From eaf62b1a3fb81933ed7540b46e3744c800a83b30 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Sat, 30 Sep 2023 03:18:28 +0000
Subject: [PATCH 01/18] section: what are tensors

---
 03_tensors.Rmd | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/03_tensors.Rmd b/03_tensors.Rmd
index 3d16e0d..1232170 100644
--- a/03_tensors.Rmd
+++ b/03_tensors.Rmd
@@ -4,10 +4,24 @@
 
 - THESE ARE NICE TO HAVE BUT NOT ABSOLUTELY NECESSARY
 
-## SLIDE 1 {-}
+## What are tensors? {-}
+
+```{r}
+library(torch)
+t1 <- torch_tensor(2)
+summary(t1)
+t1$dtype
+t1$device
+t1$shape
+t2 <- t1$to(dtype = torch_int())
+t2$dtype
+t2 <- t1$to(device = "cuda")
+t2$device
+t3 <- t1$view(c(1,1))
+t3$shape
+```
 
-- ADD SLIDES AS SECTIONS (`##`).
-- TRY TO KEEP THEM RELATIVELY SLIDE-LIKE; THESE ARE NOTES, NOT THE BOOK ITSELF.
+## Creating tensors
 
 ## Meeting Videos {-}
 

From c4661b3b1cab73ee0ffa86e54e4d4aa86794816a Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Mon, 2 Oct 2023 16:33:09 +0000
Subject: [PATCH 02/18] Added material for pages 9-17 of book.

---
 03_tensors.Rmd | 90 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 88 insertions(+), 2 deletions(-)

diff --git a/03_tensors.Rmd b/03_tensors.Rmd
index 1232170..99ffc26 100644
--- a/03_tensors.Rmd
+++ b/03_tensors.Rmd
@@ -6,23 +6,109 @@
 
 ## What are tensors? {-}
 
+> "*tensors* are 'just' multi-dimensional arrays optimized for fast computation - 
+not on the CPU only but also on specialized devices such as GPUs and TPUs.
+
+Create a tensor:
+
 ```{r}
 library(torch)
 t1 <- torch_tensor(2)
+
+t3 <- t1$view(c(1,1))
+t3$shape
+```
+
+Parameters of `torch_tensor()` (see help file for this function):
+
+* `data`
+* `dtype`
+* `device`
+* `requires_grad`
+* `pin_memory`
+
+Look at the attributes of the tensor:
+
+```{r}
 summary(t1)
 t1$dtype
 t1$device
 t1$shape
+```
+
+Change attributes:
+
+```{r}
+# to integer:
 t2 <- t1$to(dtype = torch_int())
 t2$dtype
+
+# utilize GPU:
 t2 <- t1$to(device = "cuda")
 t2$device
-t3 <- t1$view(c(1,1))
-t3$shape
 ```
 
+
+
+
 ## Creating tensors
 
+### Tensors from values
+
+Defaults: long integer type and CPU device.
+
+```{r}
+torch_tensor(1:5, dtype = torch_float(), device = "cuda")
+```
+
+Matrix:
+
+```{r}
+torch_tensor(matrix(1:9, ncol = 3, byrow = TRUE))
+```
+
+Higher dimensions:
+
+```{r}
+torch_tensor(array(1:24, dim = c(4,3,2)))
+```
+
+### Tensors from specifications
+
+```{r}
+#normal distribution:
+torch_randn(3, 3)
+
+#unfiorm distribution
+torch_rand(3, 3)
+```
+
+```{r}
+torch_zeros(2,2)
+torch_ones(3,3)
+torch_eye(3,3)
+torch_diag(c(1,2,3))
+```
+
+See full list at https://torch.mlverse.org/docs/reference/#tensor-creation-utilities. 
+
+### Tensors from datasets
+
+```{r}
+JohnsonJohnson
+```
+
+```{r}
+library(modeldata) # Need to install 0.1.1 to obtain okc data. https://cran.r-project.org/src/contrib/Archive/modeldata/
+library(tidyverse)
+
+data(okc)
+okc |> glimpse()
+```
+
+If your data contains `NA`s, you'll need to convert them before training a neural network 
+(topic to be covered later).
+
 ## Meeting Videos {-}
 
 ### Cohort 1 {-}

From feef41ec4b9807ab531cdf27e557c8bb316d6114 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 13:17:14 +0000
Subject: [PATCH 03/18] Added additional content.

