NEWS

---

ctmm 1.2.1

• sdm.fit() and sdm.select() now support camera-trap and other count data
• new dispatch method projection()<- for ctmm class objects
• new functions pd.solve(), pd.logdet(), pd.sqrtm() for covariance matrix operations
• new default method "ECDF" for function encounter()
• periodic mean functions now estimate frequency
• periodic mean summary now uses beta CIs
• mean.ctmm() now works on periodic means
• new mean.ctmm() argument 'formula' for functional response estimation
• new grid argument dr.fn in akde(), occurrence(), pkde()
• as.telemetry() now imports ATLAS error ellipses
• new ctmm.boot() argument 'clamp'
• new convex argument 'options'
• new geometric mean ratio estimates in meta() and improvements for small DOFs
• mean() of occurrence() now time weighted by default
• mean() can now accept non-stationary mean models
• new plot method: plot.ctmm()
• new outlie() argument 'units'
• plot() argument 'col.DF' renamed to 'col.UD'
• speedups in Kalman filter for irregularly sampled
• improvements in ctmm.fit() method="pREML" on unsupported parameters
• improvements DOF[area] calculations in mean() and pkde()
• improvement to optimizer() when initial guess is on a boundary and hessian is bad
• bugfix in speed() for nearly fractal movement models
• bugfix in polygon export from bad output from grDevices::contourLines()
• bugfix in rsf.select with functions in formulas
• bugfix in raster factor expansion with more than one raster factor
• bugfix in normal meta-analysis REML correction
• bugfixes in suitability with grid projection, NA raster values, and categorical variables
• bugfixes in mean.ctmm()
• bugfix in contour exports with convex=TRUE
• bugfix in transition()

ctmm 1.2.0 (2023-09-23)

• new function names: cde() and encounter() replacing encounter() and rates()
• new functions rsf.select(), intensity()
• new functions sdm.fit(), sdm.select()
• new function writeVector(), depreciating function writeShapefile()
• new function funnel() for funnel plots
• new function midpoint()
• new population covariance models and improved model selection in mean.ctmm()
• new argument 'sqrt' in distance()
• new argument 'dt.hot' in as.telemetry()
• new argument 'variable' in Log()
• new argument 'compute' in ctmm.loglike()
• new argument 't' in proximity()
• as.telemetry() now supports GBIF format data
• as.telemetry() datum argument now works on UTM import, and is no longer to a be a complete PROJ string
• as.telemetry() timeformat='auto' now default
• as.telemetry(), plot.telemetry(), rsf.fit() updated from sp to sf transforms
• distance() can now take location arguments
• plot.telemetry() col.DF & col.level arguments can now be color() lists
• suitability() now produces a raster stack corresponding to the CIs
• suitability() on population RSFs now outputs the population suitability
• suitability() extrapolation disabled
• bugfix in tbind for conflicting location classes
• bugfix in suitability()
• bugfix in distance() method="Euclidean", debias=TRUE
• bugfix in rates() debias=TRUE
• bugfix in summary() of population mean location DOF
• bugfix in distances() for 0/0
• bugfix in UD polygon export for tiny areas
• as.telemetry() UTM import updated to new PROJ specification
• mean.ctmm() improved convergence, numerical stability, and covariance selection
• meta() stability improvements for tiny DOF estimates, and OUf support
• overlap() and meta() can now extract object names
• pkde(...) -> akde(...) -> bandwidth(...) -> mean(...) arguments now passed
• rsf.fit() AICc formula improved

ctmm 1.1.0 (2022-11-04)

• new function pkde() for population kernel density estimates
• new functions difference(), distances(), proximity() for estimating distances between individuals
• new functions Log(), Exp() to log transform parameter estimates and their uncertainties for meta-analytic regression
• new functions dimfig(), sigfig() to represent quantities with concise units and significant digits
• new argument 'sample' in mean()
• new argument 'interpolate' in rsf.fit()
• new arguments 'xlim', 'ylim' to plot.outlie()
• numerical stability improvements in rsf.fit optimization and hessian calculations
• numerical convergence improvements in location error fitting
• numerical convergence improvements in AKDE weight optimization
• plot.telemetry() can now subset and reproject rasters
• bugfix in sp::polygon derived areas (used since v1.0.0 for summary, plot, meta)
• bugfix in agde(), suitability(), akde() when reprojecting onto the same raster
• bugfix in mean() when averaging isotropic and anisotropic models together
• bugfix in speeds() without telemetry object
• bugfix in cluster() with 0/0 bias correction error
• bugfix in occurrence() with multiple error classes
• bugfix in chi dof computation
• bugfix in outlie() for error ellipses
• summary() now works on mean.ctmm() outputs from different input model structures (OUF & OUO)
• fixed log-chi^2 bias correction in mean.ctmm()

ctmm 1.0.0 (2022-07-12)

