periodigram vignette
New utility function %#% for unit conversions
New model-fit sampling function “emulate”
summary now works on lists of telemetry objects
new extent method for variogram objects
bugfixes in plot.variogram with fit UERE, tau==0
bugfixes with ctmm.fit/select/summary near boundaries
resetting Polak–Ribiere formula in weighted AKDE conjugate gradient routine
read.table fallback in as.telmetry
R 3.4 compatibility fixes
various improvements to plot.variogram
plot.UD & export can now accept multiple level.UD values
increased numerical precision in ctmm.loglike
SI speeds & diffusion fixed with units=FALSE
AICc formulas updated from univariate to multivariate
ctmm.select more aggressive on small sample sizes where AICc >> AIC
new residuals and correlogram functions
ctmm.fit now has unified options controling optimization & differentiation
ctmm.fit Hessian and pREML calculations 2x faster
new writeRaster method for UD objects
Better UD plot boxes with new extent methods
variogram fast=TRUE less biased for irregular data with new res>1 option
variogram fast=FALSE more robust to irregularity
akde() can now handle duplicate times (with an error model)
plot.variogram bugfix for fixed error models [still not quite correct]
Column name preferences in as.telemetry
as.telemetry faster with fread & fastPOSIXct
new trace option for ctmm.fit
new labels option for plot.UD
more robust CIs for pREML, REML
chi-square CIs (area, semi-variance, etc.) more robust when DOF<1
added a FAQ page to the documentation help(“ctmm-FAQ”)
bugfix in occurrence method for BM & IOU models
unit conversion can now be disabled in summary with units=FALSE argument
added trace option to ctmm.select & bandwidth/akde
improved telemetry error support in summary.ctmm and plot.variogram
as.telemetry more robust to alternative column label capitalizations
ctmm.loglike & ctmm.fit more robust when tau_velocity ~ tau_position
Kalman filter & smoother upgraded to Joseph form covariance updates
weighted AKDE implemented, fast option, covered in vignette
overlap arguments & ouput changed/generalized
method akde.bandwidth renamed to bandwidth inline with S3 standards
predict now returns covariance estimates
occurrence distributions now exportable
AKDE overlap bugfixes
summary.ctmm now returns correct RMS speed
bugfix for eccentricity errors
variogram CIs fixed for odd dimensions
variogram.fit can now accept OU models
periodogram rare index bugfix
fixed missing lag in dt-argumented variogram
as.telemetry column identification more robust
as.telemetry defined for MoveStack objects
improved import of ‘move’ objects
preliminary 3D AKDE support, debiased
new method predict for ctmm objects
akde now supports smoothing errors
variogram.fit and plot.variogram now support telemetry error
UERE fitting now possible simultaneous with tracking data
tag.local.identifier now used as backup to individual.local.identifier in as.telemetry
multiple bug fixes in uere
res.space fixed in occurrence
new function overlap for stationary Gaussian distributions and KDEs
new function uere calculates UERE from calibration data
akde debias argument removes most bias from area estimtes, now default
akde CIs further improved
variogram, periodogram generalized to arbitrary dimensions
periodic mean function option for ctmm, ctmm.fit, ctmm.select, plot.variogram, summary (not yet documented)
new method residuals for ctmm objects
ctmm.select now only considers likely model modifications
DOFs now returned in summary
new methods [.telemetry, [.variogram, [.periodogram, subset.periodogram
methods for zoom, raster, writeShapefile now properly assigned to generics
new plot.periodogram option max
new periodogram option res.time (with Lagrange interpolation). Old option res renamed to res.freq.
akde res argument is now relative to the bandwidth
occurrence res.space argument is now relative to the average diffusion
plot.telemetry with data error now uses level.UD for error radius instead of one standard deviation
gridding function for fast=TRUE variogram and periodogram now always fast
bad location removed from buffalo “Pepper”
variogram.fit now stores global variables of any name
variogram.fit sliders now use pretty units
variogram.fit range argument depreciated in favor of a more general CTMM prototype argument
akde UD CIs significantly improved for high quality datasets
akde bugfix: subscript out of bounds
circulatory model introduced via circle ctmm argument
oscillatory CPF model introduced via CPF ctmm argument
as.telemetry now imports GPS.HDOP columns with a UERE argument
summary now works on arbitrary lists of ctmm objects
ctmm.fit now tries to make sense of ML parameters that lie on boundaries
occurrence() now works when some timesteps are tiny
new function “occurrence” to estimate occurrence distributions
“akde” & “occurrence” class objects generalized to “UD” class
alpha & alpha.HR arguments simplified and generalized to level & level.UD
AKDE= and .HR= arguments generalized to UD= and .UD=
new basic telemetry error functionality in ctmm, ctmm.fit
new function ctmm.select
new methods subset.telemetry and subset.variogram
fixed a bug in the uncertainty report of uncorrelated processes
ctmm.fit is now much faster by specifying a reasonable parscale for optim
ctmm.fit now has a backup for when Brent fails
fixed a rare condition in ctmm.fit where solve would fail on correlated errors
multiscale variogram and mean variogram example in vignette
new data example Mongolian gazelle
new fast option for periodogram
improvements in plot.periodogram
bugfix in as.telemetry for numeric indentifiers
bugfix in dt array option of variogram
new resolution option and better estimation algorithms in akde
alpha, alpha.HR, res arguments made consistent across all functions
efficiency gains in as.telemetry with multiple animals
bugfix in plot.telemetry for multiple Gaussian PDFs
bugfix in variogram for rare condition when fast=TRUE
CRAN check compliance achieved.
all methods (plot, mean, summary, simulate) can and must be run without class extensions
argument names no longer clash with function names and are more explicit about their object class
cleaned up and labeled tau parameter arrays
implemented Workaround for when subset demotes S4 objects to S3 objects
plot.telemetry now enforces asp=1 even with xlim/ylim arguments
new function summary.telemetry
bugfix in as.telemetry for data$t
bugfix in ctmm.loglike for some cases with numeric underflow
periodogram and plot.periodogram can now check for spurious periodicities
minimal support for BM and IOU motion
new function SpatialPoints.telemetry returns SpatialPoints object from telemetry data
new function SpatialPolygonsDataFrame.akde returns akde home-range contour SpatialPolygons objects from akde object
new function writeShapefile.akde writes akde home-range contours to ESRI shapefile
new function raster.akde returns akde pdf raster object
new function summary.akde returns HR area of AKDE
fixed bad CI in plot.telemetry model option
as.telemetry now takes a timezone argument for as.POSIXct and defaults to UTC
telemetry, ctmm, and akde objects now have idenification and projection information slotted, with consistent naming throughout
vignettes “variogram” and “akde”
new function as.telemetry imports MoveBank formatted csv data and returns telemetry objects
new function variogram.zoom plots a variogram with zoom slider
variogram.fit and variogram.zoom default to a logarithmic-scale zoom slider, which requires much less fiddling
plot.variogram now takes multiple variogram, model, and color options
plot.telemetry now takes multiple data, model, akde, and color options
plot.telemetry can now make probability density plots for both Gaussian model and akde data
ctmm.fit no longer screws up results with initial sigma guesstimates. ML parameter estimates now match closely with published Mathematica results. CIs are improved.
ks-package was producing incorrect home-range contours and has been replaced with custom code. ML home ranges now match published Mathematica results. CIs should be improved.