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CHANGES in 0.2.3.9008 (2022-02-25)
* Fixed warnings when no animals detected in `simOcc` and `simOccCat`.
CHANGES in 0.2.3.9007 (2022-02-25)
* Additional plots in `simOccCat`.
CHANGES in 0.2.3.9006 (2022-02-21)
* New function `simOccCat` added.
CHANGES in 0.2.3.9005 (2022-02-20)
* New function `simIDS` added.
CHANGES in 0.2.3.9004 (2022-02-19)
* Tweaks to plots in `simHDSpoint`: histogram now includes undetected individuals.
CHANGES in 0.2.3.9003 (2022-02-18)
* Tweaks to `simHDSpoint`: changed default for `beta.sig`; use `base::pi` instead of `pi`.
* Output from `simHDSpoint` now includes counts of individuals detected at each site.
CHANGES in 0.2.3.9002 (2022-02-17)
* New function `simHDSpoint` added, a simplified version of `simHDS(type="point",...)`.
CHANGES in 0.2.3.9001 (2022-02-05)
* Description and contents (in AHMbook-package.Rd) modified to allow inclusion of simulation functions not in the books.
CHANGES in 0.2.3.9000 (2021-11-14)
* `simComm` now includes the simulated covariates `habitatat` and `wind` in the output.
ROLL-UP to 0.2.3 (2021-05-16)
* The stop-gap function `modSelFP` is defunct as `unmarked::modSel` now works for FP models.
CHANGES in 0.2.2.9002 (2021-05-14)
* Fixed "data length differs..." warning in zinit.Rd Examples; see Ripley's email 2021-05-13.
* Updated URL for SwissMarbledWhite data set.
CHANGES in 0.2.2.9001 (2020-11-25)
* Minor corrections to help files.
CHANGES in 0.2.2.9000 (2020-11-09)
* Additional information added to the Descriptions of `simHDS*` functions.
CHANGES in 0.2.2 (2020-10-26)
* Removed insecure URL.
ROLL-UP to 0.2.1
CHANGES in 0.2.0.9008 (2020-10-17)
* Changed publication date of AHM2 to 2021 everywhere in help files.
CHANGES in 0.2.0.9007 (2020-10-08)
* `simDSM` now returns `Ucap`, needed for plotting.
CHANGES in 0.2.0.9006 (2020-07-16)
* Corrected note about RNGkind for `simNmixSpatial` and `simOccSpatial`.
CHANGES in 0.2.0.9005 (2020-07-13)
* Added note about RNGkind to `sim*` functions using `sample`.
CHANGES in 0.2.0.9004 (2020-06-18)
* Added data wrangling code to `SwissMarbledWhite` data set.
CHANGES in 0.2.0.9003 (2020-06-16)
* Added check for plotting error to all `sim*` functions.
* Functions `simDynoccSpatial`, `simPPe` and `simSpatialDSline` get a `show.plots` argument.
CHANGES in 0.2.0.9002 (2020-06-15)
* Added check for plotting error to `simDM`. Thanks to Jonathan Cohen for reporting this.
CHANGES in 0.2.0.9001 (2020-06-13)
* Added `simFrogDisease` function.
CHANGES in 0.1.4.9114 (2020-06-05)
* Corrected section numbers on main help page.
CHANGES in 0.1.4.9113 (2020-06-05)
* 'e2dist' will now accept length 2 vector for coordinates of a single point.
CHANGES in 0.1.4.9112 (2020-06-01)
* Updated COPYRIGHTS file and dtc fields.
CHANGES in 0.1.4.9111 (2020-05-31)
* Removed commented-out code from several *.R files.
* Replace 'F' with 'FALSE' throughout.
* 'e2dist' now has default 'y = NULL', when y <- x.
CHANGES in 0.1.4.9110 (2020-05-31)
* Tidied up Authors@R and corresponding changes to help files.
* Added inst/COPYRIGHTS file.
CHANGES in 0.1.4.9109 (2020-05-30)
* Revised Authors@R, added URLs.
CHANGES in 0.1.4.9108 (2020-05-29)
* Checked Examples for compliance with CRAN requirements.
