NEWS

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secrdesign 2.9.3

New features or changed behaviour of old functions

• none

secrdesign 2.9.2 (2024-09-27)

New features or changed behaviour of old functions

• minsimRSE new method for optimalSpacing simulations

Bugs fixed

• run.scenarios() with fit="multifit" failed with default (shared) mask
• estimateSummary() lost scenario number in some grouped examples
• run.scenarios() with model2D = 'IHP' could fail with NA start value for D

Other

• internal function dfcast accepts character detectfn
• plot.optimalSpacing tweaked to allow pch other than 1 and new plottype option
• run.scenarios() with trapset functions outputs a message as each is tested
• added anchors to external documentation links

secrdesign 2.9.1 (2024-04-20)

New features or changed behaviour of old functions

• run.scenarios() default extractfn keeps raw counts (including RPSV) as attribute
• run.scenarios() acquires argument 'prefix' for saving intermediate output
• expand.arg() new utility function to generate lists of arguments
• scenarioSummary() outputs overlap index k

Bugs fixed

• estimateSummary() failed when some estimates NA

Other

• run.scenarios() tweak to allow missing detectpar in det.pars
• estimateArray() and estimateSummary() more robust to failed model fit

secrdesign 2.9.0 (2024-03-02)

New features or changed behaviour of old functions

• multi-model fits (nested fit.args for one fitindex)
• run.scenarios() acquires argument 'joinsessions'

Bugs fixed

• run.scenarios() could ignore maskset
• run.scenarios() failed with byscenario = TRUE
• Enrm() and related functions: E(m) sometimes NA due to near-zero hazard

Other

• outputtype<- in-place replacement (also reassigns class)
• transformOutput() function to recast output
• select.stats tweak to allow movingAverage
• estimateArray() and estimateSummary() more robust
• byscenario = TRUE uses cluster type = FORK on Unix-like machine
• tweaks to c.estimatetables and c.selectedstatistics()
• run.scenarios() fitarg start may be NULL (dodges binomial problem with "true")
• onAttach() options (matprod = "internal")

secrdesign 2.8.2 (2023-03-10)

New features or changed behaviour of old functions

• none

Other

• example time reduced for CRAN

secrdesign 2.8.1

New features or changed behaviour of old functions

• fit option 'design' (assumes detection model cf Fewster & Buckland 2004)
• estimateArray() and estimateSummary() new functions

Other

• summary field 'var'

secrdesign 2.8.0 (2023-01-18)

New features or changed behaviour of old functions

• run.scenarios() fit.function may be "ipsecr.fit"
• run.scenarios() acquires argument 'CH.function'
• functions to combine output from different executions of run.scenarios() (methods c, rbind for estimatetables, selectedstatistics)

Other

• suggests ipsecr
• schematic figure in help page ?secrdesign
• revised help page ?run.scenarios
• run.scenarios() sets RCPP_PARALLEL_NUM_THREADS if ncores provided

secrdesign 2.7.0 (2022-12-03)

New features or changed behaviour of old functions

• GAoptim() optimization by genetic algorithm using min(n,r) criterion (Durbach et al. 2021) and others
• minnrRSE() accepts GAoptim() output
• En2() and Qpm() for additional optimization criteria
• run.scenarios() option to create trapset dynamically with function(s)
• run.scenarios() compatible with dynamic density function in pop.args

Bugs fixed

• run.scenarios() failed with grouped scenarios if maskindex not specified

Other

• on GitHub
• added tests
• exports internal functions GApenfn() and compactSample()
• make.scenarios allows single-level 'groups'
• check for consistent traps etc. across groups within scenario
• parallel clusters not used by run.scenarios() if fit = FALSE
• shift to Rcpp, RcppArmadillo from C
• summaryScenarios() ncores defaults to 1 (usually faster than >1)

secrdesign 2.6.0 (2022-01-25)

