update lockfile, inst directions

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:

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",