CHANGES in 0.1.4.9107 (2020-05-29)
* Functions 'playRN', 'sim3occ', 'simDCM', 'simDynoccSpatial', 'simNmixSpatial', 'simNmix', 'simOccSpatial', 'simOccttd' and 'wigglyOcc' gain a 'verbose' argument; if FALSE, Console output is suppressed.
CHANGES in 0.1.4.9106 (2020-05-29)
* Spell check; changed instances of GB usage to US.
CHANGES in 0.1.4.9105 (2020-05-23)
* Added contributors to the DESCRIPTION file.
CHANGES in 0.1.4.9104 (2020-04-30)
* Added 'U' to the output of 'simDSM'.
CHANGES in 0.1.4.9103 (2020-04-27)
* Fixed bug in 'simDSM' with 1 survey.
CHANGES in 0.1.4.9102 (2020-04-27)
* Added note about 'sample.kind="Rounding"' to all simulation functions affected.
CHANGES in 0.1.4.9101 (2020-04-27)
* Corrections to help file for 'simDSM'.
CHANGES in 0.1.4.9100 (2020-04-25)
* Tweaked argument and output names for 'simDSM'.
CHANGES in 0.1.4.9099 (2020-04-25)
* Added 'N.pix' to the output of 'simDSM'.
CHANGES in 0.1.4.9098 (2020-04-25)
* Added 'simDSM' function.
CHANGES in 0.1.4.9097 (2020-04-03)
* Fixed bug in helper function 'histCount' to deal properly with large counts.
CHANGES in 0.1.4.9096 (2020-02-03)
* Fixed typo in 'simCJS'
* Updated README.md file
CHANGES in 0.1.4.9095 (2020-01-10)
* Update Title and Description in DESCRIPTION.
* Clean up References sections: chronological order, AHM1/2 with sections.
CHANGES in 0.1.4.9094 (2020-01-09)
* Rename functions 'sim.spatialDSline' and 'sim.spatialDSte' to 'simSpatial*'.
CHANGES in 0.1.4.9093 (2020-01-09)
* Corrections to help files from Andy.
CHANGES in 0.1.4.9092 (2020-01-08)
* Corrections to help files from Marc.
CHANGES in 0.1.4.9091 (2019-12-29)
* Fixed help page for 'crPiFun' and friends, added examples.
CHANGES in 0.1.4.9090 (2019-09-20)
* Increased top and bottom margins of raster plot in 'simExpCorrRF'.
CHANGES in 0.1.4.9089 (2019-08-16)
* Added plots to 'simDM0'.
CHANGES in 0.1.4.9088 (2019-07-26)
* Updated README.md file, added badges.
CHANGES in 0.1.4.9087 (2019-07-25)
* 'wigglyOcc' now returns 'x.index' and 'p.ordered', needed for plots on p.AHM1/623.
CHANGES in 0.1.4.9086 (2019-07-21)
* Changes to file names only, no change to contents. All 'sim*' files now begin with 'sim' followed by an uppercase letter (exception 'sim3Occ'). Sort order should now be the same on case-sensitive systems (eg, Github) and on Windows.
CHANGES in 0.1.4.9085 (2019-07-20)
* Chapter numbering corrected in help pages and in comments in R files; no changes to code. Not yet done in file names.
CHANGES in 0.1.4.9084 (2019-07-15)
* In 'simExpCorrRF', changes to flip the plot; 'field' output is now vector, not matrix.
CHANGES in 0.1.4.9083 (2019-07-12)
* 'image_scale' gets 'cex.legend' argument.
CHANGES in 0.1.4.9082 (2019-07-07)
* Added 'wigglyLine' data set.
CHANGES in 0.1.4.9081 (2019-07-03)
* In 'simDynoccSpatial': argument 'expo.range.XAC' renamed 'theta.XAC'.
CHANGES in 0.1.4.9080 (2019-06-27)
* Additional elements from 'BerneseOberland' data set incorporated in the output of
'simNmixSpatial' and 'simOccSpatial'.
CHANGES in 0.1.4.9079 (2019-06-15)
* Replaced 'EurasianLynx' with 'EL2', coordinates named 'xcoord' and 'ycoord'.
CHANGES in 0.1.4.9078 (2019-06-15) - not pushed to Github
* Added 'EL2' data set; similar to 'EurasianLynx' but different row order;
includes x, y and forest covariates.
