Metropolis Sampler and Supporting Functions for Estimating Animal Movement from Archival Tags and Satellite Fixes

Data handling and estimation functions for animal movement estimation from archival or satellite tags. Helper functions are included for making image summaries binned by time interval from Markov Chain Monte Carlo simulations.


tripEstimation

tripEstimation maintenance

NOTE: this package is now deprecated by SGAT, https://github.com/SWotherspoon/SGAT

News

Changes to version 0.0-42

o update CITATION process for CRAN

Changes to version 0.0-41

o maintenance build

o CITATION file added

Changes to version 0.0-40

o version number increment for r-forge build

Changes to version 0.0-39

o removed get.sst, sst.interp and supporting functions to meet CRAN licensing needs, now no need for akima or locfit

Changes to version 0.0-38

o added check for very short trips that break the windowing in position.logp

o renamed CHANGES to NEWS

Changes to version 0.0-37

o reverted to Suggests for locfit, since that package has no namespace

Changes to version 0.0-36

o added a package NAMESPACE

o reversed order of CHANGES file entries

o fixed mis-order in warning message use of CRS/CRSargs in
satellite.model and solar.model

Changes to version 0.0-35

o Sanity test for NAs and class in the data for mkLookup. 

Changes to version 0.0-34

o Added functions get.sst, sst.interp and sst.interp1. 

Changes to version 0.0-33

o added functions mkMaskObject and "set.mask<-"

o added winoffset argument to position.logp

o Modified the algorithm used by position.logp

Changes to version 0.0-30

o added time vector to output of solar.model to make keeping track of the values simpler

o Fixed bug in position.logp with incorrect check for is.null(start) 

Changes to version 0.0-30

o Fixed stray boilerplate "pkg" references in .Rd files. 

Changes to version 0.0-29

o New build version to get around problems submitting to CRAN. 

Changes to version 0.0-28

Thanks to Nick.Ellis@csiro.au for the report.  2009-05-29
    ported from Montenbruck and Pfleger (1994).  
    between the values from elevation() and the astro() functions
    o Fixed an embarassing error in POLAR that caused a disparity
    
    o Added transformation capacity to satellite.model
    
    o Added proj.string to satellite.model
    
    warning message about logical to double type conversion.
    o Fixed broken checks in solar.model that resulted in worrying
    
    match solar.model
    satellite.model with behav.dist, behav.mean and behav.sd to
    o Replaced speed.dist, speed.mean and speed.sd arguments in
    
    replaced by pmax.int, pmin.int
    o Removed fast.pmax and fast.pmin from solar/satellite.model,
    
probability control (new prob arg)
o Updated position.logp to more sensibly allow quantile

Changes to version 0.0-27

o Fixed a bad mistake from the last build in solar.model

Changes to version 0.0-26

David Pinaud)
o Fixed missing transform function from solar.model (thanks to

Changes to version 0.0-25

solar

elevation

julday
julcent

---------
SOLAR

solar.model
satellite.model

norm.proposal
mvnorm.proposal
bmvnorm.proposal

metropolis0
metropolis

        ## k.prior DELETED
------------------
GEO.METROPOLIS

        ##reynolds DELETED
        ##podaac   DELETED
mkLookup 

mkTempMask
mkSmall
mkDepthMask
get.mask

        ## fetch.topo DELETED

bits<-
bits
--------
MASKS


picksegs
pick

mkCalibration

show.segment
light.quantile
position.logp
initialize.x


----------------
MISCELLANEOUS

old.mkLookup
old.metropolis
old.find.init
old.dist.gc
mkNLPosterior
mkElevationSeg
------------------
OLD GEO.METROPOLIS

POLAR
MJD
mini.sun
lunar
LMST
FRAC
EQUHOR
astro
-----------
MINI ASTRO


    
R files
shows the grouping of functions in doc, sometimes also in the
o restructured package with documentation, the following list

Changes to version 0.0-17

distance functions appropriately - km units are assumed
o solar.model also accepts a proj4 string, and creates
    
behav.sigma
model - the arguments have become behav, behav.mean and
o solar.model now has support for "distance" as well as speed
  
  elevation "ekstrom" arguments
  outside a given range, this is specified either by light or
o solar.model can now put a larger variance on light levels

o show.segment now has "..." to pass in graphics options

class for imaging the array
o position.logp has some changes in that I've added an S3

o metropolis now reports on progress

needs some fixing in terms of naming etc.)
intersections of large logp values (not the best function yet,
o init.x.diag - added function to initialize off running

o mkCalibration now allows a single segment

o Removed model.utils and put it all in solar.model

Changes to version 0.0.10

o I'm testing automatic Subversion updating to R repository

Changes to version 0.0.9

o fetch.topo now uses rgdal to read an ESRI FLT surface

default is they are not passed in, but initialize occurs after
o Changed operation of start.x and start.z in solar.model -

Changes to version 0.0-8

o Added function findSegments

Changes to version 0.0-7

logp.behavioural
o fixed some bugs (not very well) in mkLookup and

Changes to version 0.0-6

of the time
o changed defaults in model.utils to avoid require(rgdal) most

Changes to version 0.0-5

o incorporated new functions for diagnostics

Changes to version 0.0-4

Changes to version 0.0-34

o Sanity test for NAs and class in the data for mkLookup. 

