diff --git a/README.md b/README.md index 41c5835..de68ed0 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,36 @@ The `paramix` package provides convenient functions to create both the correct a remotes::install_github("cmmid/paramix") ``` +## Demo Analysis + +In addition to the vignette introductory analysis, we provide a more extensive analysis pipeline, divided into stages and linked together via GNUMake. You will also need to have the R package `renv` installed. + +You can create a copy of this pipeline from an R console: + +```r +path_to_destination <- file.path("~", "Downloads", "paramixdemo") # or wherever +if (!dir.exists(path_to_destination)) { # if needed, create the directory + dir.create(path_to_destination, recursive = TRUE) +} +# get the analysis pipeline +system.file("analysis", package = "paramix") |> + list.files(full.names = TRUE, recursive = FALSE, include.dirs = TRUE) |> + file.copy( + from = _, + to = path_to_destination, + recursive = TRUE + ) +# should be a bunch of TRUEs indicating the files copied successfully +``` + +then go to where you created the copy and run the `make` command: + +```bash +~/Downloads/paramixdemo$ make +``` + +This should result in a fair bit of environment setup (to ensure setup for reproducibility) + ## Usage Briefly, there are three steps: diff --git a/inst/analysis/renv.lock b/inst/analysis/renv.lock index 4d0acc9..5ee0264 100644 --- a/inst/analysis/renv.lock +++ b/inst/analysis/renv.lock @@ -146,14 +146,14 @@ }, "data.table": { "Package": "data.table", - "Version": "1.16.0", + "Version": "1.16.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "fb24e05d4a91d8b1c7ff8e284bde834a" + "Hash": "2e00b378fc3be69c865120d9f313039a" }, "deSolve": { "Package": "deSolve", @@ -508,18 +508,19 @@ }, "paramix": { "Package": "paramix", - "Version": "0.0.0.9001", + "Version": "0.0.1", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "cmmid", "RemoteRepo": "paramix", "RemoteRef": "main", - "RemoteSha": "f5f50e2139cdf644a40f9463269c06978413dd44", + "RemoteSha": "692b48cf1f78e6a90ef466ae0d00430a080f7a23", "Requirements": [ + "R", "data.table" ], - "Hash": "f97c85805577f5e692bb7ddbea81bfb3" + "Hash": "dd002317271792088f2e514cd409f4a6" }, "patchwork": { "Package": "patchwork",