Changes in version 5.2.1 (2025-03-18)
New features or changed behaviour of old functions
o secr.fit() saveprogress details option
o secr.refit() new function
Bugs fixed
o sim.detect() mishandled miscparm (as used by userdist fn etc.)
o secr.fit() auto-generated multisession mask had class 'list';
class should have been c('mask','list') to pass verify() downstream
Changes in version 5.2.0 (2025-01-24)
New features or changed behaviour of old functions
o allows models for relative density with CL = TRUE
o derivedDcoef() and derivedDsurface() for conditional D models
Bugs fixed
o addCovariates() generated spurious sf warning "attribute variables are
assumed to be spatially constant throughout all geometries "
o region.N() computation of R.N ignored varying density
o derived() miscounted number of individuals when animal with exactly one
capture was lost on another occasion, hence error in D-hat
o sim.capthist() generated captures at some 'unused' multi-catch traps
Other
o tweaked OVpossum Rd example to avoid 'sp' package
o split.xxxx() functions check for NA values in split factor
o externalqx undocumented details argument
o AICcompatible check moved from AIC.secr to AIC.secrlist
o many minor edits to allow relativeD
o added tests for relativeD
Changes in version 5.1.0 (2024-11-04)
New features or changed behaviour of old functions
o MCgof() acquires 'debug' argument
o makeNewData.secr acquires 'bytrap' argument
o fxTotal extended to mixture models
o split.capthist() acquires 'bysession' argument
o simulate.secr() acquires 'poponly' argument
o sim.popn() infers 'core' from bbox of 'poly' argument if missing
Bugs fixed
o MCgof() stalled in model with trap covariates (detectpar problem)
o MCgof() error when zero unobserved AC
o direct calling of fxi.secr() disabled prematurely in 5.0.0
o simulate.secr() when D~1 generated AC in rectangular window instead of respecting mask
o esaPlot() in 5.0.0 failed with multi-session model
Other
o predict.secr() speed up when se.fit = FALSE
o detectpar() speedup (calls predict.secr with se.fit = FALSE)
o suggest.buffer() rounds to 3 sig.fig. and more robust
o expose 'externalpdot' details option
o plot.capthist() warning when petal plot rad argument large
o plot.secrtest() allows user-specified xlab
o MCgof() dots argument passed to testfn
Changes in version 5.0.0 (2024-10-02)
New features or changed behaviour of old functions
o MCgof() goodness-of-fit after Choo et al. (2024) DOI: 10.1111/2041-210X.14386
o blackbearCH new dataset of J. Laufenberg, F. van Manen and J. Clark
o default criterion for AIC and modelAverage changed from AICc to AIC
o score.table reports dAIC rather than dAICc
o detectpar() optionally returns values for each detector
o pdot() accepts detector- and occasion-specific detection parameters
o usage() method for traps objects acquires argument 'noccasions' to create from scratch
Other
o internal addzeroCH() ignores covariate dataframe with zero columns
o improved robustness of fxi.secr by setting occasional NaN to zero
o imports from mvtnorm
o list.secr.fit() now works with details$LLonly = TRUE
o trappingtransect, trappingtransectX revert to built-in integration
o some minor functions restricted to point detectors (i.e. not area search)
CVa, CVpdot, reparameterize.esa, make.mask(type=pdot)
o derivedSystematic() defunct
o purged unused code
o derived() uses nlme::fdHess for gradients
o esa(), fxTotal(), MCgof() become S3 generic
o unused HPX detectfn removed
o fxi.secr() becomes S3 generic fxi() with method for secr objects
o other fxi.xxx functions renamed fxiXxx (old ones deprecated for now)
o pdot.contour and buffer.contour renamed pdotContour and bufferContour (old names deprecated for now)
o esa.plot() renamed to esaPlot() to avoid clash with generic
Changes in version 4.6.10 (2024-08-21)
New features or changed behaviour of old functions
o sim.detect() optionally computes expected counts or retains null histories
Other
o list.secr.fit() recovers when some fits fail
o added dots argument to secr.test(), passed to statfn
o added dots argument to sim.secr(), passed to extractfn
o secr.test() fit = TRUE trim keeps mask
o internal changes to sim.detect() may change output order
o include pmix in output of detectpar() from mixture models
o as.array method for capthist objects
Bugs fixed
o code for deviance of binomial model failed (broken for years)
Changes in version 4.6.9 (2024-06-29)
New features or changed behaviour of old functions
o none
Other
o added package anchor in Rd files when linking to sf and RcppParallel functions, to satisfy CRAN
Changes in version 4.6.8 (2024-06-28)
New features or changed behaviour of old functions
o none
Bugs fixed
o bug in likelihood for 'relativeD'
Changes in version 4.6.7 (2024-06-05)
New features or changed behaviour of old functions
o sim.popn() the covariates argument may specify a function to
construct covariates
o sim.capthist() detectpar = list(individual = TRUE) uses individual
parameter values from popn covariates
o rlnormCV() is wrapper for rlnorm with inputs on the natural scale
o make.spcosa() new function for spatial coverage designs (Walvoort et al. 2010)
o append.capthist() new function to combine independent capthist
Bugs fixed
o rotate.traps added spurious polyID
o sim.capthist() with single,multi detectors did not respect 'renumber = FALSE'
o sim.popn() rLGCP saveLambda failed in one case
Other
o onLoad defaults to options()matprod = "internal"
Changes in version 4.6.6 (2024-03-01)