CHANGES in 0.1.4.9077 (2019-06-14)
* Added 'simOccSpatial' function.
CHANGES in 0.1.4.9076 (2019-06-14)
* Added 'simNmixSpatial' function.
CHANGES in 0.1.4.9074 (2019-06-12)
* Added 'simExpCorrRF' function.
CHANGES in 0.1.4.9073 (2019-06-09)
* Changed variable name 'northness' to 'north' in 'SwissAtlasHa' data set.
CHANGES in 0.1.4.9072 (2019-06-06)
* Added 'MesoCarnivores' data set.
CHANGES in 0.1.4.9071 (2019-06-03)
* 'getLVcorrMat' and 'getEcorrMat' return the MCMC chains if stat=NULL.
CHANGES in 0.1.4.9070 (2019-06-01)
* Added 'getEcorrMat' function.
CHANGES in 0.1.4.9069 (2019-05-31)
* Shorter species names for 'SwissAtlasHa' data set.
CHANGES in 0.1.4.9068 (2019-05-30)
* Tweaks to 'getLVcorrMat' function.
CHANGES in 0.1.4.9067 (2019-05-29)
* Added 'getLVcorrMat' function.
CHANGES in 0.1.4.9066 (2019-05-26)
* Tweaks to 'treeSparrow' data set, 'sim.spatialDSte' and help pages.
CHANGES in 0.1.4.9065 (2019-05-25)
* Added 'treeSparrow' data set.
CHANGES in 0.1.4.9064 (2019-05-20)
* Tweaks to 'sim.spatialDSte' and 'simPPe'.
CHANGES in 0.1.4.9063 (2019-05-20)
* Tweaks to 'sim.spatialDSte'.
CHANGES in 0.1.4.9062 (2019-05-18)
* 'simDynoccSpatial' gets input checks.
* Removed 'spatial.exp' function.
CHANGES in 0.1.4.9061 (2019-05-17)
* Added 'simDynoccSpatial' function.
CHANGES in 0.1.4.9060 (2019-05-14)
* Added SwissAtlasHa data set.
CHANGES in 0.1.4.9059 (2019-05-14)
* Added Hubbard Brook warbler data set.
CHANGES in 0.1.4.9058 (2019-05-13)
* changes to the way authors are included in DESCRIPTION file (so we can spell
Marc's name correctly).
CHANGES in 0.1.4.9057 (2019-04-29)
* 'simDataDK2' renamed 'simDataDK'; the old 'simDataDK' with 1-per-pixel limit
becomes 'simDataDK1'.
CHANGES in 0.1.4.9056 (2019-04-28)
* Changed plot titles for simDataDK*.
CHANGES in 0.1.4.9055 (2019-04-25)
* Correct correction to data set!
CHANGES in 0.1.4.9054 (2019-04-25)
* Correction to data set.
CHANGES in 0.1.4.9053 (2019-04-24)
* 'sim.spatialDSte' gets plots and input checks.
CHANGES in 0.1.4.9052 (2019-04-23)
* Added 'sim.spatialDSte'.
* Small bug fixes.
CHANGES in 0.1.4.9051 (2019-04-14)
* Fixed plots not cleaned up after 'data.fn', 'simPPe', 'sim.spatialDS', 'sim.spatialDSline' and 'spatial.exp'.
CHANGES in 0.1.4.9050 (2019-04-13)
* Added color ramps 'rampYOR', 'rampGreens', 'rampGreys', 'rampBYR', 'rampGBr'.
CHANGES in 0.1.4.9049 (2019-04-12)
* 'N' changed to 'n' in 'simPH'.
CHANGES in 0.1.4.9048 (2019-04-12)
* Small changes to plots in 'simDCM', 'simNpC' and 'graphSSM'; no change in numeric output.
CHANGES in 0.1.4.9047 (2019-04-08)
* Added 'sim.spatialDSline' function.
* Add '.onAttach' function to show version number.
CHANGES in 0.1.4.9046 (2019-04-08)
* Change to output in 'simDataDK*' functions.
CHANGES in 0.1.4.9045 (2019-04-07)
* Change to argument name 'npix' -> 'sqrt.npix' in 'simDataDK*' functions.
CHANGES in 0.1.4.9044 (2019-04-06)
* Added 'simDataDK2' function.
