make code changes

tlverse · May 3, 2022 · ae064d4 · ae064d4
1 parent 5540cd1
commit ae064d4
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Showing 9 changed files with 210 additions and 222 deletions.
diff --git a/R_code/02-roadmap.R b/R_code/02-roadmap.R
@@ -1,4 +1,4 @@
-## ----simple-DAG---------------------------------------------------------------
+## ----simple-DAG, out.width = "60%"--------------------------------------------
 library(dagitty)
 library(ggdag)
 

diff --git a/R_code/03-tlverse.R b/R_code/03-tlverse.R
@@ -4,5 +4,5 @@
 
 
 ## ----renviron-example, results="asis", eval=FALSE-----------------------------
-## GITHUB_PAT=yourPAT
-##
+## GITHUB_PAT <- yourPAT
+
diff --git a/R_code/04-data.R b/R_code/04-data.R
@@ -18,38 +18,3 @@ if (knitr::is_latex_output()) {
   skim(dat)
 }
 
-
-## ----load_ist_data_intro, message=FALSE, warning=FALSE------------------------
-# read in data
-ist <- read_csv(
-  paste0(
-    "https://raw.githubusercontent.com/tlverse/tlverse-handbook/master/",
-    "data/ist_sample.csv"
-  )
-)
-
-
-## ----skim_ist_data, results="asis", echo=FALSE--------------------------------
-if (knitr::is_latex_output()) {
-  knitr::kable(skim_no_sparks(ist), format = "latex")
-} else {
-  skim(ist)
-}
-
-
-## ----load_nhefs_data_intro----------------------------------------------------
-# read in data
-nhefs_data <- read_csv(
-  paste0(
-    "https://raw.githubusercontent.com/tlverse/tlverse-handbook/master/",
-    "data/NHEFS.csv"
-  )
-)
-
-
-## ----skim_nhefs_data, results="asis", echo=FALSE------------------------------
-if (knitr::is_latex_output()) {
-  knitr::kable(skim_no_sparks(nhefs_data), format = "latex")
-} else {
-  skim(nhefs_data)
-}
diff --git a/R_code/05-origami.R b/R_code/05-origami.R
@@ -73,7 +73,7 @@ t <- length(AP)
 
 
 ## ---- fig.cap="Rolling origin CV", results="asis", echo=FALSE-----------------
-knitr::include_graphics(path = "img/image/rolling_origin.png")
+knitr::include_graphics(path = "img/png/rolling_origin.png")
 
 
 ## ----rolling_origin-----------------------------------------------------------
@@ -86,7 +86,7 @@ folds[[2]]
 
 
 ## ---- fig.cap="Rolling window CV", results="asis", echo=FALSE-----------------
-knitr::include_graphics(path = "img/image/rolling_window.png")
+knitr::include_graphics(path = "img/png/rolling_window.png")
 
 
 ## ----rolling_window-----------------------------------------------------------
@@ -99,11 +99,11 @@ folds[[2]]
 
 
 ## ---- fig.cap="Rolling origin V-fold CV", results="asis", echo=FALSE----------
-knitr::include_graphics(path = "img/image/rolling_origin_v_fold.png")
+knitr::include_graphics(path = "img/png/rolling_origin_v_fold.png")
 
 
 ## ---- fig.cap="Rolling window V-fold CV", results="asis", echo=FALSE----------
-knitr::include_graphics(path = "img/image/rolling_window_v_fold.png")
+knitr::include_graphics(path = "img/png/rolling_window_v_fold.png")
 
 
 ## ----setup_ex-----------------------------------------------------------------
@@ -227,7 +227,8 @@ cv_rf <- function(fold, data, reg_form) {
 # now, let's cross-validate...
 folds <- make_folds(washb_data)
 cvrf_results <- cross_validate(
-  cv_fun = cv_rf, folds = folds, data = washb_data, reg_form = "whz ~ .",
+  cv_fun = cv_rf, folds = folds, 
+  data = washb_data, reg_form = "whz ~ .",
   use_future = FALSE
 )
 mean(cvrf_results$SE)
@@ -300,3 +301,4 @@ mses <- cross_validate(
 )
 mses$mse
 colMeans(mses$mse[, c("arima", "arima2")])
+