Changes in version 2.9.0 (2024-03-01) New features or changed behaviour of old functions o multi-model fits (nested fit.args for one fitindex) o run.scenarios() acquires argument 'joinsessions' Bugs fixed o run.scenarios() could ignore maskset o run.scenarios() failed with byscenario = TRUE o Enrm() and related functions: E(m) sometimes NA due to near-zero hazard Other o outputtype<- in-place replacement (also reassigns class) o transformOutput() function to recast output o select.stats tweak to allow movingAverage o estimateArray() and estimateSummary() more robust o byscenario = TRUE uses cluster type = FORK on Unix-like machine o tweaks to c.estimatetables and c.selectedstatistics() o run.scenarios() fitarg start may be NULL (dodges binomial problem with "true") Changes in version 2.8.2 (2023-03-11) New features or changed behaviour of old functions o none Other o example time reduced for CRAN Changes in version 2.8.1 (2023-03-10) New features or changed behaviour of old functions o fit option 'design' (assumes detection model cf Fewster & Buckland 2004) o estimateArray() and estimateSummary() new functions Other o summary field 'var' Changes in version 2.8.0 (2023-01-19) New features or changed behaviour of old functions o run.scenarios() fit.function may be "ipsecr.fit" o run.scenarios() acquires argument 'CH.function' o functions to combine output from different executions of run.scenarios() (methods c, rbind for estimatetables, selectedstatistics) Other o suggests ipsecr o schematic figure in help page ?secrdesign o revised help page ?run.scenarios o run.scenarios() sets RCPP_PARALLEL_NUM_THREADS if ncores provided Changes in version 2.7.0 (2022-12-04) New features or changed behaviour of old functions o GAoptim() optimization by genetic algorithm using min(n,r) criterion (Durbach et al. 2021) and others o minnrRSE() accepts GAoptim() output o En2() and Qpm() for additional optimization criteria o run.scenarios() option to create trapset dynamically with function(s) o run.scenarios() compatible with dynamic density function in pop.args Bugs fixed o run.scenarios() failed with grouped scenarios if maskindex not specified Other o on GitHub o added tests o exports internal functions GApenfn() and compactSample() o make.scenarios allows single-level 'groups' o check for consistent traps etc. across groups within scenario o parallel clusters not used by run.scenarios() if fit = FALSE o shift to Rcpp, RcppArmadillo from C o summaryScenarios() ncores defaults to 1 (usually faster than >1) Changes in version 2.6.0 (2022-01-26) New features or changed behaviour of old functions o run.scenarios() 'fit' option uses multithreading capability of secr o run.scenarios() 'ncores' defaults to NULL (then uses value of environment variable RCPP_PARALLEL_NUM_THREADS set by setNumThreads()) o run.scenarios() 'byscenario' defaults to FALSE Bugs fixed o Enrm() expected movement could fail when some of mask far from detectors Other o removed openCR options and imports (deprecated from 2.5.8) o initial value of RCPP_PARALLEL_NUM_THREADS (usually 2) is set by secr onload o depends R (>= 3.5.0), secr (>= 4.2.0) Changes in version 2.5.11 (2020-04-10) New features or changed behaviour of old functions o none Bugs fixed o run.scenarios() default extractfn (no model fitted) mistake in RSEp approximation Changes in version 2.5.10 (2020-01-31) New features or changed behaviour of old functions o run.scenarios() default extractfn (no model fitted) uses RSEp approximation of Efford & Boulanger 2019 Bugs fixed o optimalSpacing() with simulations, fit.function = "openCR.fit" and nrepeats>1 miscalculated RB(D-hat) o summary.selectedstatistics() failed when run.scenarios() pop.args included poly o header() stumbled on non-numeric (covariate) specification of D o run.scenarios() spurious warning for non-numeric D Bug not fixed (see Other) o With fit.function 'openCR.fit', the calculation of RB(D-hat) in summarized simulations does not reflect nrepeats>1 Other o fit.function 'openCR.fit' is deprecated, and will be removed in a later version; secr.fit is now fast enough o optimalSpacing() catches bad root finding when limits inappropriate o optimalSpacing() only passes valid fit.args to run.scenarios o force ncores = 1 when fitting model (internal function processCH) Changes in version 2.5.7 (2019-02-04) New features or changed behaviour of old functions o none Bugs fixed o count.summary() failed with fit.function = "openCR.fit" Changes in version 2.5.6 (2019-01-26) New features or changed behaviour of old functions o make.scenarios() allows uniform (detectfn = 4) o count and predict methods for simulation objects inheriting from 'summary' o select.stats() respects count statistics Bugs fixed o plot.optimalSpacing() failed if any values missing (NA) o optimalSpacing() did not apply nrepeats when computing binomial rotRSE o scenarioSummary() failed with single-detector arrays Other o vignette removed (had been re-introduced by mistake in 2.5.5) (see www.otago.ac.nz/density/pdfs) Changes in version 2.5.5 (2018-12-07) New features or changed behaviour of old functions o optimalSpacing() new argument 'fit.function' to select openCR.fit/secr.fit o optimalSpacing() new argument 'distribution' o optimalSpacing() adjusts rotRSE for binomial distribution of n o plot.optimalSpacing() does not