
CHANGES in 0.2.6 (2022-05-05)

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

CHANGES in 0.2.5 (2022-04-20)

  * 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.

CHANGES in 0.2.3 (2021-05-16)

  * 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.

CHANGES in 0.2.2 (2020-10-26)

  * Removed insecure URL.

CHANGES in 0.2.1 (2020-10-24)

  * 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.

CHANGES in 0.2.0 (2020-06-05)

  * 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.

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 `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.

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.
