v1.1.0

.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -37,3 +37,4 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+.Rproj.user

DESCRIPTION

@@ -1,24 +1,31 @@
 Package: paleopop
 Type: Package
-Title: Toolset for Coupled Niche-population Paleo-climatic Models
-Version: 1.0.0
+Title: Pattern-oriented Modelling Framework for Coupled Niche-population Paleo-climatic Models
+Version: 1.1.0
 Author: Global Ecology Lab
 Maintainer: Sean Haythorne <[email protected]>
-Description: The toolset provides a collection of interoperable R6 classes for simulating multiple
-    spatially-explicit demographic-based population models that utilize paleo-climatic niche model 
-    data. Included are classes for building population models and associated models for representing 
-    niche carrying capacities (derived from paleo-climatic niche models), spatial dispersal, and 
-    human density (for impact/harvesting functionality). A Latin hypercube sampling tool is provided 
-    to generate sampled parameters for multiple model simulations. A multi-simulation manager tool 
-    is provided to run and log simulations, with the assistance of model generator and simulator 
-    classes, and to collect simulation results. The toolset utilizes a hierarchy of class 
-    inheritance, with additional abstract classes being defined with reusable attributes and 
-    methods.
+Description: This pattern-oriented modelling (POM) framework provides a collection of 
+    interoperable R6 classes for simulating multiple spatially-explicit demographic-based
+    population models that utilize paleo-climatic niche model data, and for selecting the
+    simulation models that best fit observed data via an Approximate Bayesian Analysis
+    (ABC) validation method.
+    Included are classes for building population models and associated generative models
+    for representing niche carrying capacities (derived from paleo-climatic niche models),
+    spatial dispersal, and human density (for impact/harvesting functionality). A Latin
+    hypercube sampling class is provided to generate sampled parameters for multiple model
+    simulations. A multi-simulation manager class is provided to run and log simulations,
+    and to collect simulation results. A simulator class is provided to wrap a simulation
+    function, the default being the paleopop simulation function, which is optimized for
+    single-generation transitions and large populations. Finally, classes for collating
+    results into summary metrics and for running ABC validation and model selection are 
+    provided. The framework utilizes a hierarchy of class inheritance, with additional 
+    abstract classes being defined with reusable attributes and methods.
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.0.2
 Imports:
+    abc (>= 2.1),
     doParallel (>= 1.0.14),
     foreach (>= 1.4.4),
     gdistance (>= 1.2.2),
@@ -27,4 +34,30 @@ Imports:
     metRology (>= 0.9.28.1),
     R6 (>= 2.4.0),
     raster (>= 2.8.19),
-    sf (>= 0.7.7)
+    sf (>= 0.7.7),
+    trend (>= 1.1.1)
+Collate: 
+    'GenericClass.R'
+    'GenericModel.R'
+    'AbcValidationModel.R'
+    'BarrierSeaIceModel.R'
+    'CorrelationModel.R'
+    'GenerativeTemplate.R'
+    'DispersalTemplate.R'
+    'GenerativeModel.R'
+    'DispersalModel.R'
+    'HumanDensityTemplate.R'
+    'HumanDensityModel.R'
+    'NicheCarryingCapacityTemplate.R'
+    'NicheCarryingCapacityModel.R'
+    'GenericResultsManager.R'
+    'GenericResultsModel.R'
+    'LatinHypercubeSampler.R'
+    'PopulationModel.R'
+    'PopulationSimulator.R'
+    'MultiSimulationManager.R'
+    'PaleoPopModel.R'
+    'PaleoPopResultsModel.R'
+    'ResultsSummaryManager.R'
+    'paleopop_simulator.R'
+    'region_subset.R'

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(AbcValidationModel)
+export(BarrierSeaIceModel)
+export(CorrelationModel)
+export(DispersalModel)
+export(DispersalTemplate)
+export(GenerativeModel)
+export(GenerativeTemplate)
+export(GenericClass)
+export(GenericModel)
+export(GenericResultsManager)
+export(GenericResultsModel)
+export(HumanDensityModel)
+export(HumanDensityTemplate)
+export(LatinHypercubeSampler)
+export(MultiSimulationManager)
+export(NicheCarryingCapacityModel)
+export(NicheCarryingCapacityTemplate)
+export(PaleoPopModel)
+export(PaleoPopResultsModel)
+export(PopulationModel)
+export(PopulationSimulator)
+export(ResultsSummaryManager)
+export(paleopop_simulator)
+export(region_subset)
+importFrom(R6,R6Class)
+importFrom(foreach,"%dopar%")
+importFrom(foreach,foreach)