Solving conflicts

.gitattributes

@@ -1,2 +1,2 @@
 configure.ac text eol=lf
-
+inst/include/epiworld/** linguist-vendored

.github/workflows/coverage.yaml

@@ -0,0 +1,39 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: Coverage
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    name: Coverage
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2.9.0
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: check
+
+      - name: Running coverage
+        run: |
+          # Files to exclude
+          files <- list.files("inst/", full.names = TRUE, recursive = TRUE)
+
+          # Run coverage
+          covr::codecov(
+            line_exclusions = as.list(files),
+            token = Sys.getenv("CODECOV_TOKEN")
+            )
+        shell: Rscript {0}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+

README.Rmd

@@ -20,6 +20,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/UofUEpiBio/epiworldR/actions/workflows/r.yml/badge.svg)](https://github.com/UofUEpiBio/epiworldR/actions/workflows/r.yml)
 [![CRANlogs downloads](https://cranlogs.r-pkg.org/badges/grand-total/epiworldR)](https://cran.r-project.org/package=epiworldR)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/UofUEpiBio/epiworldR/blob/master/LICENSE.md)
+[![codecov](https://codecov.io/gh/UofUEpiBio/epiworldR/graph/badge.svg?token=ZB8FVLI7GN)](https://codecov.io/gh/UofUEpiBio/epiworldR)
 <!-- badges: end -->
 
 This R package is a wrapper of the C++ library [epiworld](https://github.com/UofUEpiBio/epiworld){target="_blank"}. It provides a general framework for modeling disease transmission using [agent-based models](https://en.wikipedia.org/w/index.php?title=Agent-based_model&oldid=1153634802){target="_blank"}. Some of the main features include:

README.md

@@ -12,6 +12,7 @@ status](https://www.r-pkg.org/badges/version/epiworldR)](https://CRAN.R-project.
 downloads](https://cranlogs.r-pkg.org/badges/grand-total/epiworldR)](https://cran.r-project.org/package=epiworldR)
 [![License:
 MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/UofUEpiBio/epiworldR/blob/master/LICENSE.md)
+[![codecov](https://codecov.io/gh/UofUEpiBio/epiworldR/graph/badge.svg?token=ZB8FVLI7GN)](https://codecov.io/gh/UofUEpiBio/epiworldR)
 <!-- badges: end -->
 
 This R package is a wrapper of the C++ library
@@ -140,8 +141,8 @@ summary(sir)
 #> Number of entities  : 0
 #> Days (duration)     : 50 (of 50)
 #> Number of viruses   : 1
-#> Last run elapsed t  : 163.00ms
-#> Last run speed      : 30.49 million agents x day / second
+#> Last run elapsed t  : 165.00ms
+#> Last run speed      : 30.23 million agents x day / second
 #> Rewiring            : off
 #> 
 #> Global events:
@@ -228,8 +229,8 @@ summary(model_seirconn)
 #> Number of entities  : 0
 #> Days (duration)     : 100 (of 100)
 #> Number of viruses   : 2
-#> Last run elapsed t  : 36.00ms
-#> Last run speed      : 27.62 million agents x day / second
+#> Last run elapsed t  : 39.00ms
+#> Last run speed      : 25.12 million agents x day / second
 #> Rewiring            : off
 #> 
 #> Global events:

inst/tinytest/test-get.R

@@ -15,7 +15,7 @@ set.seed(1231)
 # to check that.
 expect_equal(nrow(get_hist_tool(model)), 0L)
 expect_equal(nrow(get_hist_total(model)), 0L)
-expect_equal(nrow(get_hist_variant(model)), 0L)
+expect_equal(nrow(get_hist_virus(model)), 0L)
 expect_equal(nrow(get_reproductive_number(model)), 0L)
 expect_equal(dim(get_transition_probability(model)), c(3, 3))
 expect_equal(nrow(get_hist_transition_matrix(model)), 0L)

inst/tinytest/test-sir.R

@@ -16,10 +16,9 @@ agents_smallworld(
 
 # Initializing 
 queuing_off(sir_0)
-init(sir_0, days = 50, seed = 1912)
 
 # Running and printing
-run(sir_0)
+run(sir_0, ndays = 50, seed = 1912)
 
 tmat_0 <- get_transition_probability(sir_0)
 
@@ -40,19 +39,23 @@ agents_smallworld(
   p = .01
 )
 
-# Initializing 
-init(sir_1, days = 50, seed = 1912)
-
 # Running and printing
-run(sir_1)
+run(sir_1, ndays = 50, seed = 1912)
 
 tmat_1 <- get_transition_probability(sir_1)
 
 # Expected
-tmat_expected <- structure(c(0.90395575761795, 0, 0, 0.0959785506129265, 0.707067608833313, 
-                             0, 6.55534968245775e-05, 0.292932420969009, 1), dim = c(3L, 3L
-                             ), dimnames = list(c("Susceptible", "Infected", "Recovered"), 
-                                                c("Susceptible", "Infected", "Recovered")))
+tmat_expected <- structure(
+  c(
+    0.963432729244232, 0, 0, 0.0365671403706074, 0.702733814716339, 
+    0, 0, 0.297266155481339, 1
+    ),
+  dim = c(3L, 3L),
+  dimnames = list(
+    c("Susceptible", "Infected", "Recovered"), 
+    c("Susceptible", "Infected", "Recovered")
+    )
+  )
 
 expect_equivalent(tmat_0, tmat_1)
 expect_equivalent(tmat_0, tmat_expected)

playground/epiworld_presentation.qmd

@@ -90,11 +90,8 @@ agents_smallworld(
   p = .01
   )
 
-# Initializing 
-init(seir, days = 100, seed = 1912)
-
 # Running and printing
-run(seir)
+run(seir, ndays = 100, seed = 1912)
 seir
 
 ```