CHANGES in 0.1.4.9043 (2019-04-04)
* Changes to output of 'simDataDK' function.
CHANGES in 0.1.4.9042 (2019-04-04)
* Informative error messages for 'simDataDK' function.
CHANGES in 0.1.4.9041 (2019-04-03)
* Added 'simDataDK' function.
CHANGES in 0.1.4.9040 (2019-04-02)
* Tweaks to 'simPPe' function plots, SwissEagleOwls, more input checks.
CHANGES in 0.1.4.9039 (2019-04-01)
* Tweaks to 'simPPe' function plots.
CHANGES in 0.1.4.9038 (2019-03-31)
* Added 'simPPe' function.
CHANGES in 0.1.4.9037 (2019-03-23)
* Added 'simMultMix' function.
CHANGES in 0.1.4.9036 (2019-03-22)
* Corrected spelling of "Hierarachical" -> "Hierarchical" in 43 help files.
CHANGES in 0.1.4.9035 (2019-03-22)
* Changed 'valid_data' to use Mike Meredith's code.
CHANGES in 0.1.4.9034 (2019-03-21)
* Added 'EurasianLynx' data set.
* Added 'valid_data' function.
CHANGES in 0.1.4.9033 (2019-03-20)
* Added 'waterVoles' data set.
* Added 'modSelFP' function.
CHANGES in 0.1.4.9032 (2019-03-11)
* Added sanity checks to all sim* functions, incl. vol 1.
CHANGES in 0.1.4.9031 (2019-03-05)
* Eliminated use of par(no.readonly = TRUE).
CHANGES in 0.1.4.9030 (2019-03-04)
* Argument names 'nsite', 'nyear', 'nsurvey', 'nvisit' changed to plural ('nsites', etc)
for vol 1 functions.
* Argument name 'nrep' changed to plural, 'nreps', and 'nspec' changed to 'nspecies'.
CHANGES in 0.1.4.9029 (2019-03-04)
* Argument names 'nsite', 'nyear', 'nsurvey', 'nvisit' changed to plural ('nsites', etc)
for vol 2 functions.
CHANGES in 0.1.4.9028 (2019-03-01)
* Additional arguments to 'smDynocc'.
CHANGES in 0.1.4.9027 (2019-02-05)
* Pernickerty test removed from 'simDynocc' (sadly!)
CHANGES in 0.1.4.9026 (2019-01-23)
* Added duskySalamanders data set.
CHANGES in 0.1.4.9025 (2019-01-20)
* Small changes to SwissEagleOwls data set.
CHANGES in 0.1.4.9024 (2019-01-20)
* Better messages from 'stopifnot' when NAs are allowed.
* 'simDynocc' plots now have a vertical line at year of impact.
CHANGES in 0.1.4.9023 (2019-01-16)
* Corrected NAs in cswa data set.
CHANGES in 0.1.4.9022 (2019-01-15)
* Added 'simDM0' and 'simDM' functions.
* Modified SwissEagleOwls data set.
CHANGES in 0.1.4.9021 (2019-01-14)
* Added cswa (Chestnut-sided Warbler) data set.
* Improved 'fitstats' to cope with NAs in the data.
CHANGES in 0.1.4.9020 (2019-01-13)
* Added greenWoodpecker data set.
CHANGES in 0.1.4.9019 (2019-01-12)
* Added SwissEagleOwls data set.
* Updated 'simDCM' function with new argument names.
CHANGES in 0.1.4.9018 (2018-12-22)
* Changes to plots to make them color-blind-friendly.
CHANGES in 0.1.4.9017 (2018-12-21)
* Corrections to 'FrenchPeregrines' data set.
CHANGES in 0.1.4.9016 (2018-12-21)
* Function 'simDemoDynocc' added.
CHANGES in 0.1.4.9015 (2018-12-21)
* 'crossbillAHM' data set added.
CHANGES in 0.1.4.9014 (2018-12-18)
* 'SwissMarbledWhite' data set added.
CHANGES in 0.1.4.9013 (2018-12-17)
* 'FrenchPeregrines' data set added.
CHANGES in 0.1.4.9012 (2018-12-14)
* 'middleSpottedWoodpecker' data set renamed to 'spottedWoodpecker'.