---
 03_tensors.Rmd | 284 ++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 272 insertions(+), 12 deletions(-)

diff --git a/03_tensors.Rmd b/03_tensors.Rmd
index 99ffc26..f2317c4 100644
--- a/03_tensors.Rmd
+++ b/03_tensors.Rmd
@@ -2,18 +2,34 @@
 
 **Learning objectives:**
 
-- THESE ARE NICE TO HAVE BUT NOT ABSOLUTELY NECESSARY
+Learn how to:
+
+- Create and modify tensors
+- Access parts of tensors
+- Apply operations to tensors
 
 ## What are tensors? {-}
 
-> "*tensors* are 'just' multi-dimensional arrays optimized for fast computation - 
+From the book:
+
+> "... *tensors* are 'just' multi-dimensional arrays optimized for fast computation - 
 not on the CPU only but also on specialized devices such as GPUs and TPUs.
 
+Similar to an R array object.
+
+Load libraries:
+
+```{r message = FALSE, warning=FALSE}
+library(tidyverse)
+library(torch)
+library(modeldata) # Need to install 0.1.1 to obtain okc data. https://cran.r-project.org/src/contrib/Archive/modeldata/
+```
+
 Create a tensor:
 
 ```{r}
-library(torch)
 t1 <- torch_tensor(2)
+t1$shape
 
 t3 <- t1$view(c(1,1))
 t3$shape
@@ -49,8 +65,6 @@ t2$device
 ```
 
 
-
-
 ## Creating tensors
 
 ### Tensors from values
@@ -95,20 +109,266 @@ See full list at https://torch.mlverse.org/docs/reference/#tensor-creation-utili
 ### Tensors from datasets
 
 ```{r}
-JohnsonJohnson
+data(okc) # from modeldata library
+okc |> glimpse()
 ```
 
 ```{r}
-library(modeldata) # Need to install 0.1.1 to obtain okc data. https://cran.r-project.org/src/contrib/Archive/modeldata/
-library(tidyverse)
-
-data(okc)
-okc |> glimpse()
+okc |> 
+  mutate(diet = as.numeric(factor(diet)),
+         location = as.numeric(factor(location)),
+         Class = as.numeric(Class),
+         date = as.numeric(date)) |>
+  as.matrix() |>
+  torch_tensor() |>
+  print(5)
 ```
 
-If your data contains `NA`s, you'll need to convert them before training a neural network 
+Tip: Above transformation lost information. For example, you may instead want to
+use lat/long for location instead of converting to factor.
+
+If your data contains `NA`'s, you'll need to convert them before training a neural network 
 (topic to be covered later).
 