New features or changed behaviour of old functions
o list.secr.fit() replaces par.secr.fit()
o unRMarkInput() accepts '.' for missing
Deprecated
o functions par.secr.fit(), par.derived() and par.region.N() for parallel
processing of multiple models will be removed later in 2024
Bugs fixed
o detection models failed with polygon and transect detectors
o sim.popn() row numbering glitch (open population)
Changes in version 4.6.5 (2024-02-18)
New features or changed behaviour of old functions
o sim.popn() saves 'parents' and 'Lambda' attributes from rThomas
o relative density option 'relativeD'
o AICcompatible() checks for 'relativeD'
o secrlist acquires argument 'names'
o binCovariate() new function
Bugs fixed
o score.test() failed with condition length>1
o makeStart() failed with details$fixedbeta
o obscure reparameterizations param = 2,6 failed
o fxi.secr() did not allow polygon data
o static userdist not working
Other
o secr.fit() warns if factor levels inconsistent for covariates of
multi-session mask
o undocumented feature: details = list(externalpdot = 'pd') where 'pd'
is the name of a mask covariate to substitute for internally computed
p.(x|theta)
o traps<- replacement function works for multi-session capthist
Changes in version 4.6.4 (2023-10-18)
New features or changed behaviour of old functions
o none
Other
o tweak kfn.Rd to reduce CRAN check time
Changes in version 4.6.3 (2023-10-17)
New features or changed behaviour of old functions
o sim.popn() simulates log-gaussian Cox process (model2D = "rLGCP") using
packages spatstat and RandomFields
o sim.popn() simulates Thomas process (model2D = "rThomas") using spatstat
o as.popn() converts spatstat ppp objects
o randomDensity() new wrapper for randomHabitat() for use with sim.popn()
o reduce.capthist() now retains popn attribute
o trend reparameterization of density (secr.fit details 'Dlambda')
o kfn() new function for overlap index
Bugs fixed
o make.capthist() could lose individual covariates of animals later
lost on capture (negative occasion number)
Other
o suggests spatstat, spatstat.geom, spatstat.random (LGCP),
and igraph (randomHabitat)
o randomHabitat() loads igraph automatically if needed
o imports raster::flip
o Fletcher.chat() returns NA instead of error when input NA
o sim.popn() argument 'number.from' applied to multi-session data
o sim.popn() details$clone=="constant" applies scale (model2D="cluster")"
o secr.fit() distribution="binomial" warns when initial value of N less than number detected
o model.average() now defunct (replaced by modelAverage)
o LLsurface message edit
o secr.fit() attempt to use learned response with mark-resight data now blocked
o fixed \itemize in Rd files
Changes in version 4.6.1 (2023-07-10)
New features or changed behaviour of old functions
o collate() redefined as generic, behaviour mostly unchanged
Bugs fixed
o collate() failed if betanames specified for multi-session model (multi-row newdata)
o LR.test() failed when class of fitted models had length>1
Other
o read.traps() allows comma-separated usage values when binary.usage = FALSE
o sim.popn() handles IHP N=0 without crashing
o shift.mask() updates boundingbox
o chat.nk may use clusters in parallel for simulation
o internal boundarytoSF extended to sf geometry objects
o Fletcher.chat() protected against near-zero expected values
Bugs fixed
o secr.fit() crashed R for polygon data with hcov specified
Changes in version 4.6.0 (2023-05-22)
New features or changed behaviour of old functions
o exports Fletcher.chat(), nk()
o Enk() simulation option
o chat.nk() optionally simulates c-hat
o AIC and modelAverage methods acquire variance inflation argument 'chat'
for optional computation of quasi-AIC etc.
o adjustVarD() acquires optional argument 'chat'
Bugs fixed
o make.capthist() lost covariates when creating non-spatial capthist
Other
o trim() method for secrlist objects
o chat.nk() 'stats' components renamed; sbar added
o Enk() (and hence chat.nk) works for multi-catch traps
o sim.popn() model2D 'cluster' has clone-in-place option
o fast computation of spacing (PR of Philipp Jund, now ctb)
o faster C++ for transect fitting (PR of Philipp Jund)
Changes in version 4.5.9 (2023-03-09)
New features or changed behaviour of old functions
o none
Bugs fixed
o secr.fit() fitted wrong model for Poisson count detectors when
fastproximity = FALSE, giving bad estimates esp. of detectfn parameters
o make.capthist() failed with points snapped to transects
o sim.popn() model2D 'cluster' mistakenly allowed Ndist = 'fixed'
o region.N() could fail with user-provided distance function or when
detectors varied among sessions
Other
o MS.capthist() help clarified
o ip.secr() and pfn() defunct
o secr.fit() recognises time-covariate model when timecov is a
multi-session list, avoiding default to fastproximity
Changes in version 4.5.8 (2022-11-29)
New features or changed behaviour of old functions
o plot method for traps acquires argument 'frame'
o trapsPerAnimal() new capthist summary function
o Enk() new function expected individuals per detector
o chat.nk() and adjustVarD() new functions for spatial overdispersion
o summary method for capthist optionally includes frequency
distribution of traps per animal (count of tpa >= 2 if terse)
o sim.popn() with model2D = 'IHP' the density argument may be a function
Bugs fixed
o hcov failed with one level missing in some sessions
(following change in 4.5.1)
o sim.secr() crashed R when used with learned-response models (b, B etc.)
