Package: crawl 2.3.1

crawl: Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data

Fit continuous-time correlated random walk models with time indexed covariates to animal telemetry data. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.

Authors:Devin S. Johnson [aut, cre], Josh London [aut], Brett T. McClintock [ctb], Kenady Wilson [ctb]

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crawl.pdf |crawl.html✨
crawl/json (API)

# Install 'crawl' in R:
install.packages('crawl', repos = c('https://dsjohnson.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/nmml/crawl/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • beardedSeals - Bearded Seal Location Data
  • harborSeal - Harbor seal location data set used in Johnson et al.
  • harborSeal_sf - Harbor seal location data updated since Johnson et al.
  • northernFurSeal - Northern fur seal pup relocation data set used in Johnson et al.

On CRAN:

6.44 score 18 stars 3 packages 63 scripts 699 downloads 6 mentions 22 exports 36 dependencies

Last updated 1 months agofrom:89ad099738. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-win-x86_64OKNov 02 2024
R-4.5-linux-x86_64OKNov 02 2024
R-4.4-win-x86_64OKNov 02 2024
R-4.4-mac-x86_64OKNov 02 2024
R-4.4-mac-aarch64OKNov 02 2024
R-4.3-win-x86_64OKNov 02 2024
R-4.3-mac-x86_64OKNov 02 2024
R-4.3-mac-aarch64OKNov 02 2024

Exports:%>%aic.crwargosDiag2Covas.flatcrw_as_sfcrw_as_tibblecrwMLEcrwN2llcrwPostIScrwPredictcrwPredictPlotcrwSampleParcrwSimulatordetect_timescaledisplayParexpandPredfillColsfix_pathflattenintToPOSIXmergeTrackStoptidy_crwFit

Dependencies:classclassIntclicpp11DBIdplyre1071fansigenericsglueKernSmoothlatticelifecyclelubridatemagrittrMASSmvtnormpillarpkgconfigproxypurrrR6RcppRcppArmadillorlangs2sfsptibbletidyselecttimechangeunitsutf8vctrswithrwk

Readme and manuals

Help Manual

Help pageTopics
Fit Continuous-Time Correlated Random Walk Models to Animal Movement Datacrawl-package crawl
Generic subset/bracket method for crwIS classes[.crwIS
Calculates AIC for all objects of class crwFit listed as argumentsaic.crw
Transform Argos diagnostic data to covariance matrix formargosDiag2Cov
'Flattening' a list-form crwPredict object into a data.frameas.flat
Bearded Seal Location DatabeardedSeals
Coerce to sf/sfc objectcrw_as_sf crw_as_sf.crwIS crw_as_sf.crwPredict crw_as_sf.list
Coerce crawl objects (crwIS and crwPredict) to tibblescrw_as_tibble crw_as_tibble.crwIS crw_as_tibble.crwPredict crw_as_tibble.tbl
Fit Continuous-Time Correlated Random Walk Models to Animal Telemetry DatacrwMLE crwMLE.default crwMLE.sf crwMLE.SpatialPoints
-2 * log-likelihood for CTCRW modelscrwN2ll
Simulate a value from the posterior distribution of a CTCRW modelcrwPostIS
Predict animal locations and velocities using a fitted CTCRW model and calculate measurement error fit statisticscrwPredict
Plot CRW predicted objectcrwPredictPlot
Create a weighted importance sample for posterior predictive track simulation.crwSamplePar
Construct a posterior simulation object for the CTCRW state vectorscrwSimulator
Detect appropriate time scale for movement analysisdetect_timescale
Display the order of parameters along with fixed values and starting valuesdisplayPar
Expand a time indexed data set with additional prediction timesexpandPred
Fill missing values in data set (or matrix) columns for which there is a single unique valuefillCols
fix_path function id depreciated.fix_path
'Flattening' a list-form crwPredict object into a data.frameflatten
Harbor seal location data set used in Johnson et al. (2008)harborSeal
Harbor seal location data updated since Johnson et al. (2008)harborSeal_sf
Reverse as.numeric command that is performed on a vector of type POSIXctintToPOSIX
Merge a location data set with a dry time (or other stopping) covariatemergeTrackStop
Northern fur seal pup relocation data set used in Johnson et al. (2008)northernFurSeal
tidy-like method for crwFit objecttidy_crwFit