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NEWS
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Changes in version 2.9.3 (2024-09-28)
New features or changed behaviour of old functions
o none
Changes in version 2.9.2 (2024-09-27)
New features or changed behaviour of old functions
o minsimRSE new method for optimalSpacing simulations
Bugs fixed
o run.scenarios() with fit="multifit" failed with default (shared) mask
o estimateSummary() lost scenario number in some grouped examples
o run.scenarios() with model2D = 'IHP' could fail with NA start value for D
Other
o internal function dfcast accepts character detectfn
o plot.optimalSpacing tweaked to allow pch other than 1 and new plottype option
o run.scenarios() with trapset functions outputs a message as each is tested
o added anchors to external documentation links
Changes in version 2.9.1 (2024-04-20)
New features or changed behaviour of old functions
o run.scenarios() default extractfn keeps raw counts (including RPSV) as attribute
o run.scenarios() acquires argument 'prefix' for saving intermediate output
o expand.arg() new utility function to generate lists of arguments
o scenarioSummary() outputs overlap index k
Bugs fixed
o estimateSummary() failed when some estimates NA
Other
o run.scenarios() tweak to allow missing detectpar in det.pars
o estimateArray() and estimateSummary() more robust to failed model fit
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")
o onAttach() options (matprod = "internal")
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()