• new function rsf.fit() to fit integrated resource selection functions (iRSFs) with autocorrelation-adjusted weighted likelihood
• new function mean.ctmm() to calculate population average movement models
• new function revisitation() to calculate the distribution of revisitations
• new function npr() to calculate non-parametric spatial regressions
• new function agde() to calculate autocorrelated Gaussian distribution estimates, with RSF support
• new function suitability() to calculate suitability rasters from RSF fit objects
• new function rates() to calculate relative encounter rates
• new function dt.plot() to inspect sampling intervals
• akde() and occurrence() now support RSF-informed kernels and boundary-respecting kernels
• summary.ctmm() now outputs diffusion rate estimates
• new argument variable for meta() to estimate population diffusion rates, mean speeds, and autocorrelation timescales
• new arguments R and SP in plot.telemetry() and plot.UD() for plotting raster and shapefile base layers
• new option method="Encounter" in overlap()
• mean.UD() now propagates uncertainties
• mean.UD() now functions on occurrence distributions
• new convex argument to UD summary(), plot(), and export functions
• plot() and raster() now work on 3D UDs
• plot.outlie() now works on lists of outlie objects
• speed() output now includes DOF estimate for use with meta()
• tbind() now works correctly with different projections and calibrations
• %#% unit conversion operator can now interpret products and ratios
• summary() timescale confidence intervals are now gamma/inverse-gamma more inline with meta()
• progress bar added to optimizer() when trace=1
• bugfix in IID area CIs
• bugfix in ctmm.loglike() when fitting multiple error classes, where some are zero
• bugfix in ctmm.boot() when bias estimate exceeds variance parameter
• bugfixes in 3D akde()
• bugfix in time gridding code when dt is coarse
• bugfix in SpatialPoints.telemetry for single individuals

ctmm 0.6.1 (2021-07-28)

• ctmm.fit() can now fit multiple UERE parameters and update uncertain calibration parameter estimates
• new function cluster()
• new function video()
• new function as.sf()
• new function tbind()
• new argument VMM in simulate(), predict()
• new argument timeformat="auto" in as.telemetry()
• new argument verbose in meta()
• uere()<- can now assign posterior/updated error estimates from ctmm model objects
• bugfix in ctmm.loglike() for circle!=0 and REML
• bugfixes in optimzer()
• bugfix in ctmm.fit() for 1D processes
• bugfix in variogram.fit() for 1D processes
• bugfixes in simulate(), predict for 1D processes
• bugfix in ctmm.fit() with zero variance models
• bugfix in meta() colors when sort=TRUE
• bugfixes in ctmm.guess(), ctmm.fit(), speed() for tiny amounts of data
• bugfixes in occurrence(), Kalman smoother for IOU process
• ctmm.select() now stores IC and MSPE information for summary()
• extent objects now include missing columns
• extent object longitudes can now cross the international date line

ctmm 0.6.0 (2021-01-10)

