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Auto-generated via `{sandpaper}` Source : d6986b0 Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2024-12-24 06:14:37 +0000 Message : markdown source builds Auto-generated via `{sandpaper}` Source : 4b0ed0e Branch : main Author : carpenter <[email protected]> Time : 2024-12-24 06:11:26 +0000 Message : Local build seems to work with mult cores
carpentries-incubator · Dec 24, 2024 · 3c3f988 · 3c3f988
1 parent 7efead5
commit 3c3f988
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Showing 55 changed files with 2,081 additions and 1,541 deletions.
diff --git a/404.html b/404.html
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
diff --git a/LICENSE.html b/LICENSE.html
diff --git a/aio.html b/aio.html
diff --git a/basic-targets.html b/basic-targets.html
diff --git a/branch.html b/branch.html
diff --git a/cache.html b/cache.html
diff --git a/files.html b/files.html
diff --git a/files/plans/plan_10.R b/files/plans/plan_10.R
@@ -16,27 +16,26 @@ tar_plan(
     path_to_file("penguins_raw.csv"),
     read_csv(!!.x, show_col_types = FALSE)
   ),
-  # Clean data
-  penguins_data = clean_penguin_data(penguins_data_raw),
-  # Build models
-  models = list(
-    combined_model = lm(
-      bill_depth_mm ~ bill_length_mm, data = penguins_data),
-    species_model = lm(
-      bill_depth_mm ~ bill_length_mm + species, data = penguins_data),
-    interaction_model = lm(
-      bill_depth_mm ~ bill_length_mm * species, data = penguins_data)
+  # Clean and group data
+  tar_group_by(
+    penguins_data,
+    clean_penguin_data(penguins_data_raw),
+    species
   ),
-  # Get model summaries
+  # Get summary of combined model with all species together
+  combined_summary = model_glance_slow(penguins_data),
+  # Get summary of one model per species
   tar_target(
-    model_summaries,
-    glance_with_mod_name_slow(models),
-    pattern = map(models)
+    species_summary,
+    model_glance_slow(penguins_data),
+    pattern = map(penguins_data)
   ),
-  # Get model predictions
+  # Get predictions of combined model with all species together
+  combined_predictions = model_augment_slow(penguins_data),
+  # Get predictions of one model per species
   tar_target(
-    model_predictions,
-    augment_with_mod_name_slow(models),
-    pattern = map(models)
+    species_predictions,
+    model_augment_slow(penguins_data),
+    pattern = map(penguins_data)
   )
 )
diff --git a/files/plans/plan_11.R b/files/plans/plan_11.R
@@ -9,34 +9,32 @@ tar_plan(
     path_to_file("penguins_raw.csv"),
     read_csv(!!.x, show_col_types = FALSE)
   ),
-  # Clean data
-  penguins_data = clean_penguin_data(penguins_data_raw),
-  # Build models
-  models = list(
-    combined_model = lm(
-      bill_depth_mm ~ bill_length_mm, data = penguins_data),
-    species_model = lm(
-      bill_depth_mm ~ bill_length_mm + species, data = penguins_data),
-    interaction_model = lm(
-      bill_depth_mm ~ bill_length_mm * species, data = penguins_data)
+  # Clean and group data
+  tar_group_by(
+    penguins_data,
+    clean_penguin_data(penguins_data_raw),
+    species
   ),
-  # Get model summaries
+  # Get summary of combined model with all species together
+  combined_summary = model_glance(penguins_data),
+  # Get summary of one model per species
   tar_target(
-    model_summaries,
-    glance_with_mod_name(models),
-    pattern = map(models)
+    species_summary,
+    model_glance(penguins_data),
+    pattern = map(penguins_data)
   ),
-  # Get model predictions
+  # Get predictions of combined model with all species together
+  combined_predictions = model_augment(penguins_data),
+  # Get predictions of one model per species
   tar_target(
-    model_predictions,
-    augment_with_mod_name(models),
-    pattern = map(models)
+    species_predictions,
+    model_augment(penguins_data),
+    pattern = map(penguins_data)
   ),
   # Generate report
   tar_quarto(
     penguin_report,
     path = "penguin_report.qmd",
-    quiet = FALSE,
-    packages = c("targets", "tidyverse")
+    quiet = FALSE
   )
 )
diff --git a/files/plans/plan_5.R b/files/plans/plan_5.R
@@ -16,16 +16,21 @@ tar_plan(
     bill_depth_mm ~ bill_length_mm,
     data = penguins_data
   ),
-  species_model = lm(
-    bill_depth_mm ~ bill_length_mm + species,
-    data = penguins_data
+  adelie_model = lm(
+    bill_depth_mm ~ bill_length_mm,
+    data = filter(penguins_data, species == "Adelie")
   ),
-  interaction_model = lm(
-    bill_depth_mm ~ bill_length_mm * species,
-    data = penguins_data
+  chinstrap_model = lm(
+    bill_depth_mm ~ bill_length_mm,
+    data = filter(penguins_data, species == "Chinstrap")
+  ),
+  gentoo_model = lm(
+    bill_depth_mm ~ bill_length_mm,
+    data = filter(penguins_data, species == "Gentoo")
