From a76ac7f37110e2cf777b64cca882ea7b956a3217 Mon Sep 17 00:00:00 2001
From: "George G. Vega Yon" <g.vegayon@gmail.com>
Date: Fri, 20 Oct 2023 14:11:07 -0600
Subject: [PATCH] Working on makefile. Soon to merge on main branch

---
 Makefile                    | 18 +++++++++---------
 README.Rmd                  | 12 +++++++-----
 README.md                   | 27 +++++++++------------------
 playground/benchmark-seir.R | 16 ++++++++--------
 4 files changed, 33 insertions(+), 40 deletions(-)

diff --git a/Makefile b/Makefile
index d73f4ded..beeac088 100644
--- a/Makefile
+++ b/Makefile
@@ -12,14 +12,15 @@ docker-debug:
 		--no-docs --build .
 
 install-dev: clean
-	sed -i -E 's/^useDynLib\([a-zA-Z]+/useDynLib(epiworldRdev/g' NAMESPACE
+	sed -i -E 's/@useDynLib\s+[a-zA-Z]+/@useDynLib epiworldRdev/g' R/epiworldR-package.R
+	sed -i -E 's/useDynLib\(+[a-zA-Z]+/useDynLib(epiworldRdev/g' NAMESPACE
 	sed -i -E 's/^Package:.+/Package: epiworldRdev/g' DESCRIPTION 
-	sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{epiworldRdev/g' man/epiworldR-package.Rd
 	sed -i -E 's/^library\([a-zA-Z]+\)/library(epiworldRdev)/g' README.*
-	EPI_DEV=yes R CMD INSTALL .
-	$(MAKE) clean
+	Rscript --vanilla -e 'roxygen2::roxygenize()'
+	EPI_DEV=yes R CMD INSTALL .& $(MAKE) clean
 
-install: clean
+install:
+	$(MAKE) clean
 	R CMD INSTALL .
 		
 
@@ -37,11 +38,10 @@ check: build
 
 clean: 
 	Rscript --vanilla -e 'devtools::clean_dll()'
-	sed -i -E 's/^useDynLib\([a-zA-Z]+/useDynLib(epiworldR/g' NAMESPACE
+	sed -i -E 's/@useDynLib\s+[a-zA-Z]+/@useDynLib epiworldR/g' R/epiworldR-package.R
+	sed -i -E 's/useDynLib\(+[a-zA-Z]+/useDynLib(epiworldR/g' NAMESPACE
 	sed -i -E 's/^Package:.+/Package: epiworldR/g' DESCRIPTION 
-	sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{epiworldR/g' man/epiworldR-package.Rd
-	sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{epiworldR/g' R/epiworldR-package.Rd
-
+	# sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{epiworldR/g' man/epiworldR-package.Rd
 	sed -i -E 's/^library\([a-zA-Z]+\)/library(epiworldR)/g' README.*
 
 docs:
diff --git a/README.Rmd b/README.Rmd
index 43f0464c..fffefcb1 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -71,10 +71,10 @@ library(epiworldR)
 
 # Creating a SIR model
 sir <- ModelSIR(
-  name           = "COVID-19",
-  prevalence     = .01,
+  name              = "COVID-19",
+  prevalence        = .01,
   transmission_rate = .7,
-  recovery       = .3
+  recovery          = .3
   ) |>
   # Adding a Small world population 
   agents_smallworld(n = 100000, k = 10, d = FALSE, p = .01) |>
@@ -205,8 +205,10 @@ net <- get_transmissions(sir)
 
 # Plotting
 library(epiworldR)
-library(epiworldR)
-x <- graph_from_edgelist(as.matrix(net[,2:3]) + 1)
+library(netplot)
+x <- igraph::graph_from_edgelist(
+  as.matrix(net[,2:3]) + 1
+  )
 
 nplot(x, edge.curvature = 0, edge.color = "gray", skip.vertex=TRUE)
 ```
diff --git a/README.md b/README.md
index 143f5831..05625989 100644
--- a/README.md
+++ b/README.md
@@ -91,10 +91,10 @@ library(epiworldR)
 
 # Creating a SIR model
 sir <- ModelSIR(
-  name           = "COVID-19",
-  prevalence     = .01,
+  name              = "COVID-19",
+  prevalence        = .01,
   transmission_rate = .7,
-  recovery       = .3
+  recovery          = .3
   ) |>
   # Adding a Small world population 
   agents_smallworld(n = 100000, k = 10, d = FALSE, p = .01) |>
@@ -127,8 +127,8 @@ summary(sir)
 #> Number of entities  : 0
 #> Days (duration)     : 50 (of 50)
 #> Number of viruses   : 1
-#> Last run elapsed t  : 170.00ms
-#> Last run speed      : 29.29 million agents x day / second
+#> Last run elapsed t  : 166.00ms
+#> Last run speed      : 30.01 million agents x day / second
 #> Rewiring            : off
 #> 
 #> Global actions:
@@ -346,20 +346,11 @@ net <- get_transmissions(sir)
 
 # Plotting
 library(epiworldR)
+library(netplot)
 #> Loading required package: grid
-library(epiworldR)
-#> 
-#> Attaching package: 'igraph'
-#> The following object is masked from 'package:netplot':
-#> 
-#>     ego
-#> The following objects are masked from 'package:stats':
-#> 
-#>     decompose, spectrum
-#> The following object is masked from 'package:base':
-#> 
-#>     union
-x <- graph_from_edgelist(as.matrix(net[,2:3]) + 1)
+x <- igraph::graph_from_edgelist(
+  as.matrix(net[,2:3]) + 1
+  )
 
 nplot(x, edge.curvature = 0, edge.color = "gray", skip.vertex=TRUE)
 ```
diff --git a/playground/benchmark-seir.R b/playground/benchmark-seir.R
index 807de96d..0c860d18 100644
--- a/playground/benchmark-seir.R
+++ b/playground/benchmark-seir.R
@@ -1,5 +1,5 @@
-library(epiworldR)
-library(epiworldRfaster)
+# library(epiworldRdev)
+# library(epiworldR)
 
 library(microbenchmark)
 
@@ -22,23 +22,23 @@ for (n in ns) {
     epiworldR::verbose_off()
 
 
-  sirfast <- epiworldRfaster::ModelSEIR(
+  sirfast <- epiworldRdev::ModelSEIR(
     name                = "COVID-19",
     prevalence          = 0.01, 
     incubation_days     = 7, 
     transmission_rate   = 0.6,
     recovery_rate       = 0.5
   ) |> 
-    epiworldRfaster::agents_smallworld(n = n, k = 20, p = 0, d = FALSE) |>
-    epiworldRfaster::add_virus(
-      epiworldRfaster::virus("COVID-19-beta", 0.01, 0.6, 0.5, 7), .2
+    epiworldRdev::agents_smallworld(n = n, k = 20, p = 0, d = FALSE) |>
+    epiworldRdev::add_virus(
+      epiworldRdev::virus("COVID-19-beta", 0.01, 0.6, 0.5, 7), .2
       ) |>
-    epiworldRfaster::verbose_off()
+    epiworldRdev::verbose_off()
 
 
   ans[[as.character(n)]] <- microbenchmark(
     old = epiworldR::run(sir, ndays = 100, seed = 1912),
-    new = epiworldRfaster::run(sirfast, ndays = 100, seed = 1912),
+    new = epiworldRdev::run(sirfast, ndays = 100, seed = 1912),
     times = 10
   )