o secr.fit() failed occasionally with distribution = 'binomial'
o randomHabitat(..., plt = TRUE) assumed raster::plot loaded
o spotHeight() not working
Other
o make.lacework limit of 5000 detectors
o plot.traps() box always black (bty='o')
Changes in version 4.5.7 (2022-10-08)
New features or changed behaviour of old functions
o nontarget() replacement function
o addCovariates() may be applied to popn object
Bugs fixed
o Tu<- replacement failed with multi-session capthist
o region.N erroneous values with new mask
Changes in version 4.5.6 (2022-08-13)
New features or changed behaviour of old functions
o sim.popn() model2D = 'IHP' allows session-specific density
o clone() new option type = 'truncatedpoisson'
Bugs fixed
o plot.mask legend sometimes failed ("object 'cex' not found")
Other
o for CRAN, update latex specials in help pages
o nontarget documentation
Changes in version 4.5.5 (2022-05-31)
New features or changed behaviour of old functions
o verify.capthist() checks nontarget matrix if present
o plot.capthist() new type 'nontarget'
o gridCells() constructs cells around points (e.g., traps)
Bugs fixed
o make.systematic() failed because quantities from sf are class 'units'
o addCovariates could fail when source polygons overlap
o predictDsurface failed with user-provided density function and single-session
o trap.builder() failed with edgemethod 'centreinside'
Other
o on GitHub at https://github.com/MurrayEfford/secr
Changes in version 4.5.4 (2022-04-22)
New features or changed behaviour of old functions
o reinstate GRTS option in trap.builder()
o makeStart() encapsulates code for initial values
o ip.secr() is deprecated (see new package at https://github.com/MurrayEfford/ipsecr)
Bugs fixed
o distancetotrap() and hence esa.plot() failed with polygon inputs
o addSightings() did not pass extra arguments to read.table() for multisession input
o secr.fit() failed with sighting data when usage 0 for any detector (since 4.4.6 Oct 2021)
o likelihood-only evaluation failed with mark-resight models if chat not initialised
o read.traps() failed for polygon or transect data with non-contiguous data points
Other
o suggests spsurvey >= 5.3.0
o bad densities in likelihood give warning, not error
o autoini tweaked to treat 'capped' detector type as 'proximity'
o collate tweaked to allow mixture of secr, ipsecr models
Changes in version 4.5.3 (2022-02-14)
New features or changed behaviour of old functions
o more spatial data types for 'poly' and 'region' function arguments
o rast generic method for mask, Dsurface objects creates terra SpatRaster object
o read.traps() accepts ESRI shapefile of point, polygon or line features (experimental)
o fxi.contour() argument 'SPDF' replaced by 'output', with options 'sf', 'SPDF'
Bugs fixed
o moves() failed with empty capthist input when names = FALSE
o details$ignoreusage=TRUE not respected by esa(), derived(), region.N()
o secr.fit() details$ignoreusage=TRUE failed when using 'fastproximity'
Other
o classes (sf, sfc, sfg) and methods (st_) from package 'sf' largely replace 'sp' (now in Suggests)
o trap.builder() SRS sf::st_sample replaces sp::spsample
o imports functions from 'sf' and 'terra'
o no longer suggests maptools, rgeos, rgdal
o internal function boundarytoSF documented
o new vignette secr-spatialdata.pdf
o revised OVforest shapefile in extdata
o one trap.builder() example moved to \dontrun to save time
Changes in version 4.5.1 (2022-01-18)
New features or changed behaviour of old functions
o none
Bugs fixed
o secr.fit() hybrid mixture model (hcov with known-class data)
did not use class-dependent detection model, resulting in
erroneous estimate of pmix (secr >= 4.0)
o memory error getxy() C++ (transect simulation; no effect on users)
Changes in version 4.5.0 (2022-01-06)
New features or changed behaviour of old functions
o make.capthist() 'snapXY' also works for points along transects
o modelAverage() new generic supercedes model.average()
o snip() acquires 'tol' argument, now used by discretize()
o new link 'i1000' (identity x 1000) for modelling very low density
o sim.popn() 'UNI' movement model (radius move.a)
o sim.popn() models differential settlement of dispersers (model2D = 'IHP'
and core has covariate 'settle' 0-1)
o f() term in formula for non-linear density models (experimental)
Bugs fixed
o verify() error 'Duplicated or missing row names (animal ID)'
triggered when no live releases
o sim.popn() multi-session movement allowed some animals outside the
boundary on the first step (edgemethod 'truncate')
o secr.fit() failed with data from multiple transects
o snip() and discretize() failed when transectID contained '.'