• new function meta() for meta-analysis of home-range areas
• new function encounter() for the conditional distribution of encounters (CDE)
• new function distance() to calculate square Bhattacharyya, Mahalanobis, and Euclidean distances
• new function compass() to plot a north-pointing compass
• new argument 't' in speed()
• new argument 'axes' in outlie()
• as.telemetry() now accepts most tibble objects
• akde() on multiple individuals is now more memory efficient
• bugfix in ctmm.fit() for IOU model
• bugfix in occurrence() with repeated timestamps
• bugfix in summary.ctmm() rowname droped for single parameter CIs
• bugfix in outlie() with list input
• bugfixes in plot.outlie with zero error
• bugfix in variogram() with res>1 and CI="Gauss"
• bugfix in ctmm.select() if stepping OU->OUf->OUF
• bugfix in as.telemetry() for Move objects with empty idData slot
• bugfix in as.telemetry(), median() when importing single location estimate
• bugfix in plot.telemery() with add=TRUE and non-SI units
• bugfix in speed() for ctmm objects (no data), where CIs were incorrect
• bugfix in median() with >=50% repeating observations
• bugfix in summary() for periodic models with tau[velocity]==0
• bugfix in occurrence() for PDclamp() error
• bugfix in ctmm.select() giving incorrect model names when run indirectly
• bugfix in occurrence() with IID autocorrelation model
• workaround in export functions where sp objects change timezones
• workaround in as.telemetry() when Move idData() names are dropped
• workaround in plot.UD() when image() has alpha overflow
• improvements to akde(), occurrence() grid argument when incomplete
• improvements to overlap() Wishart approximation in bias correction
• improvements to cleave()

ctmm 0.5.10 (2020-05-07)

• as.telemetry() location class code improved
• as.telemetry() message for marked outliers
• jaguar data in sync with ctmmweb

ctmm 0.5.9 (2020-03-23)

• new argument CI="Gauss" in variogram()
• new argument weights in mean.UD()
• new argument datum in as.telemetry() -- input and ouput datums can now differ
• new data 'jaguar'
• bugfix in ctmm.select() for infinte loop
• improvements in ctmm.select, ctmm.loglike for collapsing variance/error estimates
• rewrite of optimizer's line search to be more exact & reliable
• improvements in optimizer for degenerate likelihood surfaces
• improvements in optimization for bad covariance estimates---fit object structure changed
• bugfix in uere.fit with multiple location classes in different orders
• bugfix in speed when fast=FALSE and sampled models lose features
• bugfix in IID pREML CIs
• bugfix in ctmm.guess with large errors causing eigen() to fail
• bugfix in optimizer expansion search step size not increasing
• bugfix in as.telemetry() -- MoveStack objects are given a common projection if not projected

ctmm 0.5.8 (2019-12-11)

• improvements to ctmm.select() stepwise selection, especially with error and/or circulation
• improvements to ctmm.fit() for nearly linear home ranges
• improvements to %#% operator -- units of speed supported
• bugfix in ctmm.loglike() for BM/IOU models with error
• new argument units in plot.outlie()
• new options(time.units='mean') and options(time.units='calendar') for %#% operator and display units
• ctmm.select() no longer warns when model features are not supported (ctmm.fit does)
• compatibility fix for R version 4

ctmm 0.5.7 (2019-10-07)

• new function optimizer()
• new function SpatialPolygonsDataFrame.telemetry() for location estimate error circles/ellipses
• 'pNewton' now the default optimization method
• 'pHREML' now the default estimator & all CI names updated
• grid argument now supported in akde and occurrence methods
• outlie() output now includes CIs with plot method
• error-adjusted variogram implemented when fast=FALSE
• LOOCV now supported in ctmm.select(), summary()
• new buffer argument in occurrence()
• head(), tail() methods for telemetry objects
• str() method for ctmm objects
• new data object 'pelican'
• SpatialPointsDataFrame now includes timestamp
• uere(data) <- numeric now overrides all location classes
• improved support for ARGOS-GPS hybrid data
• missing DOP values now correctly treated as separate location class
• bugfix in conditional simulations with dt argument
• bugfix in plot.UD gridlines
• bugfix in as.telemetry timeout argument when datasets lack timed-out values
• stability fixes in ctmm.fit() for BM/IOU models
• further stability enhancements in ctmm.loglike() and optimizer
• bugfix in simultaneously fit RMS UERE CIs
• AICc formulas fixed for tiny n
• reduced Z^2 now exactly normalized in UERE objects
• minor enhancements to cleave() function
• as.telemetry() no longer automatically calibrates e-obs errors (inconsistent with newer devices)
• as.telemetry() no longer complains on reverse-time-ordered files

ctmm 0.5.6 (2019-05-15)

