Nothing
## ----option chunk, echo = FALSE-----------------------------------------------
options(Encoding="UTF-8")
knitr::opts_chunk$set(
fig.width = 8,
fig.height = 5,
collapse = TRUE,
comment = "#>"
)
## ----library and data, fig.show='hold'----------------------------------------
library(segclust2d)
data(simulshift)
data(simulmode)
simulmode$abs_spatial_angle <- abs(simulmode$spatial_angle)
simulmode <- simulmode[!is.na(simulmode$abs_spatial_angle), ]
## ----ex df, eval = FALSE------------------------------------------------------
# segmentation(x_data.frame, lmin = 5, Kmax = 25)
## ----ex Move, eval = FALSE----------------------------------------------------
# segmentation(x_move, lmin = 5, Kmax = 25)
## ----ex ltraj, eval = FALSE---------------------------------------------------
# segmentation(x_ltraj, lmin = 5, Kmax = 25)
## ----disabling subsampling, fig.show='hold', eval = FALSE---------------------
# shiftseg <- segmentation(simulshift,
# Kmax = 30, lmin=5,
# seg.var = c("x","y"),
# subsample = FALSE)
#
# mode_segclust <- segclust(simulmode,
# Kmax = 30, lmin=5, ncluster = c(2,3,4),
# seg.var = c("speed","abs_spatial_angle"),
# subsample = FALSE)
## ----automatic subsampling, fig.show='hold', eval = FALSE---------------------
# shiftseg <- segmentation(simulshift,
# Kmax = 30, lmin=5,
# seg.var = c("x","y"),
# subsample_over = 2000)
#
# mode_segclust <- segclust(simulmode,
# Kmax = 30, lmin=5, ncluster = c(2,3,4),
# seg.var = c("speed","abs_spatial_angle"),
# subsample_over = 500)
## ----manual subsampling, fig.show='hold', eval = FALSE------------------------
# shiftseg <- segmentation(simulshift,
# Kmax = 30, lmin=5,
# seg.var = c("x","y"),
# subsample_by = 60)
#
# mode_segclust <- segclust(simulmode,
# Kmax = 30, lmin=5, ncluster = c(2,3,4),
# seg.var = c("speed","abs_spatial_angle"),
# subsample_by = 2)
## ----lmin and subsampling, echo = FALSE---------------------------------------
lmin <- 240
subsample_by <- 60
cli::cli_alert_success("Using {cli::col_green('lmin = ', lmin )}")
lmin <- max(lmin/subsample_by,5)
cli::cli_alert_success(
"Adjusting lmin to subsampling.
{cli::col_grey('Dividing lmin by ',subsample_by,', with a minimum of 5')}")
cli::cli_alert("After subsampling, {cli::col_green('lmin = ', lmin)}.
{cli::col_grey('Corresponding to lmin = ',lmin*subsample_by,
' on the original time scale')}")
## ----calculate covariate, fig.show='hold', eval = FALSE-----------------------
# simple_data <- simulmode[,c("dateTime","x","y")]
# full_data <- add_covariates(simple_data,
# coord.names = c("x","y"),
# timecol = "dateTime",
# smoothed = TRUE,
# units ="min")
# head(full_data)
## ----example repeated, eval = FALSE-------------------------------------------
# df <- data.frame(x = rep(1,500), y = rep(2, 500))
# segclust(df,
# seg.var = c("x","y"),
# lmin = 50, ncluster = 3 )
## ----example repeated message, echo = FALSE-----------------------------------
seg.var <- c("x","y")
cli::cli_alert_danger(
"Data have repetition of nearly-identical \\
values longer than lmin.
{cli::col_grey('The algorithm cannot estimate variance \\
for segment with repeated values. \\
This is potentially caused by interpolation \\
of missing values or rounding of values.')}
{cli::symbol$arrow_right} Please check for repeated \\
or very similar values of {seg.var}")
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