o nearesttrap, discretize etc. failed if no detections in some sessions
o alive() and reduce.capthist() erroneous when only one animal
o secr.fit() fastproximity failed when no detections in some sessions
o secr.fit() signal detector problem with Boost distribution function
(since 4.4.7 Oct 2021)
o secr.fit() mark resight simulations failed (since 4.4.5 July 2021)
Other
o suggests 'terra' package (potentially supercedes 'raster')
o tests added for transect and signal data
o model.average() deprecated
o update C++ code for BH 1.78
Changes in version 4.4.8 (2021-11-09)
New features or changed behaviour of old functions
o none
Bugs fixed
o 'count' detectors failed with Poisson model (reported by Ian Durbach)
owing to problem with switch to Boost statistical distributions in C++
Changes in version 4.4.7 (2021-10-18)
Other
o options requiring package 'spsurvey' suspended - trap.builder(method =
'GRTS') and derivednj(method = 'local') - because of changes in spsurvey 5.0.0
o 'spsurvey' removed from Suggests
Changes in version 4.4.6 (2021-10-18)
New features or changed behaviour of old functions
o sim.popn() exponential (RDE), gamma (RDG) and lognormal (RDL) movement distance
o sim.popn() zero-inflated movement models BVNzi, BVEzi, RDEzi, INDzi
o addCovariates() accepts RasterLayer spatialdata
o make.capthist() and read.capthist() tweaked to allow nonspatial input
Bugs fixed
o snip() failed in recent versions
o secr.fit() and bias.D() spurious warning of variable usage
Other
o Boost math library used for statistical distributions in C++ code
o number of threads explicit in calls to RcppParallel parallelFor
o sim.popn() with movement: edgemethod 'truncate' now synonym 'normalize'
o deprecated and defunct functions handled formally (see e.g., help("secr-defunct"))
Changes in version 4.4.5 (2021-07-12)
New features or changed behaviour of old functions
o 'sigmak' parameterization allows session covariates
o experimental parameter 'd' for parameterization sigma = sigmak/sqrt(D+d) + c
o sim.popn() all movement simulations use polar coords + rgamma, rweibull etc.
o extractMoves() new function for checking movement simulations
Bugs fixed
o as.data.frame.capthist() in 4.4.4 mis-assigned traps to captures
o trivial: bad trace when fixedbeta specified
Other
o 'BVN','BVE','BVT' aliases for movemodels 'normal','exponential','t2D'
Changes in version 4.4.4 (2021-05-29)
New features or changed behaviour of old functions
o animalID(), trap() etc. acquire argument 'sortorder'
Bugs fixed
o erroneous plot(), verify() and RPSV() results for multi-polygon data
o ASAN error: container overflow prwifastproximity.cpp
o rectangularMask() misaligned covariates by one cell, with
consequences for raster method for 'mask' class
Other
o multithreaded Examples now in dontrun{} to avoid TBB library in checks
o interactive dontrun{} Examples trapped to allow R CMD check --run-dontrun
o new text files in extdata for MRCH addSightings example
o flip() arguments changed F to FALSE
o new test: multi-detector polygon likelihood
o new test: join() nonspatial data
Changes in version 4.4.2 (2021-05-04)
Other
o rename generic make.newdata() to makeNewData()
o Imports RcppParallel version >= 5.1.1 to dodge problems in earlier releases
o run tests with Sys.setenv(RCPP_PARALLEL_BACKEND = "tinythread") to avoid CRAN errors
Changes in version 4.4.1 (2021-05-01)
Other
o Add final '/' to url in DESCRIPTION and fix typo in secr-package.Rd
Changes in version 4.4.0 (2021-05-01)
New features or changed behaviour of old functions
o sim.popn() movement model may be user-provided function
o sim.popn() recrmodel may be 'specified' (add number in details$Nrecruits)
o sim.popn() optional age covariate for multisession populations
o HPX new detectfn (binary detection in polygon)
o plot.traps minor change in colours used with polygon detectors
o split.capthist() accepts multi-session input
o reduce.traps() 'newxy' selects 'mean' or 'first' for coordinates of
new detector from group defined by 'newtraps'
Bugs fixed
o make.capthist() rejected some valid records as duplicates (R. Glennie)
o length > 1 in coercion to logical (internal function sessionLL x2)
o sim.popn() with movement: 'normalize' edgemethod did not normalize
o secr.make.newdata() (and predict.secr()) sometimes ignored all.levels = FALSE
o make.grid() spacing attribute missing in case of single detector
o reduce.capthist() failed with polygon input and nonspatial output
o no warning when attempt to combine capped and other detector types
o subset.capthist() by occasion could return wrong session labels
Other
o Suggests testthat, adds some unit tests in 'tests' folder
o sim.popn() with movement: 'clip' edgemethod works with constantN
o generic make.newdata() replaces secr.make.newdata() (seldom used directly; see 4.4.2)
o shareFactorLevels() when not multisession now converts ch _covariates_ to factor
Changes in version 4.3.3 (2020-12-11)
New features or changed behaviour of old functions
o subset.capthist() all-negative subset argument indicates exclusion
o shareFactorLevels() default for stringsAsFactors now TRUE
o sim.popn() with movement: new 'normalize' option for edgemethod
Bugs fixed
