Update documentation (#57)

* updated readme and links

* update function about information.

* updated multirun documentation

R/auto_manage.R

@@ -1,10 +1,9 @@
 #' PoPS (Pest or Pathogen Spread) automated management
 #'
-#' A dynamic species distribution model for pest or pathogen spread in forest
-#' or agricultural ecosystems. The model is process based meaning that it uses
-#' understanding of the effect of weather on reproduction and survival of the
-#' pest/pathogen in order to forecast spread of the pest/pathogen into the
-#' future.
+#' This function allows for treating multiple species with the same management
+#' strategy. Was designed for multiple lineages of the same species that share
+#' common hosts and are in the same study area. This functions loop straight
+#' through each stochastic realisation with the same treatment.
 #'
 #' @inheritParams pops
 #' @param infected_files file path to the infected species files for the start

R/auto_manage_nonsteering.R

@@ -1,10 +1,9 @@
 #' PoPS (Pest or Pathogen Spread) automated management
 #'
-#' A dynamic species distribution model for pest or pathogen spread in forest
-#' or agricultural ecosystems. The model is process based meaning that it uses
-#' understanding of the effect of weather on reproduction and survival of the
-#' pest/pathogen in order to forecastspread of the pest/pathogen into the
-#' future.
+#' This function allows for treating multiple species with the same management
+#' strategy. Was designed for multiple lineages of the same species that share
+#' common hosts and are in the same study area. This function is designed with
+#' computation steering based on Petrasova et al. (2020).
 #'
 #' @inheritParams pops
 #' @param infected_files file path to the infected species files for the start

R/pops.r

@@ -4,7 +4,9 @@
 #' or agricultural ecosystems. The model is process based meaning that it uses
 #' understanding of the effect of weather and other environmental factors on
 #' reproduction and survival of the pest/pathogen in order to forecast spread
-#' of the pest/pathogen into the future.
+#' of the pest/pathogen into the future. This function performs a single
+#' stochastic realisation of the model and is predmoninately used for automated
+#' tests.
 #'
 #' @param infected_file path to raster file with initial infections
 #' @param host_file path to raster files with number of hosts and standard

R/pops_multirun.R

@@ -1,10 +1,14 @@
 #' PoPS (Pest or Pathogen Spread) model Multiple Runs
 #'
-#' A dynamic species distribution model for pest or pathogen spread in forest or
-#'  agricultural ecosystems. The model is process based meaning that it uses
-#'  understanding of the effect of weather on reproduction and survival of the
-#' pest/pathogen in order to forecast spread of the pest/pathogen into the
-#' future.
+#' A dynamic species distribution model for pest or pathogen spread in forest
+#' or agricultural ecosystems. The model is process based meaning that it uses
+#' understanding of the effect of weather and other environmental factors on
+#' reproduction and survival of the pest/pathogen in order to forecast spread
+#' of the pest/pathogen into the future. Run multiple stochasitic simulations,
+#' propogating uncertainty in parameters, initial conditions, and drivers.
+#' The model is process based meaning that it uses understanding of the effect
+#' of weather on reproduction and survival of the pest/pathogen in order to
+#' forecast spread of the pest/pathogen into the future.
 #'
 #' @inheritParams pops
 #' @param number_of_iterations how many iterations do you want to run to allow

README.md

@@ -9,7 +9,9 @@
 
 ## Overview
 
-An R wrapper using RCPP for the [PoPS C++ library](https://github.com/ncsu-landscape-dynamics/PoPShttps://github.com/ncsu-landscape-dynamics/PoPS). PoPs is a stochastic spread model of pests and pathogens in forest and agricultural landscapes. It has been generalized and new features added but was originally developed for *Phytophthora ramorum* and the original version of the model was based on this reference paper: Ross K. Meentemeyer, Nik J. Cunniffe, Alex R. Cook, Joao A. N. Filipe, Richard D. Hunter, David M. Rizzo, and Christopher A. Gilligan 2011. Epidemiological modeling of invasion in heterogeneous landscapes: spread of sudden oak death in California (1990–2030). *Ecosphere* 2:art17. [http://dx.doi.org/10.1890/ES10-00192.1] (http://www.esajournals.org/doi/abs/10.1890/ES10-00192.1) 
+This is the R package for simulating spread of pests and pathogens. The package is an R package with multiple functions built around the PoPS (Pest or Pathogen Spread) model implemented in the C++ library maintained in the [PoPS Core Repository](https://github.com/ncsu-landscape-dynamics/pops-core). 
+
+PoPs is a stochastic spread model of pests and pathogens in forest and agricultural landscapes. The R package provides an easy way for researchers to calibrate, validate, and test what if scenarios of treatment interventions. The model is also available in GRASS GIS you can install and use r.pops.spread(https://github.com/ncsu-landscape-dynamics/r.pops.spread) to run the model in GRASS GIS.
 
 ## How to cite