corrections + precommit edits

.pre-commit-config.yaml

@@ -3,17 +3,17 @@
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
     rev: v0.1.3
-    hooks: 
+    hooks:
     -   id: style-files
-        args: [--style_pkg=styler, --style_fun=tidyverse_style]    
+        args: [--style_pkg=styler, --style_fun=tidyverse_style]
     -   id: roxygenize
     # codemeta must be above use-tidy-description when both are used
     # -   id: codemeta-description-updated
     -   id: use-tidy-description
     -   id: spell-check
         exclude: >
           (?x)^(
-          data/.*| 
+          data/.*|
           (.*/|)\.Rprofile|
           (.*/|)\.Renviron|
           (.*/|)\.gitignore|
@@ -32,14 +32,14 @@ repos:
           .*\.sh|
           .*\.RData
           )$
-    -   id: lintr
+    #-   id: lintr
     -   id: readme-rmd-rendered
     -   id: parsable-R
     -   id: no-browser-statement
     -   id: deps-in-desc
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.4.0
-    hooks: 
+    hooks:
     -   id: check-added-large-files
         args: ['--maxkb=200']
     -   id: end-of-file-fixer

05-origami.Rmd

@@ -212,7 +212,7 @@ washb_data <- fread(
 washb_data <- washb_data[1:30, ]
 head(washb_data) %>%
   kable() %>%
-  kableExtra:::kable_styling(fixed_thead = TRUE) %>%
+  kableExtra::kable_styling(fixed_thead = TRUE) %>%
   scroll_box(width = "100%", height = "300px")
 ```
 
@@ -655,7 +655,7 @@ covars <- colnames(washb_data)[-which(names(washb_data) == outcome)]
 
 head(washb_data) %>%
   kable() %>%
-  kableExtra:::kable_styling(fixed_thead = TRUE) %>%
+  kableExtra::kable_styling(fixed_thead = TRUE) %>%
   scroll_box(width = "100%", height = "300px")
 ```
 

06-sl3.Rmd

@@ -315,7 +315,7 @@ washb_data <- fread(
 )
 head(washb_data) %>%
   kable() %>%
-  kableExtra:::kable_styling(fixed_thead = T) %>%
+  kableExtra::kable_styling(fixed_thead = T) %>%
   scroll_box(width = "100%", height = "300px")
 ```
 
@@ -800,7 +800,7 @@ CVsl <- CV_lrnr_sl(
 )
 CVsl %>%
   kable(digits = 4) %>%
-  kableExtra:::kable_styling(fixed_thead = TRUE) %>%
+  kableExtra::kable_styling(fixed_thead = TRUE) %>%
   scroll_box(width = "100%", height = "300px")
 ```
 <!-- Explain summary!!!! -->
@@ -838,7 +838,7 @@ Let's explore the `sl3` variable importance measurements for the `washb` data.
 washb_varimp <- importance(sl_fit, loss = loss_squared_error, type = "permute")
 washb_varimp %>%
   kable(digits = 4) %>%
-  kableExtra:::kable_styling(fixed_thead = TRUE) %>%
+  kableExtra::kable_styling(fixed_thead = TRUE) %>%
   scroll_box(width = "100%", height = "300px")
 ```
 
@@ -872,7 +872,7 @@ chspred <- read_csv(file = db_data, col_names = TRUE)
 # take a quick peek
 head(chspred) %>%
   kable(digits = 4) %>%
-  kableExtra:::kable_styling(fixed_thead = TRUE) %>%
+  kableExtra::kable_styling(fixed_thead = TRUE) %>%
   scroll_box(width = "100%", height = "300px")
 ```
 

11-tmle3survival.Rmd

@@ -36,13 +36,15 @@ library(sl3)
 
 ```{r}
 vet_data <- read.csv(
-  paste0("https://raw.githubusercontent.com/tlverse/deming2019-workshop/",
-         "master/data/veteran.csv")
+  paste0(
+    "https://raw.githubusercontent.com/tlverse/deming2019-workshop/",
+    "master/data/veteran.csv"
+  )
 )
 vet_data$trt <- vet_data$trt - 1
 # make fewer times for illustration
 vet_data$time <- ceiling(vet_data$time / 20)
-k_grid <- seq_len(:max(vet_data$time))
+k_grid <- seq_len(max(vet_data$time))
 head(vet_data)
 ```
 