• new functions lasso, marquee, and cleave
• new functions annotate and color
• summary can now compare joint UERE objects to lists of individualized UERE objects
• support for UTM locations in as.telemetry
• support for GPS-ARGOS hybrid data in as.telemetry & uere.fit
• new plot option ext for extent objects
• increased numerical precision in ctmm.loglike for 0 < dt << tau, including the limit OU/OUF -> BM/OU
• BM/IOU model likelihoods are now exact limits of OU/OUF likelihoods modulo a constant
• covariance matrices can now take arbitrary eccentricty and scale
• ctmm.boot new argument iterate=FALSE and bugfixes for iterate=TRUE
• ctmm.boot now debiases the covariance matrix directly (linearly)
• occurrence default dt.max & cor.min arguments now tighter
• periodogram functionality restored for one-dimensional data
• bugfix in IID ctmm.fit with elliptical errors
• bugfix in occurrence when projection origin is far from the mean location
• bugfix in akde.list where location errors were not smoothed
• bugfix in ctmm.guess/variogram.fit for BM/IOU models
• bugfix in speed for IOU models
• e-obs calibration cross checked and fixed
• ctmm.loglike now returns -Inf when movement and error variance are zero
• stability improvements to base R optimizer usage
• bugfix in mark.rm argument of as.telemetry
• cores option added to ctmm.select
• only physical cores now counted by cores arguments
• cores option now used in Windows when appropriate
• improvements to speed, speeds, ctmm.select for short tracks of data

ctmm 0.5.5 (2019-02-11)

• bugfix in summary where timescale CIs were always (0,Inf)
• ctmm.select default now level=1
• summary on UERE lists now works with more than one axis
• R dependency increased to >=3.5 for parallel functions

ctmm 0.5.4 (2019-02-08)

• bugfix in ctmm.select where OU was not considered over the new OUO/OUf models introduced in v0.5.3
• bugfix in ctmm.boot for heteroskedastic errors
• multiplicative option depreciated from ctmm.boot

ctmm 0.5.3 (2019-01-31)

• oscillatory (and critically damped) OUO/OUf models now supported, starting with omega option of ctmm()
• summary() now works on lists of UERE objects for error model selection
• MSPE slots & arguments restructured and fully utilized in both summary and ctmm.select
• new method speeds() for estimating instantaneous speeds
• speed() more efficient on very coarse data, slightly improved CIs
• new complete argument in simulate() and predict() to calculate timestamps and geographic coordinates
• now avoiding fastPOSIXct timezone and epoch issues in as.telemetry
• outlie() now works on lists of telemetry objects
• bugfixes in overlap() CIs
• overlap() now robust to bad model fits
• new as.telemetry() argument mark.rm to delete marked outliers
• bugfix in predict() & occurrence() where eccentricity was dropped from covariances
• projection information in Move & MoveStack objects now preserved if possible
• identities preserved with newer MoveStack objects
• ctmm.boot() better handles parameter estimation near boundaries
• e-obs data with missing error/speed/altitude now importing correctly in as.telemetry
• correlogram plots now cap estimates to appropriate range
• beta optimizer now more aggressive in searching along boundaries
• bugfix in ctmm.fit with duplicate timestamps and IID processes without error
• bugfix in ctmm.select with pREML & error
• summary() on telemetry lists no longer fails on length-1 timeseries
• years updated to tropical years and calendar days updated to stellar days

ctmm 0.5.2 (2018-09-10)

• location classes (multiple UEREs) now supported by uere.fit() and uere()<-
• uere() forked into separate uere() and uere.fit() methods
• AICc slot included in UERE objects for error model selection
• overlap() telemetry and CTMM arguments depreciated
• fixed bug in as.telemetry() when importing ARGOS error ellipses
• e-obs error calibration updated
• numerical stability increased in ctmm.fit when distance scales are extreme

ctmm 0.5.1 (2018-08-07)

• Units of measurement down to microns and microseconds now supported
• ctmm.select() now builds up autocovariance features stepwise to help with fit convergence
• residuals() can now be calculated from (calibrated) calibration data---diagnostic argument removed from uere()
• summary.ctmm() now returns DOF[speed] information on individuals
• MSPE of ctmm objects was previously w.r.t. in-sample times and is now time averaged
• summary.list.ctmm() now returns MSPE when useful
• new speed() argument robust for coarse data
• options multiplicative & robust added to ctmm.boot to help with parameters near boundaries
• E-OBS errors adjusted by empirical results of Scott LaPoint's calibration data
• Telonics Gen4 errors estimates imported with results of Patricia Medici's calibration data --- Quick Fixes not yet fully supported
• fixed critical bug in speed()
• fixed bug in as.telemetry with projection argument
• fixed bugs in ctmm.loglike when !isotropic && error && circle
• fixed bug in emulate when fast=FALSE and error=TRUE
• fixed bug in new variogram error calculations (v0.5.0) used for plotting
• simultaneously fitted UERE's from ctmm slot "error" can now be assigned to data for plotting

ctmm 0.5.0 (2018-05-16)

