fix here::i_am

Novartis · Jul 31, 2024 · d91dd20 · d91dd20
1 parent 7f1b8b6
commit d91dd20
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diff --git a/src/01b_basic_workflow.qmd b/src/01b_basic_workflow.qmd
@@ -91,7 +91,8 @@ set.seed(5886935)
 #| eval: true 
 #| include: false
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 As `brms` models are translated to Stan model files, which must be

diff --git a/src/01c_priors.qmd b/src/01c_priors.qmd
@@ -34,7 +34,8 @@ theme_set(theme_bw(12))
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 Within the Bayesian regression modeling in Stan framework `brms`

diff --git a/src/02a_meta_analysis.qmd b/src/02a_meta_analysis.qmd
@@ -46,7 +46,8 @@ set.seed(593467)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 ## Background

diff --git a/src/02ab_meta_analysis_trtdiff.qmd b/src/02ab_meta_analysis_trtdiff.qmd
@@ -24,7 +24,8 @@ set.seed(979356)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 ## Background

diff --git a/src/02ac_meta_analysis_strata.qmd b/src/02ac_meta_analysis_strata.qmd
@@ -56,7 +56,8 @@ options(width=120, digits=2)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 ## Background

diff --git a/src/02b_dose_finding.qmd b/src/02b_dose_finding.qmd
@@ -52,7 +52,8 @@ set.seed(8979476)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 ```{r get_annualized_rates}

diff --git a/src/02c_dose_escalation.qmd b/src/02c_dose_escalation.qmd
@@ -72,7 +72,8 @@ set.seed(8794567)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 Such a model is straightforward to implement in `brms`. Below, we use a nonlinear formula specification, in order to allow the prior for the intercept to be specified on the log scale. 

diff --git a/src/02cb_tte_dose_escalation.qmd b/src/02cb_tte_dose_escalation.qmd
@@ -144,7 +144,8 @@ gt_format <- function(x) {
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 ## Example trial

diff --git a/src/02e_multiple_imputation.qmd b/src/02e_multiple_imputation.qmd
@@ -76,7 +76,8 @@ options(brms.normalize=FALSE)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 Let us consider some simulated data for a trial in chronic obstructive

diff --git a/src/02g_longitudinal.qmd b/src/02g_longitudinal.qmd
@@ -45,7 +45,8 @@ control_args <- list(adapt_delta = 0.95)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 ```{r get_data, echo = TRUE}

diff --git a/src/02h_mmrm.qmd b/src/02h_mmrm.qmd
@@ -51,7 +51,8 @@ options(width=120)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 ```{r include=FALSE}

diff --git a/src/02i_time_to_event.qmd b/src/02i_time_to_event.qmd
@@ -58,7 +58,8 @@ options(width=120)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 

diff --git a/src/02j_network_meta_analysis.qmd b/src/02j_network_meta_analysis.qmd
@@ -38,7 +38,8 @@ control_args <- list(adapt_delta=0.95)
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 

diff --git a/src/02l_single_arm_pos.qmd b/src/02l_single_arm_pos.qmd
@@ -47,7 +47,8 @@ theme_set(theme_bw(base_size=18))
 
 ```{r, include=FALSE, echo=FALSE, eval=TRUE}
 # invisible to the reader additional setup steps, which are optional
-{{< include setup.R >}}
+# {{< include setup.R >}}
+source("setup.R")
 ```
 
 

diff --git a/workshops/jsm2024/slides/R/02_hist_control.R b/workshops/jsm2024/slides/R/02_hist_control.R
@@ -1,4 +1,4 @@
-here::i_am("/home/beanan1/work/brms_course/slides/R/02_hist_control.R")
+here::i_am("slides/R/02_hist_control.R")
 library(here)
 
 library(here)

diff --git a/workshops/jsm2024/slides/R/05_mmrm.R b/workshops/jsm2024/slides/R/05_mmrm.R
@@ -1,4 +1,4 @@
-here::i_am("/home/beanan1/work/brms_course/slides/R/05_mmrm.R")
+here::i_am("slides/R/05_mmrm.R")
 library(here)
 
 library(here)

diff --git a/workshops/jsm2024/slides/R/06_dose_finding.R b/workshops/jsm2024/slides/R/06_dose_finding.R
@@ -1,4 +1,4 @@
-here::i_am("/home/beanan1/work/brms_course/slides/R/06_dose_finding.R")
+here::i_am("slides/R/06_dose_finding.R")
 library(here)
 
 library(here)

diff --git a/workshops/jsm2024/slides/R/07_time_to_event.R b/workshops/jsm2024/slides/R/07_time_to_event.R
@@ -1,4 +1,4 @@
-here::i_am("/home/beanan1/work/brms_course/slides/R/07_time_to_event.R")
+here::i_am("slides/R/07_time_to_event.R")
 library(here)
 
 library(here)