PRIORITY
* reference Guillaume's paper at the beginning of the periodogram vignette
* use perturb.ctmm in ctmm.guess / variogram.fit ?
* reduce uere() warning in as.telemetry to once... remove other crap... too much
* properly fillout UERE & UERE.DOF on the fly
* uere() return doesn't check for missing UEREs (in as.telemetry too)
* is.calibrated()
* uere() factor estimation
* get.error, get/set params, fit, summary, etc..
* error vignette - check back on variogram
* quiet uere() example

ERROR PAPER
* how does error change variogram DOF calculation?
* errors on x,y,z variograms
* errors on periodograms?
* exact 4x4 matrix inverse relations in PDsolve()
* UERE error propagation from calibration (do not use as prior!)
* email ARGOS about McClintock formula
* kGcluster with tpeqd projection suggestion
* predict can return VAR.xy for isotropic with UERE<4

PROJECTION
* projection() <- on all plottable objects + plot option
* project()<- ignores simulated/predicted velocities & covariances without headings & magnitudes
* error as.telemetry if user attempts lon-lat projection
* check latlon projection stop code against KT's input
* document projection projection<- dispatch methods

PARALLELIZATION
* parallelize akde.list & document overlap
* overlap() man example akde() first
* simulate nsim>1 with plapply
* parallel derivatives with upper/lower/etc.

MISC WORK
* p-value test for trend terms using variance of mu_alt-mu_null
* significant digits argument to summary()
* functionalize detrend & retrend in simulate/predict
* predict.ctmm cov
* spline velocity mean function
* variogram discrepancy rank function
* color array -> spatial segregation
* plot axes=c('x','y') by default or axes=c('t','z')
* catch optimizer failure (last best) in global variable and finish optimize() with warning
* specify grid partially/totally in akde/occurrence
* pre-standardize length data in ctmm.fit & ctmm.loglike (if not already) - ctmm.prepare?
* times can be pre-standardized according to tau_velocity as well?
* opacity option for plot
* predict isotropic VAR.xy output
* SpatialPolygonsDataFrame.ctmm
* writeShapefile.ctmm
* define print.ctmm and see if that works
* simulate prior=FALSE
* remove mean from kalman smoother - detrend, then add back
* change all sapply to vapply
* make sure terms of kalman filter are sorted by |magnitude|
* resort all arrays to put time in last index
* FAQ entry on automated time format reading in as.telemetry breaking with R update
* non-range resident in vignette
* default labels not working for UD contours
* occurrence error option
* boundry warning in help(ctmm.fit)
* standardize x,y prior to likelihood calculation
* plot3D of 2D UD
* ltraj export
* export ellipse drawing function
* effective DOF for diffusion rate?

PERIODIC 0.4.X
* DOF[mean] should just be the stationary mean
* AIC/MSPE hybrid model selection
* mean derivative not included in simulate/predict/etc?
* T-test on high frequency amplitudes
* variogram on mean detrended data with CTMM argument
* simulate.telemetry (not pure ctmm)
* smoother (non-uniform u(t) and velocity vector)
* akde... slow exact and fast approximation or block toeplitz matrix (stationary Laplace approximation?)
* plot ctmm (fall back on kde code)
* vignette: periodogram, ctmm.select

VIGNETTES & EXAMPLES
* explain effective sample sizes (DOF of summary)

OPTIMIZER
* split-parameter optimization (for periodic parameters like angle) with funnelling error target
* convex perimeter tracker
* Somehow optimizer can stop on stage 1 without proceeding to stage 2
* Stop on encapsulated
* local tangent transformation on periodic variables
* STAGE 4 - pattern search
* try to fit Gamba with error
* mc.optimize cross curvature if queue allows space
* mc.optimize fill up queue with higher-order derivatives if further space allows
* mc.genD cross correlations are wrong

Aligned Krige UDs
pregridder composite dimension?

LOW HANGING FRUIT & Nagging issues
* add acf of calibration residuals to uere diagnostic
* sort.ctmm by IC argument
* simulate conditionally with t=t returns data and t times. predict does not. (lots of low-level changes here)
* move object coordinate x1,x2 lat-lon
* Bayesian=FALSE argument for simulate() leveraging emulate()
* project(telemetry) <- function
* check IID AICc formula for isotropic case
* change default gap skip in occurrence?
* rbind on telemetry objects
* grid fix regression - weight to coarse scale when appropriate
* detrend mean in correlogram function
* plot errors with HDOP & error model in CTMM
* rainbow.telemetry
* plot telemetry/UD with reverse axes (preserve x&y orientation)s
* give writeShapefile a default folder name, maybe also separate layers into different files
* compass plot
* unit Environment on plots for points()
* individualized projections
* 1-point azimuthal equidistant projection quick option
* overload covm * / to apply to area & matrix
* str.ctmm, str.telemetry (show, print too?)
* points methods units environment
* have summary return a warning on occurrence distributions
* variogram.list <- mean-lapply-variogram
* occurrence.list
  + need to choose/enforce the same time steps?
  + weight by period of data?
* mean.UD on occurrence objects; +1 DOF
* simulate.UD
* Bayesian simulate.ctmm models (not data)
* krige velocities, activity plot
* put overlap in vignette after publication
* predict plot with transparency proportional to uncertainty (Google Earth?)
* mean.ctmm: list -> iid

generalize Gaussian area?
  UDs for both mean and population
  homerange(method=normal)
time/tube plot
periodic plot.ctmm

level.UD of summary UD/ctmm return Inf
  test p-value against sample size

summary on z-axis ctmm.fit might be buggy

sort.ctmm
sort.list
name.ctmm
name.generic

zoom.telemetry x,y offset clicker

global variable for units of current plot?

proj4: email about making north up
plot N vector in corner

dogleg splines
  degree = 1,2?
  migration = times?
  settlement = times?

model option vignette
IID, OU, OUF, (an)isotropic table in vignette

fixed circulation option?
Fixed period parameters during fitting?

3d periodogram, ctmm.fit, krige, kde

simulate nsim in both unconditioned and conditionedb by storing all objects
multiple conditional simulations loop
More efficient sampler/smoother:
store propagator results for all time-lags
store forecast/concurrent estimates
call vectorized RNG

Include telemetry errors in unconditional simulation?
krige -> predict

cross variogram

Newton-Raphson iteration at end of ctmm.fit for solution check on optim

AKDE vignette: DOF.H, DOF.mu

plot options: cex, type, abrv

AKDE with errors, weights
akde with user-specified grid (and projection)

residual acf versus data acf with correct confidence intervals for no autocorrelation null hypothesis

multi-scale variogram bias correction
variogram & periodogram: coarsening window method to avoid all bias

population fitting without correlation
population fit of list
population akde of lists

optional columns with NAs are being discarded
or maybe report if NAs are discarded?

Lapack GE solve -> Lapack PO/SY solve.

as.telemetry option: minimal columns, maximum columns, specified columns to keep

profile CIs

contour labels in plot ctmm

Email ks author about inaccuracy

Repeated times in variograms -- account for as error -- fix cap

dplyr, rolling for loops

fixed mean parameter for boundary issues

HIERARCHICAL___________
* stochastic gradient Langevin dynamics
* proximal methods of optimization