+## Operations on Tensors
+
+```{r}
+t1 <- torch_tensor(c(1,2))
+t2 <- torch_tensor(c(3,4))
+```
+
+Add:
+
+```{r}
+torch_add(t1, t2) # t1 is NOT modified
+t1$add(t2) # t1 is NOT modified
+t1$add_(t2) # t1 IS modified
+t1
+```
+
+In general: 
+
+* underscore appended to operation indicates modification in-place.
+* torch does not distinguish between row and column vectors.
+* Other examples of operations: `torch_t()`, `torch_dot()`, `torch_matmul()`, and `torch_multiply()`. 
+See https://torch.mlverse.org/docs/reference/#mathematical-operations-on-tensors.
+
+```{r}
+t1 <- torch_tensor(1:3)
+t2 <- torch_tensor(4:6)
+```
+
+```{r}
+t1$dot(t2)
+```
+
+### Summary operations
+
+```{r}
+m <- outer(1:3, 1:6)
+t <- torch_outer(torch_tensor(1:3), torch_tensor(1:6))
+```
+
+```{r}
+apply(m, 1, sum) # row sums (of R matrix)
+t$sum(dim = 2) # row sums (of tensor)
+```
+
+* In R, we *group* by row (dimension 1) for row summaries and by columns (dimension 2) for column summaries
+* In `torch, we *collapse* the columns (dimension 2) for row summaries and the rows (dimension 1) for column summaries.
+
+Time series example: Two features collected three times for four individuals. 
+
+* Dimension 1: Runs over individuals
+* Dimension 2: Runs over points in time
+* Dimension 3: Runs over features
+
+```{r}
+t <- torch_randn(4, 3, 2)
+t
+```
+
+Obtain averages of features, independent of subject (dimension 1) and time (dimension 2):
+
+```{r}
+t$mean(dim = c(1, 2))
+```
+
+
+## Accessing Parts of a Tensor (indexing and slicing)
+
+Indexing in `torch` is 1-based. Very similar to functionality in R.
+
+Example:
+
+```{r}
+t <- torch_tensor(matrix(1:9, ncol = 3, byrow = TRUE))
+t
+t[1, ] # row 1. 
+t[1, , drop = FALSE] # Same as above except that dimensionality is preserved
+```
+
+Slicing example:
+
+```{r}
+t <- torch_rand(3, 3, 3)
+t[1:2, 2:3, c(1, 3)]
+```
+
+### Beyond R
+
+Access last element:
+
+```{r}
+t <- torch_tensor(matrix(1:4, ncol = 2, byrow = TRUE))
+t[-1, -1]
+```
+
+Compare to R:
+
+```{r}
+# matrix:
+m <- matrix(1:4, ncol = 2, byrow = TRUE)
+m[-1, -1]
+
+# vector:
+m <- 1:4
+m[-1]
+```
+
+Step pattern:
+
+```{r}
+t <- torch_tensor(matrix(1:20, ncol = 10, byrow = TRUE))
+t
+t[ , 1:8:2] # every other value in columns 1 through 8
+```
+
+Use `..` to designate all dimensions not explicitly referenced.
+
+```{r}
+t2 <- torch_randn(2, 2, 2)
+t2
+t2[2, ..] # 2nd element of the 1st dimension
+```
+
+## Reshaping Tensors
+
+Two methods:
+
+* `view`: Zero-copy reshape (by changing tensor metadata). Will fail if zero-copy reshape is not possible.
+* `reshape`: Uses zero-copy reshape (via metadata) when possible. If not, then will make a copy.
+
+```{r}
+t <- torch_tensor(matrix(1:15, nrow = 3, byrow = TRUE))
+t
+t$stride()
+
+# Change shape of t using view():
+t2 <- t$view(c(5,3))
+t2
+t2$stride()
+```
+
+Check memory location:
+
+```{r}
+t$storage()$data_ptr()
+t2$storage()$data_ptr() # same location
+```
+
+
+View vs reshape:
+
+When two operations that change the stride are done in sequence, this will likely fail.
+Below is an example of transpose, `t()` followed by `view()`.
+
+```{r eval = FALSE}
+t$t()$view(15) # error
+```
+
+However, `reshape()` makes a copy of the underlying data and does not fail.
+
+```{r}
+t3 <- t$t()$reshape(15) # no error
+t3
+```
+
+
+Now the memory locations of t3 and the original data are different:
+
+```{r}
+t$storage()$data_ptr()
+t3$storage()$data_ptr() # different location
+```
+
+Two additional functions that are zero-copy operations:
+
+* `squeeze()`: Removes singleton dimensions
+* `unsqueeze()`: Adds a singleton dimension
+
+```{r}
+t <- torch_rand(3) # one dimensional tensor of shape 3
+t
+t2 <- t$unsqueeze(1) # two dimensional tensor of shape {1,3}
+t2
+```
+Inspect location:
+
+```{r}
+t$storage()$data_ptr()
+t2$storage()$data_ptr() # same location
+```
+
+
+## Broadcasting
+
+Example: Want to add two tensors of shape 3x7x1 and 1x5
+
+```
+t1 shape: 3 7 1
+t2 shape:   1 5
+```
+
+Broadcast (from right to left):
+
+```
+t1 shape: 3 7 5
+t2 shape:   7 5
+```
+
+Next, virtual expansion:
+
+```
+t1 shape: 3 7 5
+t2 shape: 1 7 5
+```
+
+And, broadcast again:
+
+```
+t1 shape: 3 7 5
+t2 shape: 3 7 5
+```
+
+Let's see it in action:
+
+```{r}
+t1 <- torch_ones(3, 7, 1)
+t2 <- torch_zeros(1, 5)
+torch_add(t1, t2)
+```
+
+The following will NOT work:
+
+```{r eval = FALSE}
+t1 <- torch_ones(3, 7, 1)
+t2 <- torch_zeros(6, 5)
+torch_add(t1, t2)
+```
+
+
+
 ## Meeting Videos {-}
 
 ### Cohort 1 {-}

From f92d14923002e236e2ed56107221e0abf3f6cfa8 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 14:58:13 +0000
Subject: [PATCH 04/18] cleanup. added torch_tensor() example and stride
 definition.

