version 2.2.6 (2023-11-28) New features and changed behaviour o static userdist option; linear mask o details may include stepmax argument passed to nlm o openCR.fit() acquires details argument 'agebreaks' o collate method for 'openCR' objects Other o makeNewData.openCR() rejects covariates with reserved names o agebreaks largely replaces agecov for defining age groups o openCR.design() acquires argument 'agebreaks', saves agelevels o age.matrix() acquires argument 'unborn' (code for age<0) o requires secr >= 4.6.1 o explicit error for integer overflow with many parameter levels version 2.2.5 (2022-09-25) New features and changed behaviour o ucare.cjs() restored Bugs fixed o modelAverage.openCR() did not pass arguments to modelAverage.openCRlist() version 2.2.4 (2022-07-02) New features and changed behaviour o ucare.cjs() temporarily removed (requires R2ucare) Other o vignette - new references and tweaked mention of ucare.cjs () version 2.2.3 (2022-07-01) New features and changed behaviour o none Bugs fixed o predict() failed with parameters b & h2 when number of sessions differed among strata o derived() not working with stratified model o bad names in openCRlist output by par.openCR.fit() o dummy variable coding failed with R>4.0 Other o fix accidental inclusion of GitHub README o depends secr >=4.5.0 o does not expect R2ucare to be on CRAN version 2.2.2 (2022-01-17) New features and changed behaviour o modelAverage() method for openCR models o openCR() new parameter 'settle' for weighted settlement o cumMove() allows settlement to be weighted by 0-1 mask covariate Bugs fixed o expected.d() failed with user-defined movement model Other o Git repository synched with GitHub o exampledata folder under inst with some previously fitted models (used in Examples e.g. ?make.kernel) version 2.2.1 (2021-11-09) New features and changed behaviour o none Bugs fixed o openCR.fit() did not correctly fit non-spatial learned response (b) models such as model = p~b, type = 'JSSAfCL' (bug undetected for some years). Other o tidied C++ code, edited vignette version 2.2.0 (2021-11-03) New features and changed behaviour o openCR.fit() new defaults: kernelradius = 30, sparsekernel = TRUE o plot.kernel() accepts meshcol argument o make.kernel() acquires argument 'session' for model input o expected.d() expected movement from movement parameters, fitted model etc. o summary.kernel() expected distances use expected.d() and may differ o matchscale() acquires argument 'expected' to match expected distance o 'BVN2' movement model (equal mixture two BVN) o bivariate Cauchy movement model 'BVC' (BVT with fixed move.b = 0.5) o log-sech movement model 'RDLS' (partial implementation) o extensions to plot.kernel Bugs fixed o openCR.fit() failed with non-binary detector usage o domain errors in inputs to Boost statistical distributions could crash R o make.table() could fail with models fitted before 2.1.0 Other o new aliases for movementmodel 'RDE', RDG','RDL','RDEzi','IND','INDzi' o RDL movementmodel no longer blocked (Boost call bypassed if scale infinite) o openCR.fit() more robust to extreme parameter values (spatial models) o more documentation of movement models o improved weighting of sparse kernels; details argument 'r0' for effective radius of zero cell version 2.1.0 (2021-08-14) New features and changed behaviour o new movement kernels based on polar distance o zero-inflated option for some movement kernels and 'uncorrelated' movement o cumMove() compounds movement kernel and applies edge effect o proportionInPolygon() sums probability within arbitrary polygon(s) o optional link 'log1' defined as log(x-1) (constrains x>1) o plot.kernel() uses par()$cex.main for title font o openCR.fit() optional dummy variable coding of factor predictors Bugs fixed o openCR.esa() failed and hence derived() failed for spatial models o openCR.make.newdata() failed if model from version <2.0.0 (details$minimumage not specified) o m.array() mis-tabulated counts when none caught on some occasions (no flow-on) o openCR.fit() version 2.0 halved variance for types 'Pradel' and 'Pradelg' Other o 'BVN','BVE','BVT' aliases for movementmodels 'normal','exponential','t2D' o openCR.fit() default move.b for BVT changed to 1.5 (from 0.6) o openCR.fit() details argument 'control' passes arguments to nlm() o openCR.fit() default iterlim for nlm() raised to 300 o makeNewData() S3 method replaces openCR.make.newdata() o C++ code uses Boost library for statistical distributions, avoiding R API o kernel code simplified (one C++ routine) and tested o long operations more responsive to interruption o plot.openCR() definition of 'turnover parameters' for intermediate.x extended to include move.a and move.b o number of threads explicit in calls to RcppParallel parallelFor o minor changes to make.kernel() and summary.kernel() o c and '[' methods for openCRlist class; separate documentation of openCRlist() o "anchored" movement (experimental) version 2.0.2 (2021-05-14) New features and changed behaviour o make.table() acquires argument 'collapse' for stratified models Bugs fixed o C++ sqrt() ambiguity on r-patched-solaris-x86 (use std::sqrt()) o clang-UBSAN overflow error in tests (read beyond array in C++ getmoveargs) o erroneous likelihood when dimensions differed among strata o openCR.make.newdata() omitted session covariates of stratified model o sumsims() failed with 'non-numeric argument to binary operator' Other o multithreaded Examples now in dontrun{} to avoid problematic TBB library version 2.0.1 (2021-05-09) New features and changed behaviour o none Other o run tests with Sys.setenv(RCPP_PARALLEL_BACKEND = "tinythread") to avoid CRAN errors o added URL to DESCRIPTION o onLoad() allows for possibility of single CPU (previous minimum 2) version 2.0.0 (2021-05-04) New features and changed behaviour o stratified models o generic method strata() for retrieving and assigning stratum names o stratify() function to arrange data for stratified model o openCR.fit() sparse movement kernels (new argument 'sparsekernel') o openCR.fit() kernelradius elevated to full argument from 'details' o make.kernel() saves empirical cumulative distribution function as attribute o make.kernel() accepts fitted model as input o pkernel() computes cumulative probability distribution of distance o qkernel() computes quantiles of distance distribution o dkernel() computes probability density of distance distribution o matchscale() kernel scale parameter giving required quantile of distance o plot.kernel() acquires argument 'title' o new movementmodel "annular" in openCR.fit(), make.kernel() etc. o HPX new detection function for binary detection Bugs fixed o age miscoded in openCR.make.newdata(), hence bad prediction for age models o summary.kernel() proportion truncated misreported for exponential movement o LLsurface.openCR() failed Other o vignette drops call for multiple cores o Age2 included in openCR.make.newdata() o plotKernel() removed (superceded by plot method for kernel objects) o 'openCR' object returned by openCR.fit includes kernel coordinates o optional logmultinomial term precalculated and not affected by covariates o fixed doi format in a citation o avoid ':::' (use local versions of unexported 'secr' functions) o Imports RcppParallel version >= 5.1.1 to dodge problems in earlier releases version 1.5.0 (2020-12-13) New features and changed behaviour o number of threads managed via RCPP_PARALLEL_NUM_THREADS as in secr o PLB... aliases for JSSA...CL type names o openCR.fit() new argument 'edgemethod' ("truncate", "wrap", "none") o par.openCR.fit() modified to allow each fit to multithread o openCR.fit() and openCR.design() new argument 'agecov' for grouping ages o openCR.fit() and openCR.design() new argument 'minimumage' o openCR.esa() now returns a list when bysession = TRUE o openCR.esa() unsqueezes result (allows for histories with freq>1) Bugs fixed o movementmodel "user" failed (typo in openCR.fit line 80) o secr LL component 3 miscalculated when some capthist repeated (biased D-hat) o movement models bias in D-hat due to edge effect o movement models failed when R = TRUE (dim(PIA) error) o derived.openCR() mistakenly report kappa for spatial models o some factor covariates mishandled by openCR.make.newdata() and hence by predict, derived Other o more robust user-defined kernel o calcpdotbd details argument of openCR.fit defunct o correct description of runsim.spatial() intervals argument o par.openCR.fit() ncores>1 is deprecated (slower than ncores=1!) o par.openCR.fit() logfile defaults to automatically generated tempfile o Suggests testthat, adds some unit tests version 1.4.4 (2020-09-01) New features and changed behaviour o none Other o suggests rmarkdown o tweak url in vignette version 1.4.2 (2020-09-01) New features and changed behaviour o reported rank takes account of possible negative eigenvalues (eigH) Other o some data.frame() calls specify stringsAsFactors = TRUE for backwards compatibility in R >= 4.0 o corrected return without () o terminal '/' on URLs in documentation as required o updated references version 1.4.1 (2019-06-29) New features and changed behaviour o sumsims() dropifnoSE condition now also rejects zero SE o print.summary.openCR() drops attributes eigH and fit Bugs fixed o multiple problems in naive CJSsecr model (CJSp1 FALSE, the default) o summary.openCR table of counts, format error with non-spatial model Other o details switch 'calcpdotbd' defaults to FALSE unless required for movement model; may affect estimates with JSSAsecr models o minor improvements to robustness when details$R = TRUE etc. version 1.4.0 (2019-06-15) New features and changed behaviour o new 2-parameter movement kernel t2D for 2-D t-distribution o new movement kernel uniform (no parameters, depends kernelradius) o new function make.kernel() and kernel methods plot and summary o plotKernel() deprecated o runsims.spatial() more robust with non-standard extractfn o see also 1.3.6 Bugs fixed o biased estimates from movement models Other o removed redundant C++ code for single-threaded execution o default details$autoini changed to NULL, meaning 'use all' o classMembership should now work with movement models version 1.3.6 (2019-04-13; not published) New features and changed behaviour o plot.openCR() invisibly returns the x coordinates of plotted points; dots argument also controls axes, line width and colour of CI o new plot method for output from derived.openCR