Fixing some small testing bugs.

.Rbuildignore

@@ -7,8 +7,9 @@
 ^.github$
 build_custom.R
 ^tmp$
+R\notes.txt
 README.RMD
-
+.here
 ^codecov\.yml$
 ^\.github$
 vignettes/transient/*

DESCRIPTION

@@ -31,7 +31,8 @@ Imports:
   stringr,
   tidyr,
   utils,
-  yaml
+  yaml,
+  zip
 Suggests:
   babelmixr2,
   cli,

R/simulate_rules.R

@@ -301,7 +301,7 @@ simulate_rules <- function(object,
     # This will force the simulation to initialize at the
     # first observed time. This will be important as wel
     # step through the different eval_time intervals:
-    rxSetIni0(FALSE)
+    rxode2::rxSetIni0(FALSE)
 
     # Simulating before the fist eval_time to get
     # a snapshot of the simulation:
@@ -1718,11 +1718,11 @@ rx2other <- function(object,
         rx_details  = fetch_rxinfo(rx_obj)
         # If no dataset has been specified we create a dummy dataset
         if(is.null(dataset)){
-          dataset = eventTable()
+          dataset = rxode2::eventTable()
 
           # Adding observations for each output
           for(tmp_output in  rx_details[["elements"]][["outputs"]]){
-            dataset = dataset |> et(id=c(1,2), time=c(0,1), evid=0, cmt=tmp_output)
+            dataset = dataset |> rxode2::et(id=c(1,2), time=c(0,1), evid=0, cmt=tmp_output)
           }
 
           # Adding default values for covariates

README.md

@@ -5,6 +5,7 @@
 
 <!-- 
 -->
+
 <!-- badges: start -->
 
 [![Codecov test
@@ -38,7 +39,7 @@ instance and if many people are using it at once it can be slow.
 
 ## From CRAN
 
-You can install the released version of `rumiante` from
+You can install the released version of `ruminate` from
 [CRAN](https://cran.r-project.org/package=ruminate) with:
 
 ``` r
@@ -54,6 +55,8 @@ install.packages("ubiquity")
 install.packages("nlmixr2lib")
 install.packages("nonmem2rx")
 install.packages("rxode2")
+install.packages("rxode2et")
+install.packages("nlmixr2")
 
 # Actual package
 install.packages("ruminate")
@@ -92,11 +95,11 @@ Note that because `{ruminate}` depends on `{formods}` and `{onbrand}`
 you will need to first install the development versions of `{onbrand}`
 and `{formods}`.
 
-# Running in ruminate
+# Running ruminate
 
 ## In RStudio
 
-This will run the default/stable version of rumiante:
+This will run the default/stable version of ruminate:
 
 ``` r
 library(ruminate)
@@ -118,7 +121,7 @@ version off of github to make sure you have the latest version.**
 ## In a Docker container
 
 This kind of assumes a basic familiarity with Docker. Keep in mind that
-these containers are built for ‘x86’ images. Basically Intel/AMD cpus.
+these containers are built for ‘x86’ images. Essentially Intel/AMD cpus.
 This means that if you have a Mac with Apple Silicon (M1, M2,etc.) it
 may not work or the performance may not be that good.
 
@@ -129,6 +132,11 @@ This will pull container from docker and run it locally
     docker pull johnmharrold/ruminate:latest
     docker run -p 3838:3838   johnmharrold/ruminate:latest &
 
+If that worked you can put the following into a web browser and then use
+ruminate there:
+
+    http://127.0.0.1:3838/
+
 ### Create your own container
 
 If you want to create your own container you can do the following:

vignettes/deployment.Rmd

@@ -13,20 +13,6 @@ vignette: >
 # require(rhandsontable)
 # require(flextable)
 # require(ruminate)
-# # Determining if ubiquity is installed
-# if(system.file(package="ubiquity") == ""){
-#   ubiquity_found = FALSE
-# } else {
-#   require(ubiquity)
-#   ubiquity_found = TRUE
-# }
-# if(system.file(package="gridExtra") == ""){
-#   gridExtra_found = FALSE
-# } else {
-#   require(gridExtra)
-#   gridExtra_found = TRUE
-# }
-# 
 # # The presim variable will contain presimulated data when eval is set to true
 # presim_loaded = FALSE
 ```