New features or changed behaviour of old functions

• run.scenarios() 'fit' option uses multithreading capability of secr
• run.scenarios() 'ncores' defaults to NULL (then uses value of environment variable RCPP_PARALLEL_NUM_THREADS set by setNumThreads())
• run.scenarios() 'byscenario' defaults to FALSE

Bugs fixed

• Enrm() expected movement could fail when some of mask far from detectors

Other

• removed openCR options and imports (deprecated from 2.5.8)
• initial value of RCPP_PARALLEL_NUM_THREADS (usually 2) is set by secr onload
• depends R (>= 3.5.0), secr (>= 4.2.0)

secrdesign 2.5.11 (2020-04-10)

New features or changed behaviour of old functions

• none

Bugs fixed

• run.scenarios() default extractfn (no model fitted) mistake in RSEp approximation

secrdesign 2.5.10 (2020-01-31)

New features or changed behaviour of old functions

• run.scenarios() default extractfn (no model fitted) uses RSEp approximation of Efford & Boulanger 2019

Bugs fixed

• optimalSpacing() with simulations, fit.function = "openCR.fit" and nrepeats>1 miscalculated RB(D-hat)
• summary.selectedstatistics() failed when run.scenarios() pop.args included poly
• header() stumbled on non-numeric (covariate) specification of D
• run.scenarios() spurious warning for non-numeric D

Bug not fixed (see Other

• With fit.function 'openCR.fit', the calculation of RB(D-hat) in summarized simulations does not reflect nrepeats>1

Other

• fit.function 'openCR.fit' is deprecated, and will be removed in a later version; secr.fit is now fast enough
• optimalSpacing() catches bad root finding when limits inappropriate
• optimalSpacing() only passes valid fit.args to run.scenarios
• force ncores = 1 when fitting model (internal function processCH)

secrdesign 2.5.7 (2019-02-04)

New features or changed behaviour of old functions

• none

Bugs fixed

• count.summary() failed with fit.function = "openCR.fit"

secrdesign 2.5.6 (2019-01-26)

New features or changed behaviour of old functions

• make.scenarios() allows uniform (detectfn = 4)
• count and predict methods for simulation objects inheriting from 'summary'
• select.stats() respects count statistics

Bugs fixed

• plot.optimalSpacing() failed if any values missing (NA)
• optimalSpacing() did not apply nrepeats when computing binomial rotRSE
• scenarioSummary() failed with single-detector arrays

Other

• vignette removed (had been re-introduced by mistake in 2.5.5) (see www.otago.ac.nz/density/pdfs)

secrdesign 2.5.5 (2018-12-07)

New features or changed behaviour of old functions

• optimalSpacing() new argument 'fit.function' to select openCR.fit/secr.fit
• optimalSpacing() new argument 'distribution'
• optimalSpacing() adjusts rotRSE for binomial distribution of n
• plot.optimalSpacing() does not plot optimum
• summarySpacing() calculates detectors per home range

Bugs fixed

• run.scenarios() tripped up on multi-session simulation
• summaryScenarios() mostly ignored nrepeats

Other

• imports from openCR

secrdesign 2.5.4 (2017-12-04)

New features or changed behaviour of old functions

• none

Other

• vignette secrdesign-vignette.pdf removed (see www.otago.ac.nz/density/pdfs)

secrdesign 2.5.3 (2017-12-03)

New features or changed behaviour of old functions

• saturation() new function for expected detector saturation (trap success)
• scenarioSummary() reports average expected detector saturation
• derived.SL() and regionN.SL() replaced by methods for generic functions derived and region.N (see 'secr')

Bugs fixed

• Enrm() etc. detectfn 'HAN' and 'HCG' failed

Other

• tweak to select.stats to allow parameters without true value in scenarios
• depends on secr >= 3.1.2

secrdesign 2.5.2 (2017-10-10)

Other

• vignettes secrdesign-Enrm.pdf and secrdesign-tools.pdf removed (see www.otago.ac.nz/density/pdfs)

secrdesign 2.5.0 (2017-10-05)

