Add instructions for contributing and add GitHub workflows

.Rbuildignore

@@ -3,3 +3,4 @@
 ^LICENSE\.md$
 ^codecov\.yml$
 .travis.yml
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,56 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v1
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/test-coverage.yaml

@@ -0,0 +1,30 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: covr
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

DESCRIPTION

@@ -41,14 +41,17 @@ Imports:
     R6,
     remotes,
     gregorian,
-    readr,
-    dplyr
+    readr
 Suggests:
-    lintr,
     covr,
+    dplyr,
+    dygraphs,
     knitr,
+    leaflet,
+    lintr,
+    rmarkdown,
     testthat,
-    rmarkdown
+    xts
 URL: https://github.com/zizroc/villager/
 BugReports: https://github.com/zizroc/villager/issues/
 VignetteBuilder: knitr

README.md

@@ -1,5 +1,8 @@
 # villager
-[![Codecov test coverage](https://codecov.io/gh/zizroc/villager/branch/master/graph/badge.svg)](https://codecov.io/gh/zizroc/villager?branch=main)
+# dplyr <img src='man/figures/logo.png' align="right" height="139" />
+
+[![R build status](https://github.com/zizroc/villager/workflows/R-CMD-check/badge.svg)](https://github.com/zizroc/villager/actions)
+[![Codecov test coverage](https://codecov.io/gh/zizroc/villager/branch/main/graph/badge.svg)](https://codecov.io/gh/zizroc/villager?branch=main)
 
 villager is a framework for creating and running agent based models in R. It's purpose is to provide an extensible framework where modeling can be done in native R.
 
@@ -227,3 +230,7 @@ simulator$run_model()
 ## Advanced Usage
 
 In the examples above, the default properties of agents and resources were used. It's possible that these won't cover all the needs for more diverse models. There are vignettes on extending the agent and resource classes to handle these situations.
+
+## Contributing
+
+Code contributions are welcome as pull requests to the `develop` branch. Bugs, comments, and questions can be submitted as Github Issues.

codecov.yml

@@ -1,4 +1,4 @@
-comment: true
+comment: false
 
 coverage:
   status:

vignettes/extending-agents.Rmd

@@ -15,7 +15,9 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup}
+
 library(villager)
+library(leaflet)
 ```
 # Extending Agents
 To create agents (winiks) that have more properties than the ones provided by _villager_, subclass the `winik` class into a new R6 class. Once sub-classed, additional properties can be added to the winik which can be used in the subsequent model. The new winik class can be tied to individual villages. This gives flexibility to model populations differently when running under the same simulation.
@@ -144,3 +146,17 @@ los_angeles <- village$new("Test_Village", initial_condition, test_model, gps_wi
 simulator <- simulation$new("100-01-01", "100-01-05", list(los_angeles))
 simulator$run_model()
 ```
+
+### Results
+```{r}
+# Load in data
+agent_data <- readr::read_csv("results/Test_Village/winiks.csv")
+
+# Grab just the location data
+agent_location <- data.frame(latitude = agent_data$latitude, longitude = agent_data$longitude)
+
+# create a map 
+leaflet::leaflet() %>% 
+  leaflet::addTiles() %>%  # Add default OpenStreetMap map tiles
+  leaflet::addMarkers (data = agent_location) # Add agent locations
+```

vignettes/extending-resources.Rmd

@@ -15,7 +15,9 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup}
+library(dygraphs)
 library(villager)
+library(xts)
 ```
 
 # Extending Resources
@@ -126,5 +128,32 @@ simulator$run_model()
 A timeseries of each resource type is plotted below. The _rice_ resource has clearly not expired while the _corn_ resource has after 10 days.
 
 ```{r}
+# Load in data
+time_series_data <- readr::read_csv("results/Expiring_Resources/resources.csv")
 
+# Get unique dates
+unique_dates<- sort(unique(time_series_data$date))
+
+# Get corn & rice quantities and dates
+corn_date_quantities <- dplyr::filter(time_series_data, name=="Corn")
+rice_date_quantities <- dplyr::filter(time_series_data, name=="Rice")
+
+# create data frame for sorted data
+reordered_time_series <- data.frame(Date = unique_dates, Corn = 0, Rice = 0)
+for (i in 1:nrow(reordered_time_series)){
+  reordered_time_series[i,2] = corn_date_quantities[which(corn_date_quantities$date == reordered_time_series$Date[i]),2]
+  reordered_time_series[i,3] = rice_date_quantities[which(rice_date_quantities$date == reordered_time_series$Date[i]),2]
+}
+
+# Convert the date field to an actual date
+reordered_time_series$Date <- strptime(reordered_time_series$Date, "%Y-%m-%d")
+
+# Create a xts time series object from the new data frame (an xts object is needed
+# for the dygraph plotting library)
+final_time_series <- xts::xts(x = reordered_time_series[,-1], order.by = reordered_time_series$Date)
+
+# Plot the graph
+dygraphs::dygraph(final_time_series, main = "Crop Quantities", xlab = "Date") %>% 
+  dygraphs::dyAxis("y", label = "Quantity", valueRange = c(0, 25)) %>%
+  dygraphs::dyOptions(drawGrid = FALSE)
 ```