Fix R code in Readme (#244)

* README.Rmd now reflects the current state of the code base * Added VScode task to run the REAMDE.Rmd program with the other unit tests to ensure its not broken
Genentech · Nov 7, 2023 · eb01931 · eb01931
1 parent b4957b2
commit eb01931
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Showing 3 changed files with 38 additions and 8 deletions.
diff --git a/.vscode/tasks.json b/.vscode/tasks.json
@@ -89,6 +89,28 @@
         },
 
 
+        {
+            "label": "JMP: Build README",
+            "type": "R",
+            "code": [
+                "devtools::build_readme()"
+            ],
+            "problemMatcher": [],
+            "group": {
+                "kind": "build",
+                "isDefault": false
+            },
+            "presentation": {
+                "echo": false,
+                "reveal": "always",
+                "focus": false,
+                "panel": "dedicated",
+                "showReuseMessage": true,
+                "clear": true
+            }
+        },
+
+
         {
             "label": "JMP: Run Vignettes",
             "type": "shell",
@@ -125,7 +147,8 @@
                 "JMP: Run Vignettes",
                 "JMP: CMD Check (no vig)",
                 "JMP: Test Pkgdown",
-                "JMP: Test (with cache)"
+                "JMP: Test (with cache)",
+                "JMP: Build README"
             ],
             "problemMatcher": []
         },

diff --git a/README.Rmd b/README.Rmd
@@ -76,17 +76,19 @@ long_data <- sim_data$lm |>
     dplyr::arrange(time, pt)
 
 joint_data <- DataJoint(
-    survival = DataSurvival(
+    subject = DataSubject(
         data = os_data,
-        formula = Surv(time, event) ~ cov_cat + cov_cont,
         subject = "pt",
         arm = "arm",
         study = "study"
     ),
+    survival = DataSurvival(
+        data = os_data,
+        formula = Surv(time, event) ~ cov_cat + cov_cont
+    ),
     longitudinal = DataLongitudinal(
         data = long_data,
         formula = sld ~ time,
-        subject = "pt",
         threshold = 5
     )
 )

diff --git a/README.md b/README.md
@@ -51,7 +51,7 @@ You can install the current development version from GitHub with:
 
 ``` r
 if (!require("remotes")) {
-  install.packages("remotes")
+    install.packages("remotes")
 }
 remotes::install_github("genentech/jmpost")
 ```
@@ -75,6 +75,9 @@ right format.
 
 ``` r
 library(jmpost)
+#> Registered S3 method overwritten by 'GGally':
+#>   method from   
+#>   +.gg   ggplot2
 set.seed(321)
 sim_data <- simulate_joint_data(
     lm_fun = sim_lm_random_slope(),
@@ -85,17 +88,19 @@ long_data <- sim_data$lm |>
     dplyr::arrange(time, pt)
 
 joint_data <- DataJoint(
-    survival = DataSurvival(
+    subject = DataSubject(
         data = os_data,
-        formula = Surv(time, event) ~ cov_cat + cov_cont,
         subject = "pt",
         arm = "arm",
         study = "study"
     ),
+    survival = DataSurvival(
+        data = os_data,
+        formula = Surv(time, event) ~ cov_cat + cov_cont
+    ),
     longitudinal = DataLongitudinal(
         data = long_data,
         formula = sld ~ time,
-        subject = "pt",
         threshold = 5
     )
 )