CHANGES in 0.1.4.9011 (2018-12-12)
* Changes to file names so data files begin 'data' and simulation functions begin 'sim...'.
* Restore settings and input checks changed in some code files.
CHANGES in 0.1.4.9010 (2018-12-11)
* Added middleSpottedWoodpecker data set.
* Moved unmarked from Depends to Imports.
CHANGES in 0.1.4.9009 (2018-12-10)
* Improved fixes and checks for input arguments for AHM2 functions
* Changed 'range' to 'trend' where appropriate in 'simDynocc'.
CHANGES in 0.1.4.9008 (2018-12-05)
* Updated simDynocc function.
* Added 'stopifnot*' functions.
CHANGES in 0.1.4.9007 (2018-12-03)
* Added 'zinit' function.
CHANGES in 0.1.4.9006 (2018-12-01)
* Fixed: NAs removed from 'forest' covariate in crestedTit
CHANGES in 0.1.4.9005 (2018-11-30)
* marbledWhite help page gets proper acknowledgement.
* simSSM renamed simPOP.
CHANGES in 0.1.4.9004 (2018-11-29)
* Fixed: graphSSM now restores graphics settings on exit.
* Fixed: in willowWarbler data, 1d arrays changed to vectors.
CHANGES in 0.1.4.9003 (2018-11-28)
* 'standardize' no longer adds attributes to output (causes problems with jagsUI).
* Added function 'standardize2match'.
CHANGES in 0.1.4.9002 (2018-11-26)
* Added new functions simPH, simNpC, simSSM (ne simpop), graphSSM (ne graph.ssm2), simCJS and ch2marray (ne marray).
* Added utility function 'standardize'.
* Updated main package help page
* Better Examples for crestedTit data set
CHANGES in 0.1.4.9001 (2018-11-22)
* Added help pages for 'crestedTit' and 'marbledWhite' data sets.
* Added 'willowWarbler' data set and documentation.
CHANGES in 0.1.4.9000 (2018-11-04)
* Added 'crestedTit' and 'marbledWhite' data sets, but not yet documented.
CHANGES in 0.1.4 (2017-05-19)
* New "logit" detection function added to sim.spatialDS function, which corresponds to the model fitted in unmarked::pcount.spDS v.0.12.2; old "hazard" detection function removed.
* Improvements to help pages and additional examples.
* Fixed: argument discard0 in simHDS now works as documented.
* Fixed: bugs in issj.sim which produced errors with argument values other than those in the book; tidied up ambiguity in help page with nsites and npoints; added example.
CHANGES in 0.1.3 (2017-04-20)
* Function pcount.spHDS and predict methods for unmarkedFit objects have moved to the unmarked package v.0.12; AHMbook now Depends on unmarked (>=0.12).
* Added the MHB2014, SwissSquirrels, SwissTits, Finnmark, ttdPeregrine and wagtail data sets; see the help pages for ways to use these instead of .csv files with the code in the book.
* Removed default arguments for the coordinates in map.Nmix.resi, making it more generally useful.
* Fixed: slew of warnings produced by simNmix, also dropping of dimensions with small numbers of individuals.
* Added more examples to the help pages for simulation functions.
CHANGES in 0.1.1 (2017-01-03)
* Full help pages for all functions.
* New names: plot.Nmix.resi -> plot_Nmix_resi and image.scale -> image_scale, to prevent clashes with R's 'plot' and 'image' generic functions.
* Fewer dependencies, and all checked when you load AHMbook: no more "there is no package called xxx" when you try to run a function.
* Changes to the "histograms" of counts, using transparent colours when two counts are plotted together.
* The dragonfly data have been tidied up; do data(dragonfly) before use.
* New functions for Volume 2: simDynocc and simDCM.
* The 'jay' dataset has moved to 'unmarked' package.
* Fixed: bugs involving 'logit'.
* Fixed: data.fn() now corresponds to the code in section 4.3.
* Fixed: simHDSg("point", ...), sim.spatialDS() and sim.spatialHDS() now work.
* Fixed: plotting functions now restore the settings of the graphics window on exit.
* Note: simComm("counts",...), simHDStr("point",...), and simHDSopen("point",...)
give slightly different results even with the same seed; all the other simulations
give the same values as before when set.seed() is used.