DOcument apps

Signed-off-by: Peter Solymos <psolymos@gmail.com>

Author: psolymos

README.Rmd

@@ -119,13 +119,20 @@ run_app("distfunH")
 run_app("distfunHER")
 ```
 
-Compare simulation settings for single landscape:
+Compare simulation settings for a single landscape:
 
 ```{r eval=FALSE}
 run_app("bsimsH")
 run_app("bsimsHER")
 ```
 
+The [Shinylive](https://shinylive.io/r/examples/) versions of the apps can be found here:
+
+- [`distfunH`](https://peter.solymos.org/bSims/apps/distfunH/)
+- [`distfunHER`](https://peter.solymos.org/bSims/apps/distfunHER/)
+- [`bsimsH`](https://peter.solymos.org/bSims/apps/bsimsH/)
+- [`bsimsHER`](https://peter.solymos.org/bSims/apps/bsimsHER/)
+
 ### Replicating simulations
 
 Interactive sessions can be used to explore different settings.

README.md

@@ -103,9 +103,6 @@ get_table(x)
 #> 50-100m       3      0       1
 #> 100-150m      4      1       0
 #> 150+m         8      3       0
-```
-
-``` r
 
 head(get_events(a))
 #>            x          y          t v   a  i
@@ -115,9 +112,6 @@ head(get_events(a))
 #> 4 -2.1041934 -1.6092706 0.03936096 1 295 19
 #> 5 -4.9531338 -0.4093427 0.04890537 1 217 11
 #> 6 -3.3127196 -0.2145475 0.08899310 1 215 15
-```
-
-``` r
 
 head(get_detections(o))
 #>             x           y          t v   a         d  f  i  j
@@ -141,13 +135,21 @@ run_app("distfunH")
 run_app("distfunHER")
 ```
 
-Compare simulation settings for single landscape:
+Compare simulation settings for a single landscape:
 
 ``` r
 run_app("bsimsH")
 run_app("bsimsHER")
 ```
 
+The [Shinylive](https://shinylive.io/r/examples/) versions of the apps
+can be found here:
+
+- [`distfunH`](https://peter.solymos.org/bSims/apps/distfunH/)
+- [`distfunHER`](https://peter.solymos.org/bSims/apps/distfunHER/)
+- [`bsimsH`](https://peter.solymos.org/bSims/apps/bsimsH/)
+- [`bsimsHER`](https://peter.solymos.org/bSims/apps/bsimsHER/)
+
 ### Replicating simulations
 
 Interactive sessions can be used to explore different settings. Settings
@@ -182,32 +184,23 @@ nc <- 2 # number of cores
 ## sequential
 system.time(bb <- b$replicate(B, cl=NULL))
 #>    user  system elapsed 
-#>   0.232   0.001   0.233
-```
-
-``` r
+#>   0.235   0.002   0.237
 
 ## parallel clusters
 cl <- makeCluster(nc)
 ## note: loading the package is optional
 system.time(clusterEvalQ(cl, library(bSims)))
 #>    user  system elapsed 
-#>   0.000   0.000   0.439
-```
-
-``` r
+#>   0.000   0.000   0.444
 system.time(bb <- b$replicate(B, cl=cl))
 #>    user  system elapsed 
-#>   0.004   0.001   0.194
-```
-
-``` r
+#>   0.004   0.001   0.189
 stopCluster(cl)
 
 ## parallel forking
 if (.Platform$OS.type != "windows") {
   system.time(bb <- b$replicate(B, cl=nc))
 }
 #>    user  system elapsed 
-#>   0.119   0.046   0.182
+#>   0.127   0.048   0.177
 ```

RELEASE.R

@@ -16,36 +16,3 @@ devtools::check()
 # install
 devtools::install()
 
-# multi-arch checks
-library(rhub)
-#validate_email("peter@analythium.io")
-platforms()
-f <- c("debian-gcc-devel",
-       "debian-gcc-release",
-       "macos-highsierra-release-cran",
-       "windows-x86_64-devel",
-       "windows-x86_64-release",
-       "windows-x86_64-oldrel")
-check(platform=f)
-list_package_checks(".")
-
-# build package to submit
-devtools::build()
-
-pkgnews <- function() {
-    x <- readLines("NEWS.md")
-    x <- x[x != ""]
-    h <- which(startsWith(x, "#"))
-    i <- (h[1]+1):(h[2]-1)
-    paste0(x[i], collapse="\n")
-}
-cat(sprintf('Dear CRAN Maintainers,
-I am submitting the %s version of the bSims R extension package to CRAN.
-The package passed R CMD check --as-cran without errors/warnings/notes on the following platforms: %s.
-I made the following changes since the last release:
-%s
-Yours,
-Peter Solymos
-maintainer', read.dcf("DESCRIPTION", fields="Version")[1],
-            paste0(f, collapse=", "),
-            pkgnews()))

inst/WORDLIST

@@ -20,6 +20,7 @@ RStudio
 Reparametrized
 SDlog
 Schmiegelow
+Shinylive
 Stralberg
 VSCode
 Voronoi

vignettes/bsims04-apps.Rmd

@@ -0,0 +1,43 @@
+---
+title: "Explore bSims with Shiny apps"
+author: "Peter Solymos"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Simulation workflow in bSims}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r setup,include=FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+par(mar = c(1, 1, 1, 1))
+set.seed(429)
+suppressPackageStartupMessages(library(bSims))
+```
+
+bSims comes with a few [Shiny](https://shiny.posit.co/) apps.
+These can be used to interactively explore the effects of different settings.
+
+Compare distance functions:
+
+```{r eval=FALSE}
+run_app("distfunH")
+run_app("distfunHER")
+```
+
+Compare simulation settings for a single landscape:
+
+```{r eval=FALSE}
+run_app("bsimsH")
+run_app("bsimsHER")
+```
+
+The [Shinylive](https://shinylive.io/r/examples/) versions of the apps can be found here:
+
+- [`distfunH`](https://peter.solymos.org/bSims/apps/distfunH/)
+- [`distfunHER`](https://peter.solymos.org/bSims/apps/distfunHER/)
+- [`bsimsH`](https://peter.solymos.org/bSims/apps/bsimsH/)
+- [`bsimsHER`](https://peter.solymos.org/bSims/apps/bsimsHER/)