• Extensive re-write of the Kalman filter & smoother, now supporting an arbitrary number of spatial dimensions, necessary for ARGOS error ellipse support. (Previously, all multi-dimensional problems were transformed into multiple one-dimensional problems.) Many new models will be supported going forward, based on the v0.5.0 code.
• telemetry error vignette "error"
• ARGOS error ellipse support in ctmm.fit() and simulate()
• plotted variogram errors now estimated from HDOP and no longer assumed to be homoskedastic
• as.telemetry() default projections now use robust ellipsoidal statistics
• new median.telemetry() method for help with projecting data
• (anisotropic & circulation & error) models now exact with 2D Kalman filter & smoother
• simulate() & predict() velocities now correct with mean="periodic"
• units argument in speed()
• REML and related methods fixed from 0.4.X 1/2 bug
• ctmm.loglike COV[mu] bugfix for circular error & elliptical movement
• summary() rotation % bugfix with circle=TRUE
• parameter boundary bugfix in ctmm.fit() and ctmm.loglike()
• fixed bandwidth() bug when weights=TRUE on IID process
• variogram.fit() manipulate more appropriate with calibrated errors
• fixed bug in plot.variogram for isotropic model fits
• fixed bug in ctmm.fit with fitted errors and any(diff(t)==0)
• fixed bug in plot.variogram() from stats::qchisq() with k<<1

ctmm 0.4.2

• new speed() method
• new ctmm.boot() method
• new outlie() method
• new export functionality for telemetry class
• overlap debias=TRUE option (approximate)
• pHREML, pREML, HREML ctmm.fit methods implemented and documented
• IID pREML & REML AICc values implemented
• MSPE values implemented
• new uere()<- assignment method
• velocity esimtates now included in predict() [fitting one model to multiple behaviors can result in wildly optimistic confidence intervals]
• velocities now included in simulate()
• simulate precompute option
• as.telemetry drop=TRUE option
• as.telemetry will no longer drop individuals with missing data columns
• as.telemetry will try to approximate DOP values
• as.telemetry imports velocity vectors
• as.telemetry default projection orientation now robust with GmedianCOV
• plot.UD resolution grid less obnoxious, NA/FALSE contour label option
• plot.telemetry error=0:3 options for data with recorded error circles/ellipses
• plot.telemetry velocity=TRUE option for data with recorded velocities
• plot.variogram bugfixes with telemetry errors
• fixed AIC bug in new parameterization code (0.4.0-0.4.1) where isotropic=TRUE model would never be selected
• fixed rare endless loop in akde/bandwidth with weights=TRUE
• outlier removed from buffalo$Cilla

ctmm 0.4.1 (2017-08-30)

• projection method for ctmm objects

ctmm 0.4.0 (2017-08-29)

• 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

ctmm 0.3.6 (2017-04-24)

• 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

ctmm 0.3.5 (2017-02-03)

• 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

ctmm 0.3.4 (2016-11-30)

• 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

ctmm 0.3.3 (2016-09-06)

• 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

ctmm 0.3.2 (2016-05-14)

• 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"

ctmm 0.3.1 (2016-02-24)

• 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

ctmm 0.3.0 (2015-11-28)

• 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

ctmm 0.2.9 (2015-10-14)

• 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

ctmm 0.2.8 (2015-08-26)

• 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

ctmm 0.2.7 (2015-07-31)

• 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

ctmm 0.2.6

• export bugfixes

ctmm 0.2.5

• IOU bug fixes in ctmm.fit and plot.variogram

ctmm 0.2.4

• 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

ctmm 0.2.3

• 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

ctmm 0.2.2

• new functions periodogram, plot.periodogram

ctmm 0.2.1

• 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

ctmm 0.2.0

• 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.