o multisession hcov failed if only one level present in one or more sessions
o plot.capthist() failed when no detections in session
o plot.mask(..., dots = FALSE) crashed when no points in mask
o secr.fit failed with hcov if only one class present in a session
o region.N() with multisession model failed using 'hcov' and otherwise not reliable
o alive() incorrect order of output
o sim.detect() renumbered multi-session capthist even when renumber = FALSE
Other
o terminal '/' on https://www.otago.ac.nz/density/ in Rd required by CRAN
o verify() suggests shareFactorLevels() when needed
o more robust handling of sessions with zero detections
o join() gives advice when table limit exceeded (2^31 elements)
o output from region.N() with multisession model uses session names
o rectangularMask() rewritten to allow disjunct mask blocks
o character sessioncov used in D~ models automatically converted to factor
o sim.popn() undocumented movement options 'radialexp' and 'radialnorm'
o reduce.capthist() more robust when no detections
o sim.capthist() now accepts character detectfn when nsessions>1
Changes in version 4.3.1 (2020-08-31)
New features or changed behaviour of old functions
o subset.traps() allows subset argument to be function, as for
subset.capthist()
o de novo calculation of spacing for traps, mask uses median instead of mean
o read.traps() enables usage and covariate input from data and xls
o summary.traps() new argument 'covariates' for covariate summaries (default FALSE)
o verify() invisible output includes detail on captures
o ORL() new function for observed range length
o centroids() new function for detection centroids
Bugs fixed
o verify() bug on covariates call to stringsAsFactors fn
o moves() lost animal order when animal IDs numeric and names = TRUE
o secr.make.newdata() (and hence predict() etc.) included superfluous
combinations of session covariates
o read.mask() assigned wrong spacing for some unusual configurations
o occasion() could result in wrong sequence, with consequences for various plots
and summaries
Other
o summary.secr() always reports detector percent usage
o plotMaskEdge() increased robustness
o make.capthist() coerces third column of captures dataframe to integer
o updateCH() recoded to avoid reduce.capthist() that now assumes 3-D
o secr.fit() calls check3D in case data pre-dates secr 3.0
o fxi.secr() and related functions work with models fitted using fastproximity = TRUE
Changes in version 4.3.0 (2020-07-14)
New features or changed behaviour of old functions
o RSE() returns matrix with one row for each row of newdata
o shareFactorLevels() gains argument stringsAsFactors to convert character to factor
Bugs fixed
o learned response models (b, B etc.) fitted incorrectly to data from multi-catch traps
(detector 'multi') and exclusive polygon-type detectors (detector 'polygonX', 'transectX')
o esa() ignored individual covariates in models with CL = TRUE, with consequences
for derived() and region.N()
Other
o internal changes for compatibility with R 4.0
o make.capthist() forces character covariates to factor for backward compatibility
o verify() converts character covariates to factor before checking levels consistent
across sessions
o derived() and region.N() now work for models fitted in secr versions before 4.0
Changes in version 4.2.2 (2020-04-08)
New features or changed behaviour of old functions
o none
Bugs fixed
o individual covariate (CL) models for proximity data failed unless fastproximity = FALSE
o Bk models for proximity data gave error unless fastproximity = FALSE
o join() sometimes failed (circumstances unclear)
Other
o adjusted protection for calls to suggested package rgdal
o suggest.buffer() trivial change to Examples
Changes in version 4.2.0 (2020-02-22)
New features or changed behaviour of old functions
o new mechanism for setting number of threads (default 2)
o setNumThreads() new function
o make.systematic() 'rotate', 'centrexy' and 'keep.design' arguments
o make.lacework() new function
o make.grid() and make.circle() acquire argument 'leadingzero') (default TRUE)
Bugs fixed
o make.systematic() unintended result when spacing of rows and columns differs
Other
o pdot() uses multithreaded C++ function pdotpointcpp2
o pdot() acquires argument ncores
o derivedSystematic() acquires argument ncores
o esa() internal limit on ncores (2) removed
o trim.secr() drops designD, designNE by default (see 4.0.0)
o rotate.traps() checks for zero rows
o suggest.buffer() minor internal changes
o distancetotrap() uses rgeos::gDistance for polygon detectors if available
o fxi.secr() and related functions enabled for polygon detector types
Changes in version 4.1.0 (2019-12-17)
New features or changed behaviour of old functions
o AICcompatible() new S3 method to check models for AIC compatibility
o AIC() warns if secr models not compatible
o LR.test() stops if secr models not compatible
o secr.fit() faster fitting of polygon and transect data
o secr.fit() option details = list(convexpolygon = FALSE) allows non-convex polygons.
o autoini() uses simpler and more robust code; secr.fit() start values differ slightly
from earlier versions; new argument 'adjustsigma'.