plot optimum o summarySpacing() calculates detectors per home range Bugs fixed o run.scenarios() tripped up on multi-session simulation o summaryScenarios() mostly ignored nrepeats Other o imports from openCR Changes in version 2.5.4 (2017-12-05) New features or changed behaviour of old functions o none Other o vignette secrdesign-vignette.pdf removed (see www.otago.ac.nz/density/pdfs) Changes in version 2.5.3 (2017-12-04) New features or changed behaviour of old functions o saturation() new function for expected detector saturation (trap success) o scenarioSummary() reports average expected detector saturation o derived.SL() and regionN.SL() replaced by methods for generic functions derived and region.N (see 'secr') Bugs fixed o Enrm() etc. detectfn 'HAN' and 'HCG' failed Other o tweak to select.stats to allow parameters without true value in scenarios o depends on secr >= 3.1.2 Changes in version 2.5.2 (2017-10-10) Other o vignettes secrdesign-Enrm.pdf and secrdesign-tools.pdf removed (see www.otago.ac.nz/density/pdfs) Changes in version 2.5.0 (2017-10-06) New features or changed behaviour of old functions o functions Lambda(), Enrm(), minnrRSE(), costing(), getdetectpar() and optimalSpacing() o new function scenarioSummary() reports deterministic summary of scenarios (e.g., expected number of individuals, costings) o run.scenarios() and fit.models() acquire argument byscenario (parallel scenarios or replicates?) o fit.models() mask may be passed as component of fit.args, when it has priority over maskset o run.scenarios() user may specify different masks as core in pop.args Bugs fixed o run.scenarios() ignored Nmark detection argument o chatnsim lost if multiple scenarios o nrepeats was ignored when method = 'none' Other o more robust outputtype when no results o packageType message if pre-release o persistent problems in header() for non-scalar arguments Changes in version 2.4.1 (2016-09-28) New features or changed behaviour of old functions o rule-of-thumb RSE added to default extractfn when fit = F o validate() acquires argument 'quietly' o detectpar list may be specified in det.args (overrides scenario) Bugs fixed o summary.selectedstatistics() failed when type = 'array' Other o all array dimensions now named in output of summary.selectedstatistics() Changes in version 2.4.0 (2016-04-23) New features or changed behaviour of old functions o mark-resight data are simulated with secr::sim.resight if traps object has markocc attribute o run.scenarios() new argument chatnsim for simulating overdispersion of sightings o header() allows for complex 'details' and 'start' components o validate reports number of problem rows Bugs fixed o header() failed with model2D="IHP" (problem in argdf - temporary fix) o run.scenarios() respects detectpar component of det.args (see makeCH) Other o number of occasions in markocc overrides noccasions in scenario o internally streamlined use of multiple cpu (no unnecessary export) o select.stats() failed with parameter not 'D' o run.scenarios() uses message instead of cat Changes in version 2.3.1 (2015-05-14) New features or changed behaviour of old functions o scenariosFromStatistics() new function to generate scenarios with specified number of first captures and recaptures. o improved output header for fit.args etc. Changes in version 2.3.0 (2015-03-25) New features or changed behaviour of old functions o fit.models() acquires arguments 'scen' and 'repl' to select a subset of rawdata o run.scenarios() and fit.models() when predict.secr returns a list the default extractfn selects first session or group, with a warning (previously crashed) o summary.selectedstatistics() has improved labelling of output o select.stats() acquires argument 'true' for user override of 'true' values Bugs fixed o fit.models() did not work with grouped populations o default extractfn failed when no detections and fit = FALSE o run.scenarios() dots argument (...) not passed to worker processes Other o more robust handling of start values for secr.fit() Changes in version 2.2.2 (2015-01-11) Other o CITATION file uses package metadata Changes in version 2.2.1 (2014-11-27) New features or changed behaviour of old functions o run.scenarios() allows value "linear" for model2D argument of sim.popn o details 'userdist' argument suppressed when printing summaries o make.scenarios() optionally generates scenarios with group structure (e.g. males and females) o run.scenarios() simulates composite (grouped) populations Bugs fixed o validate() did not catch NaN values Other o attribute 'regionarea' renamed 'regionsize' to cover linear case o workflow figure dropped from secrdesign-package.Rd (see vignette) o argument order changed in summary.selectedstatistics o default extractfn checks for non-null 'fit' of returned secr object Changes in version 2.1.3 (2014-06-04) o vignette renamed and edited o vignette source code included Changes in version 2.1.2 (2014-04-29) New features or changed behaviour of old functions o validate() function to set out-of-range values to NA o min, max as fields in summary.selectedstatistics o secrdesign.pdf vignette o header in summary output now includes pop.args o run.scenarios() allows IHP population simulation as alternative to specifying uniform density Bugs fixed o maskset was not saved when specified in run.scenarios()