NEWS.md

In ianjonsen/foieGras: Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement

aniMotum 1.2-06 (05/06/2024)

• various minor issues fixed including: build against TMB 1.9.11, fixes error when grad specified in sim_fit().

aniMotum 1.2 (03/11/2023)

• addition of sim_post(), a function for posterior simulations from SSM fits, conditional on data and movement parameters
• addition of plot method for sim_post objects
• sim_filter() can now use arbitrary variables, including user-appended environmental variables, for filtering tracks simulated with sim_fit()
• sim_fit() now simulates tracks from user-specified start and end locations that differ from the estimated track start and end.
• fit_ssm() now handles "generic location" data provided the locations have x and y standard errors. These data can be light-level geolocations, acoustic telemetry positions, or other location data. Input data should have lc = "GL" for all generic locations.
• a change to the min.dt argument in fit_ssm(), the default is now min.dt = 0 (no minimum time interval between observations, but any subsequent observations that occur at the same time are ignored when fitting an SSM).
• fixed an issue with high temporal resolution data, where prediction times exactly match observation times when observations occur 1 s apart. This caused an error when fitting SSM's.

aniMotum 1.1-06 (13/07/2023)

• fixes issue with route_path() where simulated tracks that are entirely on land resulted in an error

aniMotum 1.1-04 (01/03/2023)

• fixes issue with grab() where multiple data sets with lon modulo 0,360 resulted in an error
• fixes issue with route_path() where rerouting tracks that have no locations on land resulted in an error. In these cases, route_path() now returns a tibble identical to that supplied (fitted or predicted locations) and issues a message on the console.

aniMotum 1.1-02 (13/02/2023)

• update citations to include new aniMotum R package paper in Methods in Ecology and Evolution as the primary reference.

aniMotum 1.1-01 (01/02/2023)

• fixes issue with map() where function could become paused one some calls.

aniMotum 1.1 (10/12/2022)

• package name change to coincide with Methods in Ecology and Evolution manuscript: Jonsen et al. aniMotum, an R package for animal movement data: rapid quality control, behavioural estimation and simulation. Accepted 06/12/2022.

foieGras 1.1 (01/12/2022)

• adds format_data() to pre-process non-default data formats into that expected by fit_ssm
• adds greater flexibility for input data formats (via new arguments to fit_ssm), related to format_data
• fixes an issue with input data as an sf-tibble or sf-data.frame that caused an error when fitting SSM's via fit_ssm
• when installing package from source, C++ code is automatically compiled against the existing TMB package version. This should eliminate the warning message on installation and package load that some users may have experienced previously
• updated Overview vignette, describing input data structures in greater detail

foieGras 1.0-5 (15/05/2022)

• adds route_path() a wrapper function calling pathroutr to re-route fit_ssm estimated or simfit simulated tracks around land barriers
• adds a move persistence model via fit_ssm(model = "mp") to allow simultaneous estimation of locations and move persistence. This approach may be preferable to using fit_mpm() on a fit_ssm model object. fit_mpm() is retained for less error-prone (GPS) location data
• adds option for move persistence estimates to be normalised to 0,1 in grab(), either on tracks separately or as a group for a relative measure that spans 0 - 1.
• adds sim_filter() to calculate similarity between simulated and ssm-estimated tracks, and returns the most similar simulated tracks based on a user-specified quantile
• adds mapping function map() to replace fmap() for faster, more flexible estimated track maps & fixes to coastline and other mapping issues for tracks that cross -180,180
• adds rosm map tile layers to map() via ggspatial::annotation_map_tile for more detailed coastlines on large-scale maps
• adds faster crw model fitting via fit_ssm() by turning off travel rate standard error (s.se) estimation in ssm_control() as the default. SE estimation can be turned on via control = ssm_control(se = TRUE).
• adds a summary function for displaying information about SSM fits.
• replaces hcl.colors("Zissou1") palette for most plots - Zissou1 was fun but not colour blind-friendly; in most cases "Cividis" is now the default but users can specify any hcl.pals() palette, using the pal argument in many of the plot functions.
• fit object s3 classes fG_ssm, fG_mpm migrated to ssm_df, mpm_df
• generic plot method s3 classes migrated to plot.ssm_df, plot.mpm_df, plot.osar, plot.sim, plot.simfit
• adds new vignettes for more comprehensive documentation of package features

foieGras 0.7-6 (26/04/2021)

