NEWS

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AHMbook 0.2.10 (2024-09-11)

• Remove plotrix from dependencies
• Move coda, fields, raster, sp, spdep to suggests

AHMbook 0.2.9 (2023-08-23)

• Ken Kellner takes over as Maintainer
• 'RandomFields' removed from suggests
• Old versions of 'simExpCorrRF', 'simDynoccSpatial', and 'simPPe' can be found in 'inst/RandomFieldsSupport'; see the corresponding help files for how to access these functions from within R.

AHMbook 0.2.8

• Bump version number.

AHMbook 0.2.7

• Andy Royle takes over as Maintainer.

AHMbook 0.2.6 (2022-06-14)

• 'RandomFields' moved to Suggests; when not available, use package 'fields' in functions 'simExpCorrRF', 'simDynoccSpatial' and 'simPPe'.

AHMbook 0.2.5 (2022-05-02)

• New functions added: 'simOccCat', 'simIDS', 'simHDSpoint' (an enhanced version of 'simHDS(type="point",...)').
• Description and contents (in AHMbook-package.Rd) modified to allow inclusion of simulation functions not in the books.
• Fixed: warnings when no animals detected in 'simOcc' and 'simOccCat' are now meaningful.
• Fixed: 'simComm' now includes the simulated covariates 'habitat' and 'wind' in the output.
• Fixed: 'pi' replaced with 'utils::pi' where appropriate.
• The stop-gap function 'modSelFP' has been removed, as 'unmarked::modSel' now works for FP models.

AHMbook 0.2.3 (2021-05-17)

• Fixed: "data length differs..." warning in zinit.Rd Examples (thanks to Prof Ripley's report).
• The stop-gap function 'modSelFP' is deprecated, as 'unmarked::modSel' now works for FP models.
• Updated URL for 'SwissMarbledWhite' data set.
• Minor corrections to help files.
• Additional information added to the Descriptions of 'simHDS*' functions.

AHMbook 0.2.2 (2020-10-26)

• Removed insecure URL.

AHMbook 0.2.1

• Changed publication date of AHM2 to 2021 everywhere in help files.
• 'simDSM' now returns 'Ucap', needed for plotting Fig.11.17 p.AHM2/710.
• Added data wrangling code to 'SwissMarbledWhite' help file.
• Added check for plotting error to all 'sim*' functions; numeric output is still produced even if plotting fails.
• Functions 'simDynoccSpatial', 'simPPe' and 'simSpatialDSline' get a 'show.plots' argument.
• Added 'simFrogDisease' function.

AHMbook 0.2.0 (2020-06-09)

• Added simulation functions for AHM vol 2: 'simNpc', 'simPOP', 'simPH', 'simDM0', 'simDM', 'simMultMix', 'simCJS', 'simDemoDynocc', 'simDM', 'simDynOccSpatial', 'simExpCorrRF', 'simOccSpatial', 'simNmixSpatial', 'simPPe', 'simDataDK', 'simSpatialDSline', 'simSpatialDSte', 'simDSM'.
• Added data sets for AHM vol 2: 'BerneseOberland', 'crestedTit', 'cswa', 'crossbillAHM', 'duskySalamanders', 'EurasianLynx', 'FrenchPeregrines', 'greenWoodpecker', 'HubbardBrook', 'MesoCarnivores', 'spottedWoodpecker', 'SwissAtlasHa', 'SwissEagleOwls', 'SwissMarbledWhite', 'treeSparrow', 'UKmarbledWhite', 'waterVoles', 'wigglyLine', 'willowWarbler'.
• Added utility functions: 'graphSSM', 'ch2marray', 'valid_data', 'modSelFP', 'getLVcorrMat', 'zinit', 'Color_Ramps', 'standardize', 'standardize2match'.
• 'e2dist' now has default 'y = NULL', when y <- x; now accepts length 2 vector for coordinates of a single point.
• Authors and contributors now listed as 'Authors@R' in DESCRIPTION file.
• Added inst/COPYRIGHTS file.
• Functions 'playRN', 'sim3occ', 'simNmix', 'simOccttd' and 'wigglyOcc' gain a 'verbose' argument; if FALSE, Console output is suppressed.
• Added note about 'sample.kind="Rounding"' to help files for all simulation functions affected.
• 'wigglyOcc' now returns 'x.index' and 'p.ordered', needed for plots on p.AHM1/623.
• 'image_scale' gets 'cex.legend' argument.
• Added input checks to all 'sim*' functions.
• Argument names 'nsite', 'nyear', 'nsurvey', 'nvisit', 'nrep', 'nspec' changed to plural ('nsites', etc) for all functions.
• Changes to plots to make them more color-blind friendly.
• Moved package 'unmarked' from Depends to Imports.

AHMbook 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.

AHMbook 0.1.3 (2017-04-20)

• Function 'count.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.

AHMbook 0.1.1

• 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.