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