_NULL = "TRUE") } ## ----setup-------------------------------------------------------------------- library(QuAnTeTrack) ## ----eval=FALSE--------------------------------------------------------------- # PaluxyRiver <- tps_to_track( # system.file("extdata", "PaluxyRiver.tps", package = "QuAnTeTrack"), # scale = 0.004341493, # missing = FALSE, # NAs = NULL # ) ## ----echo=FALSE--------------------------------------------------------------- PaluxyRiver <- tps_to_track( system.file("extdata", "PaluxyRiver.tps", package = "QuAnTeTrack"), scale = 0.004341493, missing = FALSE, NAs = NULL ) ## ----eval=FALSE--------------------------------------------------------------- # MountTom <- tps_to_track( # system.file("extdata", "MountTom.tps", package = "QuAnTeTrack"), # scale = 0.004411765, # missing = TRUE, # NAs = matrix(c(7, 3), nrow = 1, ncol = 2), # R.L.side = c( # "R", "L", "L", "L", "R", "L", "R", "R", "L", "L", "L", "L", "L", # "R", "R", "L", "R", "R", "L", "R", "R", "R", "R" # ) # ) ## ----echo=FALSE--------------------------------------------------------------- MountTom <- tps_to_track( system.file("extdata", "MountTom.tps", package = "QuAnTeTrack"), scale = 0.004411765, missing = TRUE, NAs = matrix(c(7, 3), nrow = 1, ncol = 2), R.L.side = c( "R", "L", "L", "L", "R", "L", "R", "R", "L", "L", "L", "L", "L", "R", "R", "L", "R", "R", "L", "R", "R", "R", "R" ) ) ## ----eval=FALSE--------------------------------------------------------------- # sbMountTom <- subset_track(MountTom, tracks = c(1, 2, 3, 4, 7, 8, 9, 13, 15, 16, 18)) # print(sbMountTom) ## ----echo=FALSE--------------------------------------------------------------- sbMountTom <- subset_track(MountTom, tracks = c(1, 2, 3, 4, 7, 8, 9, 13, 15, 16, 18)) print(sbMountTom) ## ----echo=TRUE---------------------------------------------------------------- plot_track(PaluxyRiver) ## ----echo=TRUE---------------------------------------------------------------- plot_track(MountTom) ## ----echo=TRUE---------------------------------------------------------------- plot_track(PaluxyRiver, plot = "Footprints") ## ----echo=TRUE---------------------------------------------------------------- plot_track(MountTom, plot = "Footprints") ## ----echo=TRUE---------------------------------------------------------------- plot_track(PaluxyRiver, plot = "Tracks") ## ----echo=TRUE---------------------------------------------------------------- plot_track(MountTom, plot = "Tracks") ## ----echo=TRUE---------------------------------------------------------------- labels <- paste("Track", seq_along(MountTom[[1]])) plot_track(MountTom, plot.labels = TRUE, labels = labels, cex.l = 4, box.p = 0.3, alpha.l = 0.7) ## ----echo=TRUE---------------------------------------------------------------- plot_track(PaluxyRiver, plot = "Footprints", colours = c("red", "orange"), shape.f = c(15, 18)) ## ----eval=FALSE--------------------------------------------------------------- # params_paluxy <- track_param(PaluxyRiver) ## ----echo=FALSE--------------------------------------------------------------- params_paluxy <- track_param(PaluxyRiver) ## ----eval=FALSE--------------------------------------------------------------- # params_mount <- track_param(MountTom) ## ----echo=FALSE--------------------------------------------------------------- params_mount <- track_param(MountTom) ## ----eval=FALSE--------------------------------------------------------------- # H_paluxyriver <- c(3.472, 2.200) # velocity_paluxyriver <- velocity_track(PaluxyRiver, H = H_paluxyriver) ## ----echo=FALSE--------------------------------------------------------------- H_paluxyriver <- c(3.472, 2.200) velocity_paluxyriver <- velocity_track(PaluxyRiver, H = H_paluxyriver) ## ----eval=FALSE--------------------------------------------------------------- # H_mounttom <- c( # 1.380, 1.404, 1.320, 1.736, 1.364, 1.432, 1.508, 1.768, 1.600, # 1.848, 1.532, 1.532, 0.760, 1.532, 1.688, 1.620, 0.636, 1.784, 1.676, 1.872, # 1.648, 1.760, 1.612 # ) # velocity_mounttom <- velocity_track(MountTom, H = H_mounttom) ## ----echo=FALSE--------------------------------------------------------------- H_mounttom <- c( 1.380, 1.404, 1.320, 1.736, 1.364, 1.432, 1.508, 1.768, 1.600, 1.848, 1.532, 1.532, 0.760, 1.532, 1.688, 1.620, 0.636, 1.784, 1.676, 1.872, 1.648, 1.760, 1.612 ) velocity_mounttom <- velocity_track(MountTom, H = H_mounttom) ## ----eval=FALSE--------------------------------------------------------------- # H_paluxyriver <- c(3.472, 2.200) # Method_paluxyriver <- c("A", "B") # velocity_paluxyriver_diff <- velocity_track(PaluxyRiver, H = H_paluxyriver, method = Method_paluxyriver) ## ----echo=FALSE--------------------------------------------------------------- H_paluxyriver <- c(3.472, 2.200) Method_paluxyriver <- c("A", "B") velocity_paluxyriver_diff <- velocity_track(PaluxyRiver, H = H_paluxyriver, method = Method_paluxyriver) ## ----echo=TRUE---------------------------------------------------------------- plot_velocity(PaluxyRiver, velocity_paluxyriver_diff, param = "RSL") ## ----echo=TRUE---------------------------------------------------------------- plot_velocity(MountTom, velocity_mounttom, param = "V") ## ----echo=TRUE---------------------------------------------------------------- plot_velocity(PaluxyRiver, velocity_paluxyriver_diff, param = "RSL", lwd = 1.5, colours = c("purple", "orange", "pink", "gray"), legend = FALSE) ## ----echo=TRUE---------------------------------------------------------------- plot_velocity(MountTom, velocity_mounttom, param = "V", lwd = 2, colours = c("blue", "green", "yellow", "red")) ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(PaluxyRiver, plot_type = "boxplot") ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(MountTom, plot_type = "boxplot") ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(PaluxyRiver, plot_type = "polar_steps") ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(MountTom, plot_type = "polar_steps") ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(PaluxyRiver, plot_type = "polar_average") ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(MountTom, plot_type = "polar_average") ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(PaluxyRiver, plot_type = "faceted") ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(MountTom, plot_type = "faceted") ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(PaluxyRiver, plot_type = "polar_average", y_breaks_manual = c(1, 2)) ## ----echo=TRUE, results='hide'------------------------------------------------ plot_direction(PaluxyRiver, plot_type = "polar_steps", y_labels_position = -90) ## ----eval=FALSE--------------------------------------------------------------- # test_velocity(PaluxyRiver, velocity_paluxyriver_diff, analysis = "ANOVA") ## ----echo=FALSE--------------------------------------------------------------- test_velocity(PaluxyRiver, velocity_paluxyriver_diff, analysis = "ANOVA") ## ----eval=FALSE--------------------------------------------------------------- # test_velocity(MountTom, velocity_mounttom, analysis = "ANOVA") ## ----echo=FALSE--------------------------------------------------------------- test_velocity(MountTom, velocity_mounttom, analysis = "ANOVA") ## ----eval=FALSE--------------------------------------------------------------- # test_velocity(PaluxyRiver, velocity_paluxyriver_diff, analysis = "Kruskal-Wallis") ## ----echo=FALSE--------------------------------------------------------------- test_velocity(PaluxyRiver, velocity_paluxyriver_diff, analysis = "Kruskal-Wallis") ## ----eval=FALSE--------------------------------------------------------------- # test_velocity(MountTom, velocity_mounttom, analysis = "Kruskal-Wallis") ## ----echo=FALSE--------------------------------------------------------------- test_velocity(MountTom, velocity_mounttom, analysis = "Kruskal-Wallis") ## ----eval=FALSE--------------------------------------------------------------- # test_velocity(PaluxyRiver, velocity_paluxyriver_diff, analysis = "GLM") ## ----echo=FALSE--------------------------------------------------------------- test_velocity(PaluxyRiver, velocity_paluxyriver_diff, analysis = "GLM") ## ----eval=FALSE--------------------------------------------------------------- # test_velocity(MountTom, velocity_mounttom, analysis = "GLM") ## ----echo=FALSE--------------------------------------------------------------- test_velocity(MountTom, velocity_mounttom, analysis = "GLM") ## ----eval=FALSE--------------------------------------------------------------- # mode_velocity(velocity_paluxyriver_diff) ## ----echo=FALSE--------------------------------------------------------------- mode_velocity(velocity_paluxyriver_diff) ## ----eval=FALSE--------------------------------------------------------------- # mode_velocity(velocity_mounttom) ## ----echo=FALSE--------------------------------------------------------------- mode_velocity(velocity_mounttom) ## ----eval=FALSE--------------------------------------------------------------- # test_direction(PaluxyRiver, analysis = "ANOVA") ## ----include=FALSE------------------------------------------------------------ test_dir_paluxy_anova <- test_direction(PaluxyRiver, analysis = "ANOVA") ## ----echo=FALSE--------------------------------------------------------------- print(test_dir_paluxy_anova) ## ----eval=FALSE--------------------------------------------------------------- # test_direction(MountTom, analysis = "ANOVA") ## ----include=FALSE------------------------------------------------------------ test_dir_mount_anova <- test_direction(MountTom, analysis = "ANOVA") ## ----echo=FALSE--------------------------------------------------------------- print(test_dir_mount_anova) ## ----eval=FALSE--------------------------------------------------------------- # test_direction(PaluxyRiver, analysis = "Kruskal-Wallis") ## ----include=FALSE------------------------------------------------------------ test_dir_paluxy_Kruskal <- test_direction(PaluxyRiver, analysis = "Kruskal-Wallis") ## ----echo=FALSE--------------------------------------------------------------- print(test_dir_paluxy_Kruskal) ## ----eval=FALSE--------------------------------------------------------------- # test_direction(MountTom, analysis = "Kruskal-Wallis") ## ----include=FALSE------------------------------------------------------------ test_dir_mount_Kruskal <- test_direction(MountTom, analysis = "Kruskal-Wallis") ## ----echo=FALSE--------------------------------------------------------------- print(test_dir_mount_Kruskal) ## ----eval=FALSE--------------------------------------------------------------- # test_direction(PaluxyRiver, analysis = "GLM") ## ----include=FALSE------------------------------------------------------------ test_dir_paluxy_GLM <- test_direction(PaluxyRiver, analysis = "GLM") ## ----echo=FALSE--------------------------------------------------------------- print(test_dir_paluxy_GLM) ## ----eval=FALSE--------------------------------------------------------------- # test_direction(MountTom, analysis = "GLM") ## ----include=FALSE------------------------------------------------------------ test_dir_mount_GLM <- test_direction(MountTom, analysis = "GLM") ## ----echo=FALSE--------------------------------------------------------------- print(test_dir_mount_GLM) ## ----eval=FALSE--------------------------------------------------------------- # sim_unconstrained_paluxy <- simulate_track(PaluxyRiver, nsim = 100, model = "Unconstrained") # print(sim_unconstrained_paluxy[1:10]) ## ----echo=FALSE--------------------------------------------------------------- sim_unconstrained_paluxy <- simulate_track(PaluxyRiver, nsim = 100, model = "Unconstrained") print(sim_unconstrained_paluxy[1:10]) ## ----eval=FALSE--------------------------------------------------------------- # sim_directed_paluxy <- simulate_track(PaluxyRiver, nsim = 100, model = "Directed") # print(sim_directed_paluxy[1:10]) ## ----echo=FALSE--------------------------------------------------------------- sim_directed_paluxy <- simulate_track(PaluxyRiver, nsim = 100, model = "Directed") print(sim_directed_paluxy[1:10]) ## ----eval=FALSE--------------------------------------------------------------- # sim_constrained_paluxy <- simulate_track(PaluxyRiver, nsim = 100, model = "Constrained") # print(sim_constrained_paluxy[1:10]) ## ----echo=FALSE--------------------------------------------------------------- sim_constrained_paluxy <- simulate_track(PaluxyRiver, nsim = 100, model = "Constrained") print(sim_constrained_paluxy[1:10]) ## ----eval=FALSE--------------------------------------------------------------- # sim_unconstrained_mount <- simulate_track(sbMountTom, nsim = 100, model = "Unconstrained") # print(sim_unconstrained_mount[1:10]) ## ----echo=FALSE--------------------------------------------------------------- sim_unconstrained_mount <- simulate_track(sbMountTom, nsim = 100, model = "Unconstrained") print(sim_unconstrained_mount[1:10]) ## ----eval=FALSE--------------------------------------------------------------- # sim_directed_mount <- simulate_track(sbMountTom, nsim = 100, model = "Directed") # print(sim_directed_mount[1:10]) ## ----echo=FALSE--------------------------------------------------------------- sim_directed_mount <- simulate_track(sbMountTom, nsim = 100, model = "Directed") print(sim_directed_mount[1:10]) ## ----eval=FALSE--------------------------------------------------------------- # sim_constrained_mount <- simulate_track(sbMountTom, nsim = 100, model = "Constrained") # print(sim_constrained_mount[1:10]) ## ----echo=FALSE--------------------------------------------------------------- sim_constrained_mount <- simulate_track(sbMountTom, nsim = 100, model = "Constrained") print(sim_constrained_mount[1:10]) ## ----echo=TRUE---------------------------------------------------------------- plot_sim(PaluxyRiver, sim_unconstrained_paluxy) ## ----echo=TRUE---------------------------------------------------------------- plot_sim(PaluxyRiver, sim_directed_paluxy, colours_sim = c("#E69F00", "#56B4E9"), alpha_sim = 0.4, lwd_sim = 1, colours_act = c("black", "black"), alpha_act = 0.7, lwd_act = 2 ) ## ----echo=TRUE---------------------------------------------------------------- plot_sim(PaluxyRiver, sim_constrained_paluxy, colours_sim = c("#E69F00", "#56B4E9"), alpha_sim = 0.6, lwd_sim = 0.1, alpha_act = 0.5, lwd_act = 2 ) ## ----echo=TRUE---------------------------------------------------------------- plot_sim(sbMountTom, sim_unconstrained_mount) ## ----echo=TRUE---------------------------------------------------------------- plot_sim(sbMountTom, sim_directed_mount, colours_sim = c("#6BAED6", "#FF7F00", "#1F77B4", "#D62728", "#2CA02C", "#9467BD", "#8C564B", "#E377C2", "#7F7F7F", "#BCBD22", "#17BECF"), alpha_sim = 0.3, lwd_sim = 1.5, alpha_act = 0.8, lwd_act = 2 ) ## ----echo=TRUE---------------------------------------------------------------- plot_sim(sbMountTom, sim_constrained_mount, colours_sim = c("#6BAED6", "#FF7F00", "#1F77B4", "#D62728", "#2CA02C", "#9467BD", "#8C564B", "#E377C2", "#7F7F7F", "#BCBD22", "#17BECF"), alpha_sim = 0.5, lwd_sim = 0.2, alpha_act = 0.6, lwd_act = 2 ) ## ----eval=FALSE--------------------------------------------------------------- # simil_dtw_directed_paluxy <- simil_DTW_metric(PaluxyRiver, test = TRUE, # sim = sim_directed_paluxy, # superposition = "Centroid") ## ----include=FALSE------------------------------------------------------------ simil_dtw_directed_paluxy <- simil_DTW_metric(PaluxyRiver, test = TRUE, sim = sim_directed_paluxy, superposition = "Centroid") ## ----echo=FALSE--------------------------------------------------------------- print(simil_dtw_directed_paluxy) ## ----eval=FALSE--------------------------------------------------------------- # simil_frechet_directed_paluxy <- simil_Frechet_metric(PaluxyRiver, test = TRUE, # sim = sim_directed_paluxy, # superposition = "Centroid") ## ----include=FALSE------------------------------------------------------------ simil_frechet_directed_paluxy <- simil_Frechet_metric(PaluxyRiver, test = TRUE, sim = sim_directed_paluxy, superposition = "Centroid") ## ----echo=FALSE--------------------------------------------------------------- print(simil_frechet_directed_paluxy) ## ----eval=FALSE--------------------------------------------------------------- # simil_dtw_constrained_mount <- simil_DTW_metric(sbMountTom, test = TRUE, # sim = sim_constrained_mount, # superposition = "Origin") ## ----include=FALSE------------------------------------------------------------ simil_dtw_constrained_mount <- simil_DTW_metric(sbMountTom, test = TRUE, sim = sim_constrained_mount, superposition = "Origin") ## ----echo=FALSE--------------------------------------------------------------- print(simil_dtw_constrained_mount) ## ----eval=FALSE--------------------------------------------------------------- # simil_frechet_constrained_mount <- simil_Frechet_metric(sbMountTom, test = TRUE, # sim = sim_constrained_mount, # superposition = "Origin") ## ----include=FALSE------------------------------------------------------------ simil_frechet_constrained_mount <- simil_Frechet_metric(sbMountTom, test = TRUE, sim = sim_constrained_mount, superposition = "Origin") ## ----echo=FALSE--------------------------------------------------------------- print(simil_frechet_constrained_mount) ## ----eval=FALSE--------------------------------------------------------------- # int_directed_paluxy <- track_intersection(PaluxyRiver, test = TRUE, H1 = "Lower", # sim = sim_directed_paluxy, # origin.permutation = "None") # print(int_directed_paluxy) ## ----include=FALSE------------------------------------------------------------ int_directed_paluxy <- track_intersection(PaluxyRiver, test = TRUE, H1 = "Lower", sim = sim_directed_paluxy, origin.permutation = "None") ## ----echo=FALSE--------------------------------------------------------------- print(int_directed_paluxy) ## ----eval=FALSE--------------------------------------------------------------- # int_constrained_mount <- track_intersection(sbMountTom, test = TRUE, H1 = "Higher", # sim = sim_constrained_mount, # origin.permutation = "Conv.Hull") # print(int_constrained_mount) ## ----include=FALSE------------------------------------------------------------ int_constrained_mount <- track_intersection(sbMountTom, test = TRUE, H1 = "Higher", sim = sim_constrained_mount, origin.permutation = "Conv.Hull") ## ----echo=FALSE--------------------------------------------------------------- print(int_constrained_mount) ## ----eval=FALSE--------------------------------------------------------------- # combined_metrics_paluxy <- combined_prob(PaluxyRiver, metrics = list( # simil_dtw_directed_paluxy, # simil_frechet_directed_paluxy, # int_directed_paluxy # )) ## ----include=FALSE------------------------------------------------------------ combined_metrics_paluxy <- combined_prob(PaluxyRiver, metrics = list( simil_dtw_directed_paluxy, simil_frechet_directed_paluxy, int_directed_paluxy )) ## ----echo=FALSE--------------------------------------------------------------- print(combined_metrics_paluxy) ## ----eval=FALSE--------------------------------------------------------------- # H_mounttom_subset <- c( # 1.380, 1.404, 1.320, 1.736, 1.432, 1.508, 1.768, 0.760, 1.688, 1.620, 1.784 # ) # velocity_sbmounttom <- velocity_track(sbMountTom, H = H_mounttom_subset) ## ----echo=FALSE--------------------------------------------------------------- H_mounttom_subset <- c( 1.380, 1.404, 1.320, 1.736, 1.432, 1.508, 1.768, 0.760, 1.688, 1.620, 1.784 ) velocity_sbmounttom <- velocity_track(sbMountTom, H = H_mounttom_subset) ## ----eval=FALSE--------------------------------------------------------------- # clustering_mounttom <- cluster_track( # data = sbMountTom, # veltrack = velocity_sbmounttom, # variables = c("Sinuosity", "Straightness", "Velocity", "TurnAng") # ) ## ----include=FALSE------------------------------------------------------------ clustering_mounttom <- cluster_track( data = sbMountTom, veltrack = velocity_sbmounttom, variables = c("Sinuosity", "Straightness", "Velocity", "TurnAng") ) ## ----echo=FALSE--------------------------------------------------------------- print(clustering_mounttom) ## ----eval=FALSE--------------------------------------------------------------- # clustering_mounttom$clust$classification ## ----echo=FALSE--------------------------------------------------------------- clustering_mounttom$clust$classification ## ----eval=FALSE--------------------------------------------------------------- # clustering_mounttom$clust$z ## ----echo=FALSE--------------------------------------------------------------- clustering_mounttom$clust$z