o openCR.fit checks whether autoini required (incomplete or no start provided) o runsim.nonspatial() and runsim.spatial() return NULL for failed replicates rather than crashing Bugs fixed o derived method for openCR SECR models wrongly adjusted per capita recruitment when intervals varied, with consequences for derived D-hat o JSSAsecrXXX models gave erroneous estimates, particularly of lambda0 and sigma, for count data with binomN = 0 (Poisson counts) o predict.openCR failed when one parameter estimated (others fixed) version 1.3.5 (2019-03-10) New features and changed behaviour o none Bugs fixed o vignette rebuild failed on r-devel-linux-x86_64-debian-gcc (double \vec) version 1.3.4 (2019-02-05) Bugs fixed o bad keyword in classMembership.Rd Other o removed unnecessary pdf from inst/doc version 1.3.3 (2019-02-04) New features and changed behaviour o enabled detector-level covariates o summary method compatible with secr 3.2.0 (moves) Bugs fixed o openCR.make.newdata() and dependent methods (print, predict, summary etc.) failed with learned responses (~b etc.) version 1.3.2 (2018-12-09) New features and changed behaviour o none Other o conditional use of R2ucare in Examples, vignette version 1.3.1 (2018-12-08) New features and changed behaviour o sumsims accepts simulated fits with method = "none" Other o R2ucare now in Suggests not Imports, with tweak to ucare.cjs() version 1.3.0 (2018-11-26) New features and changed behaviour o canned predictors for learned responses (b, bk etc.) redefined and extended o AIC method acquires argument n to override the default effective sample size o openCR.fit() no longer computes 'posterior' component for mixture models o classMembership method for finite mixture models ('posterior' component removed) o specifying native R routines for the likelihood forces ncores = 1 o print and AIC methods for summary.openCR o openCR.fit() acquires argument dframe0 for pesky custom models with learned response o par.openCR.fit() default trace = FALSE o rev method for reversing primary sessions of capthist objects Bugs fixed o varying usage unreliable with 'multi' detector type in some circumstances o summary method for openCR objects: erroneous counts in capthist component (ignored freq) o finite mixture model posterior class membership crashed openCR.fit() for spatial models o finite mixture models failed for 'multi' detector type Other o help page for openCR.design corrected version 1.2.1 (2018-10-31) New features and changed behaviour o runsim.spatial() acquires intervals argument o summary method for openCR objects o sumsims() accepts output from summary.openCR o sumsims() acquires argument 'true' and adds summaries of bias, coverage etc. o CJSp1 = TRUE details argument respected by openCR.design etc. Bugs fixed o sumsims() failed with parameters superN and superD o derived method for openCR objects: erroneous f and lambda for some models when intervals not 1.0 o print.derivedopenCR did not apply Dscale to session-specific D Other o changed default starting value for superD o tweaks to print method for derivedopenCR class o not published on CRAN version 1.2.0 (2018-05-25) New features and changed behaviour o multithreaded execution of some functions (up to 4x speed gain) o openCR.fit() types 'secrCL' and 'secrD' emulate closed-population analyses of 'secr' o openCR.fit() trace may be a positive integer (frequency of reporting) o ucare.cjs() wrapper for R2ucare test functions o moving.fit() and extractFocal() functions for moving window of sessions o m.array() reports releases on final session (last.session = TRUE) o openCR.fit() details ignoreusage option o runsim.spatial() and runsim.nonspatial() ncores argument defaults to NULL for multithreading o cyclic.fit() exposed as internal function but not exported o derived() method for openCR objects acquires arguments newdata and all.levels Bugs fixed o usage of count detectors not properly accounted for (noted by Richard Glennie) o fixedbeta clashed with start argument (some options) o session covariates not matched correctly with robust design sessions o LLonly reported x -1 o details$hessian = FALSE failed Other o Links to RcppParallel o Additional check for nonidentifiable parameters in print.openCR() version 1.1.2 (2018-04-16) New features and changed behaviour o none Other o tweaks to C++ code for CRAN (fabs -> abs) o check for availability of RMark o better failure criterion in bd.array() o http changed to https where possible version 1.1.1 (2018-04-11) New features and changed behaviour o movement kernel exposed o bd.array() probability of (b,d) o improved simulation functions o start may be named numeric vector Other o first CRAN submission o consolidates CJS and JSSA C code (e.g. prwisecrcpp) o timevaryingcov<- disabled until next release secr version 1.0.2 (2018-03-26) New features and changed behaviour o movement kernel unsuppressed version 1.0.1 (2018-03-25) New features and changed behaviour o movement kernel [temporarily suppressed] o plotKernel() o movementmodel argument replaces staticHR o experimental timevarying individual covariates version 1.0.0 (2018-03-11) Known bugs o CI of predicted b[1] Other o renumbered 1.0.0 (previously unreleased 2.2.3)