version 0.2.1 (2022-11-30) -- Add dcatState1Alive1Dead(), dcatState1Alive2Dead(), and dcatState2Alive2Dead() to sample state transition based on spatial probabilities. -- Add sampler_categorical_general() to allow the addition of categorical samplers -- Add calculateDensity() to calculate the density of individual in each habitat cell. -- fix bug in the registration of dbernppDetection_normal(). version 0.2.0 (2022-08-31) -- removed deprecated functions: dbinom_sparseLocalSCR and getLocalTraps -- fix bug in getLocalTraps() with newest version of R 4.2.1 -- fix bug in getSparseY() when max number of detections per id is 1. -- fix bug in dbernppLocalACmovement_exp() when resizeFactor >1. -- added a point process wolverine vignette. -- added a dmultiLocal_normal() to allow multi-catch SCR -- added dbinomLocal_normalPlateau() and dbinomLocal_exp() to simulate and fit binomial SCR data with half-normal plateau and exponential detection functions, respectively. -- added function to compute home range radius and area from custom detection functions: getHomeRangeArea() -- added a vignette describing how to use dbinomLocal_normalPlateau() (to simulate and fit SCR models) and to compute home range radius and area using different detection functions: Fit_with_dbinomLocal_normalPlateau_and_HomeRangeAreaComputation.rmd version 0.1.3 (2021-10-22) -- added point process distribution functions: Density: dbernppAC; dpoisppAC.R Movement/density: dbernppACmovement_normal.R; dbernppACmovement_exp.R Movement/density (LocalVersion): dbernppLocalACmovement_normal.R; dbernppLocalACmovement_exp.R Detection: dbernppDetection_normal.R; dpoisppDetection_normal.R Detection (LocalVersion): dbernppLocalDetection _normal.R; dpoisppLocalDetection_normal.R Normalizing constant for Semi-likelihood: dnormalizer.R -- added point process functions used internally in the distribution function (calcWindowSizes; getWindowIndex; integrateIntensityLocal_normal; integrateIntensityLocal_exp; integrateIntensity_normal; integrateIntensity_exp; stratRejectionSampler_normal; stratRejectionSampler_exp; makeConstantNimbleFunction; marginalVoidProbIntegrand) -- added function to do the numerical integration of the marginal void probability: marginalVoidProbNumIntegration() -- added function to obtain lower and upper habitat coordinates and the habitat grid to do the fast look-up of cell id from x and y coordinates: getWindowCoords. -- added function to obtain midpoint nodes coordinates for numerical integration : getMidPointNodes -- added a vignette describing how to use the point process functions: Point_Process.Rmd version 0.1.2 (2021-07-01) -- added extra arguments for the dbinomLocal_normal() function so it can also model trap covariates on p0. -- added dpoisLocal_normal(), and the possibility to model trap covariates on lambda. -- added the ‘r’ version dbinomLocal_normal() and dpoisLocal_normal() function to simulate SCR data. -- added the possibility to use getSparseY() to merge all information about individual detections in one single vector, instead of 3 separate objects (necessary when using the “r” version of dbinomLocal_normal() and dpoisLocal_normal()). -- added Soumen Dey as an author. -- moved wolverine vignette in the package. Added the wolverine dataset in the package (in the testthat folder). The working directory to load the wolverine data is based on ‘Sys.info()['user']’ (same as we do in makePackage.R). -- created a vignette describing how to use nimble and dbinomLocal_normal() to simulate and fit SCR models. -- fixed bug in scaleCoordsToHabitatGrid when scaleToGrid=F. -- fixed typo in scaleCoordsToHabitatGrid and getSparseY. -- added unit-testing using the testthat package: - tested UtilityFunctions (getSparseY, scaleCoordsToHabitatGrid,getLocalObjects). - tested dbinomLocal_normal (Make sure we obtain the same model$calculate() than reported in Daniel’s paper for the wolverine example, simulate and fit binomial SCR data with a nimble model and check that estimates are ‘close’ to the simulated ones). - tested dpoisLocal_normal (simulate and fit poisson SCR data with a nimble model and check that estimates are ‘close’ to the simulated ones). version 0.1.1 (2021-01-07) -- getLocalTraps(): added a check (return an error) so that we make sure that the ‘dmax’ value we picked is large enough so that an AC location located far away in the buffer still has a chance of being detected with the local detectirs. Basically all habitat cell center should have >0 one “local” trap. This function is deprecated and getLocalObjects() should be used instead. I added a “deprecated” warning message that appears when running the function. -- Added a new function to replace getLocalTraps() now called getLocalObjects(). -- dbinom_sparseLocalSCR(): Some internal changes where we don’t fully re-construct the y and gain in efficiency. dbinom_sparseLocalSCR(): function is deprecated and dbinomLocal_normal() should be used instead. I couldn’t add a deprecated message for the nimble function. So the warnings about the deprecated functions are printed when loading the package by adding a packageStartupMessage() in the zzz.R file. -- Added a new function to replace dbinom_sparseLocalSCR(), now called dbinomLocal_normal (). -- Added a scaleCoordsToHabitatGrid() function. Rescale the coordinates is necessary to run all our functions (i.e. fast habitat cell lookup. I guess we should do a proper vignette on this). I added credits to Mike Meredith for this technique in the description of the function. It can take as input up to 5 dimensions (5 should be enough for now) array of coordinates and scale it to the grid or rescale it back to its original coordinate with the argument “scaleToGrid = F”. It requires the dimnames (“x” and “y”) to be specified but x and y can be in any dimension of the array (useful as posterior x and y coordinates are not always on the same dimensions depending on open-pop, and indexing the user is using…). -- Adjusted the wolverine vignette with the use of the new functions . -- Added in the description file that it is now: -- Corrected a few typos here and there.