Nothing
## ---- include = F-------------------------------------------------------------
options(rmarkdown.html_vignette.check_title = FALSE)
knitr::opts_chunk$set(eval = F)
## ---- fig.show='hold', fig.cap="test"-----------------------------------------
# library(anipaths)
# vultures$POSIX <- as.POSIXct(vultures$timestamp, tz = "UTC")
# vultures_paths <- vultures[format(vultures$POSIX, "%Y") == 2009, ] ## limit attention to 2009
# animate_paths(paths = vultures_paths,
# delta.t = "day",
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier")
## ----map_logical--------------------------------------------------------------
# library(ggmap)
# animate_paths(paths = vultures_paths,
# delta.t = 2 * 24 * 60 * 60, ## number of seconds in two days
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# background = TRUE, img.name = "background_TRUE")
## ----map_google---------------------------------------------------------------
# vultures_paths <- vultures[format(vultures$POSIX, "%Y") == 2009:2010, ]
# background <- list(center = c(-90, 10),
# zoom = 3,
# maptype = "satellite")
# animate_paths(paths = vultures_paths,
# delta.t = 3 * 24 * 60 * 60, ## number of seconds in three days
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# background = background, img.name = "background_google")
## ----map_simple---------------------------------------------------------------
# background <- rworldmap::getMap(resolution = "coarse")
# sp::proj4string(background) ## matches default projection in animate_paths()
# # background <- data.frame(x = range(vultures_paths$location.long)[c(1, 2, 2, 1, 1)],
# # y = range(vultures_paths$location.lat)[c(1, 1, 2, 2, 1)])
# animate_paths(paths = vultures_paths,
# delta.t = "week",
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# background = background, img.name = "background_user")
## ----make_covariates----------------------------------------------------------
# behaviors <- c("exploratory", "directed", "stationary")
# set.seed(1)
# vultures_paths$behavior <-
# unlist(sapply(unique(vultures_paths$individual.local.identifier), function(id){
# v_id <- vultures_paths[vultures_paths$individual.local.identifier == id, ]
# switches <- c(0, sort(sample(1:nrow(v_id), 2)), nrow(v_id))
# rep(behaviors[sample(1:3, 3)], diff(switches))
# }))
## ----plot_covariates----------------------------------------------------------
# delta.t <- "day"
# background <- rworldmap::getMap(resolution = "coarse")
# sp::proj4string(background)
# animate_paths(paths = vultures_paths,
# delta.t = delta.t,
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# covariate = "behavior", covariate.colors = viridis::viridis(3),
# ID.name = "individual.local.identifier",
# background = background, img.name = "covariates")
## -----------------------------------------------------------------------------
# interp <- animate_paths(paths = vultures_paths,
# delta.t = "day",
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# s_args = rep(list(list(k = 10)), 10),
# return.paths = T)
# plot(interp, i = 2)
## -----------------------------------------------------------------------------
# obs_counts <- merge(data.frame(individual.local.identifier = unique(vultures_paths$individual.local.identifier)),
# aggregate(timestamp ~ individual.local.identifier, data = vultures_paths, FUN = length),
# by = "individual.local.identifier", sort = F)
# obs_counts
# s_args <- lapply(obs_counts$timestamp, function(x) c(k = floor(min(x / 4, 306))))
# interp <- animate_paths(paths = vultures_paths,
# delta.t = "day",
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# s_args = s_args,
# return.paths = T)
# plot(interp, i = 2)
## -----------------------------------------------------------------------------
# interp <- animate_paths(paths = vultures_paths,
# delta.t = "day",
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# return.paths = T, verbose = T)
# plot(interp, i = 2)
## ----whole_path_anim----------------------------------------------------------
# animate_paths(paths = vultures_paths,
# delta.t = delta.t,
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# background = background,
# whole.path = TRUE, tail.length = 0, img.name = "whole_traj")
## ----dim_anim-----------------------------------------------------------------
# vultures_paths <- vultures[format(vultures$POSIX, "%Y") == 2009 &
# vultures$location.lat > 32, ]
# animate_paths(paths = vultures_paths,
# delta.t = delta.t,
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# background = background, dimmed = c(1, 3, 5), img.name = "dim")
## ----make_network-------------------------------------------------------------
# vultures_paths <- vultures[format(vultures$POSIX, "%Y") == 2009, ]
# set.seed(1)
# n_indiv <- length(unique(vultures_paths$individual.local.identifier))
# change_pts <- 5
# network.times <- seq(min(vultures_paths$POSIX), max(vultures_paths$POSIX), l = change_pts + 2)
# network <- array(NA, dim = c(n_indiv, n_indiv, length(network.times)))
# for(time_i in 2:length(network.times)){
# network_mat <- matrix(sample(1:0, n_indiv^2, prob = c(0.1, 0.9), replace = T),
# n_indiv, n_indiv)
# network_mat[lower.tri(network_mat)] <- t(network_mat)[lower.tri(network_mat)]
# diag(network_mat) <- 1
# network[, , (time_i - 1):time_i] <- network_mat
# }
## ----network_anim-------------------------------------------------------------
# delta.t <- 3600*24*2
# animate_paths(paths = vultures_paths,
# delta.t = delta.t,
# coord = c("location.long", "location.lat"),
# Time.name = "POSIX",
# ID.name = "individual.local.identifier",
# background = background, network = network, network.times = network.times,
# img.name = "network")
## ----remove files, eval = F---------------------------------------------------
# system("rm -r js; rm -r css; rm -r images; rm index.html")
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.