New features or changed behaviour of old functions

• functions Lambda(), Enrm(), minnrRSE(), costing(), getdetectpar() and optimalSpacing()
• new function scenarioSummary() reports deterministic summary of scenarios (e.g., expected number of individuals, costings)
• run.scenarios() and fit.models() acquire argument byscenario (parallel scenarios or replicates?)
• fit.models() mask may be passed as component of fit.args, when it has priority over maskset
• run.scenarios() user may specify different masks as core in pop.args

Bugs fixed

• run.scenarios() ignored Nmark detection argument
• chatnsim lost if multiple scenarios
• nrepeats was ignored when method = 'none'

Other

• more robust outputtype when no results
• packageType message if pre-release
• persistent problems in header() for non-scalar arguments

secrdesign 2.4.1

New features or changed behaviour of old functions

• rule-of-thumb RSE added to default extractfn when fit = F
• validate() acquires argument 'quietly'
• detectpar list may be specified in det.args (overrides scenario)

Bugs fixed

• summary.selectedstatistics() failed when type = 'array'

Other

• all array dimensions now named in output of summary.selectedstatistics()

secrdesign 2.4.0 (2016-04-24)

New features or changed behaviour of old functions

• mark-resight data are simulated with secr::sim.resight if traps object has markocc attribute
• run.scenarios() new argument chatnsim for simulating overdispersion of sightings
• header() allows for complex 'details' and 'start' components
• validate reports number of problem rows

Bugs fixed

• header() failed with model2D="IHP" (problem in argdf - temporary fix)
• run.scenarios() respects detectpar component of det.args (see makeCH)

Other

• number of occasions in markocc overrides noccasions in scenario
• internally streamlined use of multiple cpu (no unnecessary export)
• select.stats() failed with parameter not 'D'
• run.scenarios() uses message instead of cat

secrdesign 2.3.1

New features or changed behaviour of old functions

• scenariosFromStatistics() new function to generate scenarios with specified number of first captures and recaptures.
• improved output header for fit.args etc.

secrdesign 2.3.0 (2015-03-27)

New features or changed behaviour of old functions

• fit.models() acquires arguments 'scen' and 'repl' to select a subset of rawdata
• run.scenarios() and fit.models() when predict.secr returns a list the default extractfn selects first session or group, with a warning (previously crashed)
• summary.selectedstatistics() has improved labelling of output
• select.stats() acquires argument 'true' for user override of 'true' values

Bugs fixed

• fit.models() did not work with grouped populations
• default extractfn failed when no detections and fit = FALSE
• run.scenarios() dots argument (...) not passed to worker processes

Other

• more robust handling of start values for secr.fit()

secrdesign 2.2.2 (2015-01-11)

Other

• CITATION file uses package metadata

secrdesign 2.2.1 (2014-11-27)

New features or changed behaviour of old functions

• run.scenarios() allows value "linear" for model2D argument of sim.popn
• details 'userdist' argument suppressed when printing summaries
• make.scenarios() optionally generates scenarios with group structure (e.g. males and females)
• run.scenarios() simulates composite (grouped) populations

Bugs fixed

• validate() did not catch NaN values

Other

• attribute 'regionarea' renamed 'regionsize' to cover linear case
• workflow figure dropped from secrdesign-package.Rd (see vignette)
• argument order changed in summary.selectedstatistics
• default extractfn checks for non-null 'fit' of returned secr object

secrdesign 2.1.3 (2014-06-04)

• vignette renamed and edited
• vignette source code included

secrdesign 2.1.2 (2014-05-02)

New features or changed behaviour of old functions

• validate() function to set out-of-range values to NA
• min, max as fields in summary.selectedstatistics
• secrdesign.pdf vignette
• header in summary output now includes pop.args
• run.scenarios() allows IHP population simulation as alternative to specifying uniform density

Bugs fixed

• maskset was not saved when specified in run.scenarios()