---
 03_tensors.Rmd | 53 +++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 42 insertions(+), 11 deletions(-)

diff --git a/03_tensors.Rmd b/03_tensors.Rmd
index f2317c4..5fae80f 100644
--- a/03_tensors.Rmd
+++ b/03_tensors.Rmd
@@ -15,24 +15,23 @@ From the book:
 > "... *tensors* are 'just' multi-dimensional arrays optimized for fast computation - 
 not on the CPU only but also on specialized devices such as GPUs and TPUs.
 
-Similar to an R array object.
-
 Load libraries:
 
+Note: Need to install `modeldata` 0.1.1 to obtain `okc` data. Download package from https://cran.r-project.org/src/contrib/Archive/modeldata/.
+
 ```{r message = FALSE, warning=FALSE}
-library(tidyverse)
 library(torch)
-library(modeldata) # Need to install 0.1.1 to obtain okc data. https://cran.r-project.org/src/contrib/Archive/modeldata/
+library(tidyverse)
+library(modeldata) 
 ```
 
+
+
 Create a tensor:
 
 ```{r}
 t1 <- torch_tensor(2)
 t1$shape
-
-t3 <- t1$view(c(1,1))
-t3$shape
 ```
 
 Parameters of `torch_tensor()` (see help file for this function):
@@ -46,10 +45,10 @@ Parameters of `torch_tensor()` (see help file for this function):
 Look at the attributes of the tensor:
 
 ```{r}
-summary(t1)
 t1$dtype
 t1$device
 t1$shape
+summary(t1)
 ```
 
 Change attributes:
@@ -69,7 +68,28 @@ t2$device
 
 ### Tensors from values
 
-Defaults: long integer type and CPU device.
+**Defaults**: long integer type and CPU device.
+
+Let's test this:
+
+```{r}
+torch_tensor(1:2)
+```
+
+
+```{r}
+torch_tensor(c(1,2))
+```
+
+My guess is that the difference is due to the data types of `1:2` and `c(1,2)`:
+
+```{r hold=TRUE}
+class(c(1,2))
+class(1:2)
+```
+
+
+Set the type and device:
 
 ```{r}
 torch_tensor(1:5, dtype = torch_float(), device = "cuda")
@@ -224,6 +244,11 @@ t <- torch_tensor(matrix(1:4, ncol = 2, byrow = TRUE))
 t[-1, -1]
 ```
 
+```{r}
+t <- torch_tensor(1:4)
+t[-1]
+```
+
 Compare to R:
 
 ```{r}
@@ -263,13 +288,19 @@ Two methods:
 t <- torch_tensor(matrix(1:15, nrow = 3, byrow = TRUE))
 t
 t$stride()
+```
+
+`$stride()` tells us the jump necessary to go from one element to the next in a single dimension (e.g. the stride necessary to get from one row to the next).
 
-# Change shape of t using view():
+Next, change shape of `t` using `view()`:
+
+```{r}
 t2 <- t$view(c(5,3))
 t2
 t2$stride()
 ```
 
+
 Check memory location:
 
 ```{r}
@@ -278,7 +309,7 @@ t2$storage()$data_ptr() # same location
 ```
 
 
-View vs reshape:
+`view()` vs `reshape()`:
 
 When two operations that change the stride are done in sequence, this will likely fail.
 Below is an example of transpose, `t()` followed by `view()`.

From 18f33f0776873824775019f2505f8e8b0aba4ab7 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 16:40:08 +0000
Subject: [PATCH 05/18] Removed cuda specific operations for push to GitHub.