Changes to version 0.0-33

o Added functions get.sst, sst.interp and sst.interp1. 

Changes to version 0.0-30

o Modified the algorithm used by position.logp

o added winoffset argument to position.logp

o added functions mkMaskObject and "set.mask<-"

Changes to version 0.0-30

o Fixed bug in position.logp with incorrect check for is.null(start) 

o added time vector to output of solar.model to make keeping
track of the values simpler

Changes to version 0.0-29

o Fixed stray boilerplate "pkg" references in .Rd files. 

Changes to version 0.0-28

o New build version to get around problems submitting to CRAN. 

Changes to version 0.0-27

o Updated position.logp to more sensibly allow quantile
probability control (new prob arg)
    
    o Removed fast.pmax and fast.pmin from solar/satellite.model,
    replaced by pmax.int, pmin.int
    
    o Replaced speed.dist, speed.mean and speed.sd arguments in
    satellite.model with behav.dist, behav.mean and behav.sd to
    match solar.model
    
    o Fixed broken checks in solar.model that resulted in worrying
    warning message about logical to double type conversion.
    
    o Added proj.string to satellite.model
    
    o Added transformation capacity to satellite.model
    
    o Fixed an embarassing error in POLAR that caused a disparity
    between the values from elevation() and the astro() functions
    ported from Montenbruck and Pfleger (1994).  
Thanks to Nick.Ellis@csiro.au for the report.  2009-05-29

Changes to version 0.0-26

o Fixed a bad mistake from the last build in solar.model

Changes to version 0.0-25

o Fixed missing transform function from solar.model (thanks to
David Pinaud)

Changes to version 0.0-17

o restructured package with documentation, the following list
shows the grouping of functions in doc, sometimes also in the
R files
    


MINI ASTRO
-----------
astro
EQUHOR
FRAC
LMST
lunar
mini.sun
MJD
POLAR

OLD GEO.METROPOLIS
------------------
mkElevationSeg
mkNLPosterior
old.dist.gc
old.find.init
old.metropolis
old.mkLookup

MISCELLANEOUS
----------------


initialize.x
position.logp
light.quantile
show.segment

mkCalibration

pick
picksegs


MASKS
--------
bits
bits<-

        ## fetch.topo DELETED

get.mask
mkDepthMask
mkSmall
mkTempMask

mkLookup 
        ##podaac   DELETED
        ##reynolds DELETED

GEO.METROPOLIS
------------------
        ## k.prior DELETED

metropolis
metropolis0

bmvnorm.proposal
mvnorm.proposal
norm.proposal

satellite.model
solar.model

SOLAR
---------

julcent
julday

elevation

solar

Changes to version 0.0.10 o Removed model.utils and put it all in solar.model

o mkCalibration now allows a single segment

o init.x.diag - added function to initialize off running
intersections of large logp values (not the best function yet,
needs some fixing in terms of naming etc.)

o metropolis now reports on progress

o position.logp has some changes in that I've added an S3
class for imaging the array

o show.segment now has "..." to pass in graphics options

o solar.model can now put a larger variance on light levels
  outside a given range, this is specified either by light or
  elevation "ekstrom" arguments
  
o solar.model now has support for "distance" as well as speed
model - the arguments have become behav, behav.mean and
behav.sigma
    
o solar.model also accepts a proj4 string, and creates
distance functions appropriately - km units are assumed

Changes to version 0.0.9 o I'm testing automatic Subversion updating to R repository

Changes to version 0.0-8

o Changed operation of start.x and start.z in solar.model -
default is they are not passed in, but initialize occurs after

o fetch.topo now uses rgdal to read an ESRI FLT surface

Changes to version 0.0-7

o Added function findSegments

Changes to version 0.0-6

o fixed some bugs (not very well) in mkLookup and
logp.behavioural

Changes to version 0.0-5

o changed defaults in model.utils to avoid require(rgdal) most
of the time

Changes to version 0.0-4

o incorporated new functions for diagnostics

Changes to version 0.0-3

o Fixed a bug in reynolds, it needs some stray integers stripped out
(old Fortran something) - comments in the code show how to
replicate the test output from the site.  o Added capability
for gzipped files to reynolds, as well as "data" option to
return sst, ice, err, land or water.

o Added k0 attenuation offset to find.init - seems to perform
better.

o Fixed a bug! in mkTempMask - it was using only the
initialized Reynolds dataset.

Changes to Version 0.0-2 o Recreated package completely

Changes to version 0.0-1 o Created package with all latest code

Reference manual

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install.packages("tripEstimation")

0.0-44 by Michael D. Sumner, 8 months ago


https://github.com/mdsumner/tripEstimation


Browse source code at https://github.com/cran/tripEstimation


Authors: Michael D. Sumner [aut, cre], Simon Wotherspoon [ctb]


Documentation:   PDF Manual  


Task views: Analysis of Spatial Data, Handling and Analyzing Spatio-Temporal Data


GPL-3 license


Imports lattice, mgcv, rgdal, sp, zoo


See at CRAN