• adds fixes to example data for testing/examples so pkg builds on solaris and various linux boxes with older GDAL/PROJ libraries

foieGras 0.7-5 (23/04/2021)

• adds sim() to simulate animal tracks using the rw, crw or mpm process models. The rw and crw models can also be specified with state-switching between multiple behavioural states. Tracks can be simulated with or without Argos (LS or KF) errors, as time-regular or time-irregular
• adds simfit() to simulate animal tracks from fit_ssm fit objects
• adds generic plot() methods for sim and simfit objects
• adds fit_mpm can take a fit_ssm object directly as input, removing need for user to manipulate data prior to calling fit_mpm
• adds fit_mpm can fit to SSM-predicted (time regular) or SSM-fitted (time irregular) locations, via what argument
• adds fit_mpm can fit to lon,lat or x,y coordinates, via coords argument
• adds ssm_control() for centralized control over optimizer and optimization method choices, optimizer parameters, and foieGras model parameter bounds
• adds faster and more stable optimization
• adds time-series and acf() plots as option when visualising prediction residuals calculated from osar()
• removes hist plots as option when visualising prediction residuals calculated from osar()
• removes (with deprecation errors) verbose, optim, optMeth, and lpsi arguments to fit_ssm
• replaces wesanderson::wes_palette("Zissou1") with hcl.colors("Zissou1") and provides arguments to change this default palette

foieGras 0.6-9

• adds wesanderson::wes_palette("Zissou1") as default palette for plots/maps
• generic plot method for fG_ssm objects can now plot individuals all on 1 page (pages = 1) or on separate pages (pages = 0)
• 2-d (track) plots now include confidence ellipses on estimated locations
• generic plot method for fG_mpm objects now available
• mapping function (fmap) can optionally take an fG_mpm object to colour locations by behavioural index (gamma_t)

foieGras 0.6-7

• adds ability to fit move persistence models to temporally regular OR irregular location data
• adds ability to turn off predicted locations by setting time.step=NA causing locations to be estimated only at observation times
• adds ability to fit to Argos - GPS or Argos - GLS locations simultaneously when combined in a single input data.frame
• adds ability to specify an alternate emf (Error Multiplication Factor) data.frame for Least-Squares and/or GPS locations
• adds human-readable/understandable errors and warnings with (occasional) advice
• turns off estimation of psi parameter (ellipse semi-minor axis re-scaling factor) when rw process model is fit to Argos KF/KS data
• removes reliance on dplyr::do, which is superseded as of dplyr 1.0.0
• replaces dplyr progressbar with parameter trace when fitting SSM to single or multiple data sets in default verbose mode 1
• replaces argosfilter::sdafilter in favour of trip::sda (which is a faster, vectorized version of the former) to prefilter outlier locations

foieGras 0.4.0

• adds move persistence models for behavioural inference along animal tracks, via fit_mpm()
• adds ability to fit SSM's to processed light-level geolocation or GPS data by adding lonerr, laterr variables to input data
• adds One-Step-Ahead prediction residuals for evaluating SSM fits, via osar() and generic plot() method for osar output
• adds diagnostic plot functions that handle multi-individual fits, via generic plot() method for fG_ssm fit objects
• adds sf-enabled mapping function, via fmap()
• fixes CRAN check errors from last version, where proj4string syntax +init:epsg= was not supported in non-PROJ4 emulation mode on some linux platforms

foieGras 0.2.2

• patch for compatibility with latest sf version

foieGras 0.2.1

• patch to improve C++ portability

foieGras 0.2.0

• first release, updates will follow regularly and be documented here

ianjonsen/foieGras documentation built on Jan. 17, 2025, 11:15 p.m.