   ),
   # Get model summaries
   combined_summary = glance(combined_model),
-  species_summary = glance(species_model),
-  interaction_summary = glance(interaction_model)
+  adelie_summary = glance(adelie_model),
+  chinstrap_summary = glance(chinstrap_model),
+  gentoo_summary = glance(gentoo_model)
 )
diff --git a/files/plans/plan_6.R b/files/plans/plan_6.R
@@ -11,19 +11,18 @@ tar_plan(
   ),
   # Clean data
   penguins_data = clean_penguin_data(penguins_data_raw),
-  # Build models
-  models = list(
-    combined_model = lm(
-      bill_depth_mm ~ bill_length_mm, data = penguins_data),
-    species_model = lm(
-      bill_depth_mm ~ bill_length_mm + species, data = penguins_data),
-    interaction_model = lm(
-      bill_depth_mm ~ bill_length_mm * species, data = penguins_data)
+  # Group data
+  tar_group_by(
+    penguins_data_grouped,
+    penguins_data,
+    species
   ),
-  # Get model summaries
+  # Build combined model with all species together
+  combined_summary = model_glance(penguins_data),
+  # Build one model per species
   tar_target(
-    model_summaries,
-    glance(models[[1]]),
-    pattern = map(models)
+    species_summary,
+    model_glance(penguins_data_grouped),
+    pattern = map(penguins_data_grouped)
   )
 )
diff --git a/files/plans/plan_6b.R b/files/plans/plan_6b.R
@@ -0,0 +1,28 @@
+options(tidyverse.quiet = TRUE)
+source("R/packages.R")
+source("R/functions.R")
+
+tar_plan(
+  # Load raw data
+  tar_file_read(
+    penguins_data_raw,
+    path_to_file("penguins_raw.csv"),
+    read_csv(!!.x, show_col_types = FALSE)
+  ),
+  # Clean data
+  penguins_data = clean_penguin_data(penguins_data_raw),
+  # Group data
+  tar_group_by(
+    penguins_data_grouped,
+    penguins_data,
+    species
+  ),
+  # Build combined model with all species together
+  combined_summary = model_glance_orig(penguins_data),
+  # Build one model per species
+  tar_target(
+    species_summary,
+    model_glance_orig(penguins_data_grouped),
+    pattern = map(penguins_data_grouped)
+  )
+)
diff --git a/files/plans/plan_7.R b/files/plans/plan_7.R
@@ -11,19 +11,26 @@ tar_plan(
   ),
   # Clean data
   penguins_data = clean_penguin_data(penguins_data_raw),
-  # Build models
-  models = list(
-    combined_model = lm(
-      bill_depth_mm ~ bill_length_mm, data = penguins_data),
-    species_model = lm(
-      bill_depth_mm ~ bill_length_mm + species, data = penguins_data),
-    interaction_model = lm(
-      bill_depth_mm ~ bill_length_mm * species, data = penguins_data)
+  # Group data
+  tar_group_by(
+    penguins_data_grouped,
+    penguins_data,
+    species
   ),
-  # Get model summaries
+  # Get summary of combined model with all species together
+  combined_summary = model_glance(penguins_data),
+  # Get summary of one model per species
   tar_target(
-    model_summaries,
-    glance_with_mod_name(models),
-    pattern = map(models)
+    species_summary,
+    model_glance(penguins_data_grouped),
+    pattern = map(penguins_data_grouped)
+  ),
+  # Get predictions of combined model with all species together
+  combined_predictions = model_augment(penguins_data_grouped),
+  # Get predictions of one model per species
+  tar_target(
+    species_predictions,
+    model_augment(penguins_data_grouped),
+    pattern = map(penguins_data_grouped)
   )
 )
diff --git a/files/plans/plan_8.R b/files/plans/plan_8.R
@@ -9,27 +9,26 @@ tar_plan(
     path_to_file("penguins_raw.csv"),
     read_csv(!!.x, show_col_types = FALSE)
   ),
-  # Clean data
-  penguins_data = clean_penguin_data(penguins_data_raw),
-  # Build models
-  models = list(
-    combined_model = lm(
-      bill_depth_mm ~ bill_length_mm, data = penguins_data),
-    species_model = lm(
-      bill_depth_mm ~ bill_length_mm + species, data = penguins_data),
-    interaction_model = lm(
-      bill_depth_mm ~ bill_length_mm * species, data = penguins_data)
+  # Clean and group data
+  tar_group_by(
+    penguins_data,
+    clean_penguin_data(penguins_data_raw),
+    species
   ),
-  # Get model summaries
+  # Get summary of combined model with all species together
+  combined_summary = model_glance(penguins_data),
+  # Get summary of one model per species
   tar_target(
-    model_summaries,
-    glance_with_mod_name(models),
-    pattern = map(models)
+    species_summary,
+    model_glance(penguins_data),
+    pattern = map(penguins_data)
   ),
-  # Get model predictions
+  # Get predictions of combined model with all species together
+  combined_predictions = model_augment(penguins_data),
+  # Get predictions of one model per species
   tar_target(
-    model_predictions,
-    augment_with_mod_name(models),
-    pattern = map(models)
+    species_predictions,
+    model_augment(penguins_data),
+    pattern = map(penguins_data)
   )
 )