---
 03_tensors.Rmd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/03_tensors.Rmd b/03_tensors.Rmd
index 5fae80f..3917c72 100644
--- a/03_tensors.Rmd
+++ b/03_tensors.Rmd
@@ -59,8 +59,8 @@ t2 <- t1$to(dtype = torch_int())
 t2$dtype
 
 # utilize GPU:
-t2 <- t1$to(device = "cuda")
-t2$device
+#t2 <- t1$to(device = "cuda")
+#t2$device
 ```
 
 
@@ -91,7 +91,7 @@ class(1:2)
 
 Set the type and device:
 
-```{r}
+```{r eval=FALSE}
 torch_tensor(1:5, dtype = torch_float(), device = "cuda")
 ```
 

From fa5bbe0f14c17ef16e69e2f29c8f5c4162423ec3 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 17:34:26 +0000
Subject: [PATCH 06/18] adding torch

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7dd5b88..a51d3a6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,5 +9,6 @@ Depends:
     R (>= 3.1.0)
 Imports: 
     bookdown,
-    rmarkdown
+    rmarkdown,
+    torch
 Encoding: UTF-8

From d36bbd5bbf1b42eeee76707e856fe1e682ab47ad Mon Sep 17 00:00:00 2001
From: Jon Harmon <jonthegeek@gmail.com>
Date: Wed, 4 Oct 2023 13:28:20 -0500
Subject: [PATCH 07/18] Add tidyverse and modeldata to DESCRIPTION

---
 DESCRIPTION | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index a51d3a6..eebe0fb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,6 +9,8 @@ Depends:
     R (>= 3.1.0)
 Imports: 
     bookdown,
+    modeldata,
     rmarkdown,
+    tidyverse,
     torch
 Encoding: UTF-8

From 8ca99c43dc783c7bfba237aa9e54e8173fadd234 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 21:23:57 +0000
Subject: [PATCH 08/18] Changed okc data to presidential data. Removed
 modeldata package.

---
 03_tensors.Rmd | 52 ++++++++++++++++++++++++++------------------------
 1 file changed, 27 insertions(+), 25 deletions(-)

diff --git a/03_tensors.Rmd b/03_tensors.Rmd
index 3917c72..e1b34be 100644
--- a/03_tensors.Rmd
+++ b/03_tensors.Rmd
@@ -17,16 +17,11 @@ not on the CPU only but also on specialized devices such as GPUs and TPUs.
 
 Load libraries:
 
-Note: Need to install `modeldata` 0.1.1 to obtain `okc` data. Download package from https://cran.r-project.org/src/contrib/Archive/modeldata/.
-
 ```{r message = FALSE, warning=FALSE}
 library(torch)
 library(tidyverse)
-library(modeldata) 
 ```
 
-
-
 Create a tensor:
 
 ```{r}
@@ -57,10 +52,12 @@ Change attributes:
 # to integer:
 t2 <- t1$to(dtype = torch_int())
 t2$dtype
+```
 
+```{r eval=FALSE}
 # utilize GPU:
-#t2 <- t1$to(device = "cuda")
-#t2$device
+t2 <- t1$to(device = "cuda")
+t2$device
 ```
 
 
@@ -68,34 +65,34 @@ t2$dtype
 
 ### Tensors from values
 
-**Defaults**: long integer type and CPU device.
+**Defaults**: long integer type and CPU device
 
 Let's test this:
 
 ```{r}
 torch_tensor(1:2)
 ```
-
+In the example above, the type is long integer.
 
 ```{r}
 torch_tensor(c(1,2))
 ```
 
-My guess is that the difference is due to the data types of `1:2` and `c(1,2)`:
+In this example, the type is float instead of a long integer. 
+My guess is that the difference is due to the difference in data types of `1:2` and `c(1,2)`:
 
-```{r hold=TRUE}
+```{r}
 class(c(1,2))
 class(1:2)
 ```
 
+Explicitly set the type and device:
 
-Set the type and device:
-
-```{r eval=FALSE}
+```{r eval = FALSE}
 torch_tensor(1:5, dtype = torch_float(), device = "cuda")
 ```
 
-Matrix:
+Two-dimensional tensor:
 
 ```{r}
 torch_tensor(matrix(1:9, ncol = 3, byrow = TRUE))
@@ -128,30 +125,31 @@ See full list at https://torch.mlverse.org/docs/reference/#tensor-creation-utili
 
 ### Tensors from datasets
 
+We'll look at the `presidential` dataset from the `ggplot2` package:
+
 ```{r}
-data(okc) # from modeldata library
-okc |> glimpse()
+data(presidential) # from ggplot2 
+presidential |> glimpse()
 ```
 