Bugs fixed
o reduce.capthist() subtracted dead animals when outputdetector = "count"
o verify.capthist() spurious warning for transect data with character animalID
o derived() bad for polygon and transect data in secr 4.0 because esa() corrupted
o secr.fit() in secr 4.0 bad likelihood and estimates for some covariate models
(bad indexing of parameter array PIA)
o secr.fit() failed with multi-session mark-resight data (fixed pID, non-null Tm)
o suggest.buffer() failed with input from multi-session fitted model
o make.systematic() unintended result when spacing of rows and columns differ
Other
o RcppNumerical used for numerical integration with polygon and transect detectors
o requires R >= 3.5.0 for obscure reasons (serialization of data objects)
o suppressed new warnings from regularize.values in approx()
o internal function secr.design.MS() argument bygroup replaced with CL
o LLsurface() returns value matrix when plot = FALSE (otherwise invisibly as before)
(NA where likelihood could not be evaluated)
o mark-resight sighting only, partial identification re-enabled
Changes in version 4.0.2 (2019-11-11)
New features or changed behaviour of old functions
o secr.fit() LLonly = TRUE stores number of parameters and timing information
o secr.fit() LLonly = TRUE uses default or autoini start values if none provided
o summary.secr() versiontime includes elapsed time
o summary.capthist() includes summary of individual covariates
Other
o CRAN release of 4.0
Changes in version 4.0.0 (2019-10-27)
New features or changed behaviour of old functions
o 'ncores' argument defaults to NULL in most functions (meaning one less than number
of available cores for multi-threading)
o fx functions 'normal' argument dropped
o 'ncores' argument dropped from mask.check(), pmixProfileLL() and simulate.secr()
o autoini(), region.N() and suggest.buffer() acquire 'ncores' argument
o fast secr.fit() for binary and count proximity detectors (default details$fastproximity = TRUE)
o make.systematic() new argument 'order' to control cluster sequence
o RSE() extract precision of estimated parameter from fitted model
o par.secr.fit() no longer automatically sets ncores=1 in the separate calls to 'secr.fit'
o secr.fit() details option autoini = 'all' for start values from multi-session data
Bugs fixed
o sim.secr() with 'multi' detectors slightly understated detection rate owing to mis
-assignment of detection locations
o make.systematic() and trap.builder() ignored region polygon when cluster not
specified (edgemethod set internally to 'allowoverlap'
Other
o converted C code to C++ with multithreading in RcppParallel as appropriate
o some features of earlier versions have yet to be implemented in 4.0
o secr object from secr.fit() includes design matrices for D and noneuc
o functions read.SPACECAP() and write.SPACECAP() removed
Changes in version 3.2.2 (2019-07-02)
New features or changed behaviour of old functions
o summary method for popn objects
o write.mask() function
Bugs fixed
o sim.popn() exponential
o plotMaskEdge() sometimes shows internal lines (non-integer spacing)
Other
o write.capthist help wrote files to disk; now in \dontrun{}
Changes in version 3.2.1 (2019-06-01)
New features or changed behaviour of old functions
o sim.popn() allows exponential and t2D movement between sessions
o sim.popn() new details arguments movemodel, move.a; sigma.m deprecated
Bugs fixed
o make.capthist() with transect data gave error when points did not lie on transect
o moves() failed with nonspatial capthist (also summary.capthist(moves = T) etc.)
o plot.popn() ignored frame argument when collapse = TRUE
Changes in version 3.2.0 (2019-01-25)
New features or changed behaviour of old functions
o derivednj() extended for weighted variance (R2, R3), with subtle argument changes
o derivednj() and dependent functions return 2-line dataframe (rows 'esa', 'D') as for derived()
o derivedSession() extended for weighted variance
o derivedCluster() extended for weighted variance
o derived() for secr and secrlist objects acquires argument 'bycluster'
o split method for mask objects (split.mask)
o trap.builder() new edgemethod and exclmethod options "anyinside", "centreinside" etc.
o derived.secr() improved handling of sessions with zero detections
o derivedSystematic() implements Fewster 2011 variance for systematic cluster designs
o make.systematic() acquires argument "chequerboard", saves originbox,
argument 'originoffset' replaces 'bufferorigin'
o spacing.traps() returns numeric(0) instead of NULL for 1-trap arrays
o write.traps() removed single quotes around objectname
o secr.fit() allows mixture models when detector 1 unused on occasion 1
o make.mask() more explicit warning when nrow = 0
o plot.traps() gridlines = TRUE respected for add = TRUE (default gridlines = !add)
o pdot.contour() and related functions acquire argument 'poly.habitat'
o summary method for capthist objects (summary.capthist) optionally reports movements
Bugs fixed
o make.systematic() grid didn't span extremes of some region polygons
o sighting-only did not allow unidentified marked sightings
o reduce.traps() failed for reduced number of occasions when both usage and markocc specified
Changes in version 3.1.8 (2018-11-19)
New features or changed behaviour of old functions
o make.systematic() saves origin and centres as attributes
o make.systematic() new argument bufferorigin controls random origin
o summary method for secr objects, with print and AIC methods for summary (may change)
o clone.popn() rownames consistent with clone.capthist() (1.1, 1.2...)