@@ -70,14 +72,20 @@ speficy W (covariates), A (treatment/intervention), T_tilde (time-to-event
 vector), Delta (censoring indicator vector), and row ids for the nodelist.
 
 ```{r}
-var_types <- list(T_tilde = Variable_Type$new("continuous"),
-                  t = Variable_Type$new("continuous"),
-                  Delta = Variable_Type$new("binomial"))
-survival_spec <- tmle_survival(treatment_level = 1, control_level = 0,
-                                 target_times = intersect(1:10, k_grid),
-                                 variable_types = var_types)
-node_list <- list(W = c("celltype", "karno", "diagtime", "age", "prior"),
-                  A = "trt", T_tilde = "time", Delta = "status", id ="X")
+var_types <- list(
+  T_tilde = Variable_Type$new("continuous"),
+  t = Variable_Type$new("continuous"),
+  Delta = Variable_Type$new("binomial")
+)
+survival_spec <- tmle_survival(
+  treatment_level = 1, control_level = 0,
+  target_times = intersect(1:10, k_grid),
+  variable_types = var_types
+)
+node_list <- list(
+  W = c("celltype", "karno", "diagtime", "age", "prior"),
+  A = "trt", T_tilde = "time", Delta = "status", id = "X"
+)
 
 long_data_tuple <- survival_spec$transform_data(vet_data, node_list)
 df_long <- long_data_tuple$long_data
@@ -98,8 +106,10 @@ learner_list <- list(A = sl_A, N = sl_A, A_c = sl_A)
 
 ```{r}
 tmle_task <- survival_spec$make_tmle_task(df_long, long_node_list)
-initial_likelihood <- survival_spec$make_initial_likelihood(tmle_task,
-                                                            learner_list)
+initial_likelihood <- survival_spec$make_initial_likelihood(
+  tmle_task,
+  learner_list
+)
 ```
 
 ### Perform TMLE adjustment of the initial conditional survival estimate
@@ -116,11 +126,12 @@ up <- tmle3_Update_survival$new(
   delta_epsilon = 1e-2,
   fit_method = "l2",
   use_best = TRUE,
-  verbose=FALSE
+  verbose = FALSE
 )
 
 targeted_likelihood <- Targeted_Likelihood$new(initial_likelihood,
-                                               updater = up)
+  updater = up
+)
 tmle_params <- survival_spec$make_params(tmle_task, targeted_likelihood)
 tmle_fit_manual <- fit_tmle3(
   tmle_task, targeted_likelihood, tmle_params,

Makefile

@@ -12,6 +12,6 @@ style:
 	Rscript -e "styler::style_dir(filetype = 'rmd')"
 
 code:
-	rm R/*.R
+	rm -f R_code/*.R
 	R CMD BATCH purl.R
 	rm purl.Rout .RData

R/02-roadmap.R → R_code/02-roadmap.R

@@ -18,4 +18,3 @@ tidy_dag <- tidy_dagitty(dag)
 # visualize DAG
 ggdag(tidy_dag) +
   theme_dag()
-

R/03-tlverse.R → R_code/03-tlverse.R

@@ -1,4 +1,3 @@
 ## ----installation, eval=FALSE-------------------------------------------------
-## install.packages("usethis")
-## usethis::install_github("tlverse/tlverse")
-
+## install.packages("devtools")
+## devtools::install_github("tlverse/tlverse")

R/04-data.R → R_code/04-data.R

@@ -60,4 +60,3 @@ if (knitr::is_latex_output()) {
 } else {
   skim(nhefs_data)
 }
-

R/05-origami.R → R_code/05-origami.R

@@ -16,7 +16,7 @@ washb_data <- fread(
 washb_data <- washb_data[1:30, ]
 head(washb_data) %>%
   kable() %>%
-  kableExtra:::kable_styling(fixed_thead = TRUE) %>%
+  kableExtra::kable_styling(fixed_thead = TRUE) %>%
   scroll_box(width = "100%", height = "300px")
 
 
@@ -122,7 +122,7 @@ covars <- colnames(washb_data)[-which(names(washb_data) == outcome)]
 
 head(washb_data) %>%
   kable() %>%
-  kableExtra:::kable_styling(fixed_thead = TRUE) %>%
+  kableExtra::kable_styling(fixed_thead = TRUE) %>%
   scroll_box(width = "100%", height = "300px")
 
 
@@ -285,4 +285,3 @@ mses <- cross_validate(
 )
 mses$mse
 colMeans(mses$mse[, c("arima", "arima2")])
-