 ```{r}
-okc |> 
-  mutate(diet = as.numeric(factor(diet)),
-         location = as.numeric(factor(location)),
-         Class = as.numeric(Class),
-         date = as.numeric(date)) |>
+presidential |> 
+  mutate(name = as.numeric(factor(name)),
+         start = as.numeric(start),
+         end = as.numeric(end),
+         party = as.numeric(factor(party))) |>
   as.matrix() |>
   torch_tensor() |>
   print(5)
 ```
 
-Tip: Above transformation lost information. For example, you may instead want to
-use lat/long for location instead of converting to factor.
-
 If your data contains `NA`'s, you'll need to convert them before training a neural network 
 (topic to be covered later).
 
 ## Operations on Tensors
 
+Define two tensors:
+
 ```{r}
 t1 <- torch_tensor(c(1,2))
 t2 <- torch_tensor(c(3,4))
@@ -173,6 +171,8 @@ In general:
 * Other examples of operations: `torch_t()`, `torch_dot()`, `torch_matmul()`, and `torch_multiply()`. 
 See https://torch.mlverse.org/docs/reference/#mathematical-operations-on-tensors.
 
+Another example:
+
 ```{r}
 t1 <- torch_tensor(1:3)
 t2 <- torch_tensor(4:6)
@@ -184,6 +184,8 @@ t1$dot(t2)
 
 ### Summary operations
 
+Create a matrix and a tensor using outer products:
+
 ```{r}
 m <- outer(1:3, 1:6)
 t <- torch_outer(torch_tensor(1:3), torch_tensor(1:6))

From 9736b8a7f86c3379a84a07328b3ae36cc6ac48f8 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 21:27:20 +0000
Subject: [PATCH 09/18] added ggplot2 to DESCRIPTION file (needed for dataset)

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index a51d3a6..7e3a12e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,6 +9,7 @@ Depends:
     R (>= 3.1.0)
 Imports: 
     bookdown,
+    ggplot2,
     rmarkdown,
     torch
 Encoding: UTF-8

From 7754857b811dfcae53d8dcbd9b88df1179f9d7c9 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 21:29:03 +0000
Subject: [PATCH 10/18] Added dplyr

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7e3a12e..f9dc574 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,6 +9,7 @@ Depends:
     R (>= 3.1.0)
 Imports: 
     bookdown,
+    dplyr,
     ggplot2,
     rmarkdown,
     torch

From c90b062eb8e76d9e16959430621f4e3e0a72e1a4 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 21:32:46 +0000
Subject: [PATCH 11/18] Removed tidyverse dependency. Added dplyr and ggplot2
 (specific dependencies).

---
 03_tensors.Rmd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/03_tensors.Rmd b/03_tensors.Rmd
index e1b34be..0cfcf64 100644
--- a/03_tensors.Rmd
+++ b/03_tensors.Rmd
@@ -19,7 +19,8 @@ Load libraries:
 
 ```{r message = FALSE, warning=FALSE}
 library(torch)
-library(tidyverse)
+library(dplyr)
+library(ggplot2)
 ```
 
 Create a tensor:

From 10a1cb057f754f6a6e8d7b900d8ffa6ff54a30f8 Mon Sep 17 00:00:00 2001
From: Amanda Peterson <amanda@dekleineorchards.com>
Date: Wed, 4 Oct 2023 21:34:04 +0000
Subject: [PATCH 12/18] resolve merge conflicts. update package dependencies.

---
 DESCRIPTION | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e72fa8b..f9dc574 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,13 +9,8 @@ Depends:
     R (>= 3.1.0)
 Imports: 
     bookdown,
-<<<<<<< HEAD
     dplyr,
     ggplot2,
-=======
-    modeldata,
->>>>>>> d36bbd5bbf1b42eeee76707e856fe1e682ab47ad
     rmarkdown,
-    tidyverse,
     torch
 Encoding: UTF-8

From f4c606e9f6cbb47013e0246827d3187be8faa3ba Mon Sep 17 00:00:00 2001
From: Jon Harmon <jonthegeek@gmail.com>
Date: Fri, 13 Oct 2023 09:57:12 -0500
Subject: [PATCH 13/18] Try a potentially easy fix for installing torch.