Bugs fixed
o make.mask() not using keep.poly and check.poly arguments for multi-session masks
o detector usage not correctly included in some models with detector type "multi"
o clone methods not robust - freq now rounded to avoid quirky behaviour of rep()
Other
o some models (e.g., g0~bk with detector type "multi") fit more quickly than before
Changes in version 3.1.7 (2018-10-03)
New features or changed behaviour of old functions
o esa.plot() computes CVpdot for varying buffer width
o esa.plot 'as.density' argument replaced with 'type' and new argument 'conditional'
o sim.popn() edgemethod new options 'stop' and 'reflect'
Bugs fixed
o OVpossumCH dataset Ageclass covariate placed 1-year-olds in >=2 year class
o join() detector attribute not expanded correctly for some inputs
o reduce.capthist() bug introduced in 3.1.6
o subset.popn() failed for multi-session populations
o region.N() gave misleading R.N for models with individual variation in detection,
including h2
o trap.builder() failed when projection specified for 'region'
o addTelemetry() failed with mark-resight data
o write.capthist() lost non-numeric detector names (since 2017-11-30)
Other
o secr-manual.pdf is no longer distributed with package - see
https://www.otago.ac.nz/density/pdf/secr-manual.pdf or https://CRAN.R-project.org/package=secr/secr.pdf.
Changes in version 3.1.6 (2018-05-14)
New features or changed behaviour of old functions
o sim.popn() details (turnover) argument "wrap" deprecated; use "edgemethod"
o plot method for capthist object copes with missing rownames
o CVpdot() new function for CV of p. across mask
o improved handling of attributes (intervals and sessionlabels) in subset and reduce
methods for capthist objects
o join() allows site matching by name, which is faster
o timevaryingcov() extended to capthist objects for openCR - see ?join
Bugs fixed
o internal fn predictD returned matrix instead of vector, causing problems in region.N
o sim.capthist() failed for signal detectors (df0 error reported by Ben S)
Changes in version 3.1.5 (2018-02-25)
New features or changed behaviour of old functions
o rotate method for capthist objects
o secrlist() returns input secrlist object unchanged
o plotMaskEdge() accepts multi-session input
o secr.make.newdata() rewritten; acquires logical argument 'all.levels'
o predict method for secr objects passes dots argument to secr.make.newdata()
o join() intervals optionally passed as attribute 'intervals'
o coef method for secrlist objects
o unRMarkInput() assumes all freq = 1 if freq field missing
o new detectfn 19 (HVP hazard variable power)
o RMarkInput ignores 'covariates' argument when no covariates
o reduce and subset methods for capthist objects allow nonspatial input and output
when verify = FALSE
o reduce and subset methods for capthist objects honour 'intervals' attribute
o summary method for nonspatial capthist objects drops detectors from table of counts
o plot method for popn objects acquires new arguments for overlaying multiple sessions
o sim.popn() argument sigma.m < 0 causes random relocation
o sim.popn() open population recruitment model "multinomial"
o LLsurface now a generic function with method for 'secr' objects
o new capthist attribute 'sessionlabels' useful for joined capthist
Bugs fixed
o secr.fit gave misleading estimates with binomial count data when size derived from usage
(reported by Mathias Tobler)
o predict.secr misreported pmix for other than simple h2 models (pmix = 0.5 for some levels)
o detectfnplot() in error when detectfn = 'HAN'
o sim.capthist() and sim.resight() failed in 3.1.3 when detector type varied by occasion
o make.poly() failed with some polygon list inputs
Other
o optional 'interval' attribute of capthist objects renamed 'intervals' (see ?join)
o export internal function insertdim()
o minor tweaks for compatibility with open population code
o NEWS for versions before 3.0.0 archived
o some old documentation removed to online vignette secr-models.pdf
Changes in version 3.1.3 (2017-12-02)
New features or changed behaviour of old functions
o secr.design.MS() acquires argument 'contrasts' (used internally)
Bugs fixed
o sim.capthist() ignored recapfactor provided in detectpar
Other
o region.N now a generic method with functions for secr and secrlist objects
o corrected some obsolete documentation references to maptools package
Changes in version 3.1.1 (2017-11-30)
New features or changed behaviour of old functions
o new detector type 'capped' in make.grid(), sim.capthist(), reduce(), verify(), secr.fit() etc.
o as.data.frame methods for capthist and traps objects
o secrlist() and MS.capthist() generate names from input objects
o circular.r() and circular.p() acquire argument 'upper' for explicit upper limit of integration
o LR.test generalised to any fitted models with a logLik method
o plot method for secr objects: confidence limits now computed on log scale
for hazard detectfn HHN, HEX etc. to match predict.secr
o rbind method for traps adds suffix to names only when needed to avoid any duplication
o verify method for capthist objects checks for all-zero histories and missing rownames
o summary method for capthist objects: 'terse' option activated for single-session objects
o subset method for capthist objects: subset may be defined as function (useful for covariate-based selection)
o join() acquires arguments interval, to set between-session intervals directly, and sessions, for session names
o secr.fit() details argument 'contrasts' for specialised coding of factor predictors (example in secr-multisession.pdf)
o secr.fit() details argument 'newdetector' to override detector type
o 'newdetector' reported by print.secr
Bugs fixed
o predict method for secr objects failed to report SE for parameters with some fixed coefficients (fixedbeta)
o verify.capthist failed to report detections at unused detectors
Other
o requires package stringr for some functions
o class attribute of multisession objects changed to place "list" last --
c("list", "capthist") becomes c("capthist", "list")
o LLsurface.secr automatically substitutes lambda0 for g0 given detectfn 14:18
o experimental "nontarget" capthist attribute
o make.mask() explicit error when capthist passed
o derived is now a generic method with functions for secr and secrlist objects
o derived.nj() renamed derivednj(), derived.mash() renamed derivedMash() etc.
o && changed to & throughout - should have no effect except fixes verify bug, but be wary
Changes in version 3.1.0 (2017-09-20)
New features or changed behaviour of old functions
o par.secr.fit() acquires arguments save.intermediate and LB to allow
load balancing (thanks to Mathias Tobler)
o par.secr.fit() default value of 'seed' changed from 123 to NULL
o rbind.popn() now an S3 method; no longer accepts list input
o rbind.capthist() now an S3 method
o randomHabitat() acquires argument 'seed', saved as an attribute
(thanks to Erin Peterson)
o detectfnplot() acquires argument 'hazard' for plotting hazard
Other
o adjustment to 'ts' predictor for secr.fit mark-resight models
o documentation of random number seeds in ?secrRNG
o start vector returned by secr.fit now named
Bugs fixed
o faulty start vector when model included both h2 and noneuc
Changes in version 3.0.2 (2017-06-07)
New features or changed behaviour of old functions
o make.grid() and make.circle() acquire argument 'markocc'
o read.traps() accepts Excel xls or xlsx input (requires readxl)
Bugs fixed
o plot.secr misleading axis label 'Detection lambda'
o sim.resight() could fail with markingmask and predefined popn
Other
o imports file_ext from tools package
o attributes of output from sim.popn now include Nbuffer and D
o speed increase for "count" detectors
o miinor adjustments to sim.popn for compatibility R 3.4.0
Changes in version 3.0.1 (2017-05-03)
New features or changed behaviour of old functions
o 'unresolved' sightings now stored in Tn attribute of capthist
o sim.resight() acquires argument 'unresolved'
o plot.secrlist() accepts colour vector
o new function as.mask() to coerce traps objects for plotting
o moves() acquires argument 'names' to control sort order (new default)
Bugs fixed
o sightingPlot() legend ignored fill argument
Documentation
o addTelemetry omitted 'single' and 'multi' from permitted detectionCH types
Other
o discretize() updated for 3.0
o native routine registration completed
Changes in version 3.0.0 (2017-04-11)
New features or changed behaviour of old functions
o 3-D data structure used for trapping data
o updateCH() for easy conversion of old data
o multiple detector types may be used in one session
(point detectors only: single, multi, proximity or count)
o marking and sighting occasions may be interspersed
o rbind.traps acquires argument 'checkdetector'
o user-provided distance matrix may be session-specific
o esa 'noccasions' may be less than ncol(usage)
o function occasionKey() to embellish petal plots
o explicit handling of 'uncertain' sightings Tn
o plotMCP() now works with data from point detectors
o details$debug in secr.fit() now integer with multiple levels
o sightingPlot() new function
o plot.capthist() new option "centres"
o secr.fit() argument 'details' may be given as character value
o telemetrytype attribute of traps objects replaces details$telemetrytype
o new addTelemetry() function and revised handling of telemetry data
o addTelemetry() allows multi-session data
o secr.fit() etc. auto predictor 'tt' nontelemetry vs telemetry occasions
o addCovariates() acquires argument 'replace'
o c new method for combining secrlist objects
o make.capthist() discards repeat detections at exclusive detectors, with a warning
o models for polygon or transect detectors requre hazard detection functions
o esa.plot() accepts secrlist as input (curves overlaid)
o par.secr.fit() acquires argument 'prefix'
o predict.secr() acquires argument 'realnames' to select a subset of 'real' parameters
Bugs fixed
o make.grid() did not assign polyID attribute for polygon detectors
o snip() and discretize() for transects dropped occasions with no detections
o sim.capthist() failed when 'userdist' supplied (non-Euclidean distances)
Other
o ovenbird dataset provided with detector type "proximity"
o esa() more robust to variation when noccasions specified
o new details option 'splitmarked' for resightings (default FALSE)
o usagePlot() argument occasion renamed occasions
o more compact 'call' component of secr.fit output
o discontinued warning when detectfn requires changed parameters (g0 -> lambda0)
o plot method for traps enables box around plot (bty = 'o')
o plotMaskEdge faster
o secr.fit() details savecall = FALSE suppresses call (default in par.secr.fit)
o new function shareFactorLevels() to force factor covariates to use the same levels
o rgdal::readOGR used instead of deprecated maptools::readShapeSpatial
o minor speed improvments for models without learned response
o ip.secr() faster default predictorfn