I'm not confident this will work but we might as well try!
---
 .github/workflows/deploy_bookdown.yml | 2 ++
 .github/workflows/pr_check.yml        | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/.github/workflows/deploy_bookdown.yml b/.github/workflows/deploy_bookdown.yml
index eaa103f..b6bdd93 100644
--- a/.github/workflows/deploy_bookdown.yml
+++ b/.github/workflows/deploy_bookdown.yml
@@ -7,4 +7,6 @@ on:
 
 jobs:
   bookdown:
+    env:
+      TORCH_INSTALL: 1
     uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index b7b9756..6e3e3a8 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -7,4 +7,6 @@ on:
 
 jobs:
   pr_check:
+    env:
+      TORCH_INSTALL: 1
     uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main

From b9307c54d34b474df8356c037861b62c46de8aa9 Mon Sep 17 00:00:00 2001
From: Jon Harmon <jonthegeek@gmail.com>
Date: Fri, 13 Oct 2023 09:59:36 -0500
Subject: [PATCH 14/18] Use before env.

One more try at a quick fix before reading documentation.
---
 .github/workflows/deploy_bookdown.yml | 2 +-
 .github/workflows/pr_check.yml        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deploy_bookdown.yml b/.github/workflows/deploy_bookdown.yml
index b6bdd93..07f3625 100644
--- a/.github/workflows/deploy_bookdown.yml
+++ b/.github/workflows/deploy_bookdown.yml
@@ -7,6 +7,6 @@ on:
 
 jobs:
   bookdown:
+    uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
     env:
       TORCH_INSTALL: 1
-    uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index 6e3e3a8..3caa020 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -7,6 +7,6 @@ on:
 
 jobs:
   pr_check:
+    uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main
     env:
       TORCH_INSTALL: 1
-    uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main

From 04071304be16b68c7bfe4ccd02e954ee395497c1 Mon Sep 17 00:00:00 2001
From: Jon Harmon <jonthegeek@gmail.com>
Date: Fri, 13 Oct 2023 10:02:48 -0500
Subject: [PATCH 15/18] Fix formatting.

Probably still won't work but it's closer.
---
 .github/workflows/deploy_bookdown.yml | 3 ++-
 .github/workflows/pr_check.yml        | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deploy_bookdown.yml b/.github/workflows/deploy_bookdown.yml
index 07f3625..aa75756 100644
--- a/.github/workflows/deploy_bookdown.yml
+++ b/.github/workflows/deploy_bookdown.yml
@@ -7,6 +7,7 @@ on:
 
 jobs:
   bookdown:
-    uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
+    runs-on: ubuntu-latest
     env:
       TORCH_INSTALL: 1
+    uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index 3caa020..a6238f4 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -7,6 +7,7 @@ on:
 
 jobs:
   pr_check:
-    uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main
+    runs-on: ubuntu-latest
     env:
       TORCH_INSTALL: 1
+    uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main

From cefd9548d4e296759c3dd1b7486725b7ce5cebf1 Mon Sep 17 00:00:00 2001
From: Jon Harmon <jonthegeek@gmail.com>
Date: Fri, 13 Oct 2023 10:03:52 -0500
Subject: [PATCH 16/18] Move uses to steps.

---
 .github/workflows/deploy_bookdown.yml | 3 ++-
 .github/workflows/pr_check.yml        | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deploy_bookdown.yml b/.github/workflows/deploy_bookdown.yml
index aa75756..7705a17 100644
--- a/.github/workflows/deploy_bookdown.yml
+++ b/.github/workflows/deploy_bookdown.yml
@@ -10,4 +10,5 @@ jobs:
     runs-on: ubuntu-latest
     env:
       TORCH_INSTALL: 1
-    uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
+    steps:
+      - uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index a6238f4..cc3f874 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -10,4 +10,5 @@ jobs:
     runs-on: ubuntu-latest
     env:
       TORCH_INSTALL: 1
-    uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main
+    steps:
+      - uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main

From 721a41547d85e2fac06057a44a3b766212649732 Mon Sep 17 00:00:00 2001
From: Jon Harmon <jonthegeek@gmail.com>
Date: Fri, 13 Oct 2023 10:05:28 -0500
Subject: [PATCH 17/18] Copy/paste reusable workflow.

---
 .github/workflows/pr_check.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index cc3f874..d5b3a72 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -11,4 +11,13 @@ jobs:
     env:
       TORCH_INSTALL: 1
     steps:
-      - uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.2.2'
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+      - name: Render Book
+        run: Rscript -e 'bookdown::render_book("index.Rmd")'

From 4dcfa3038afdb85ec9ca04858f5805b8d944a901 Mon Sep 17 00:00:00 2001
From: Jon Harmon <jonthegeek@gmail.com>
Date: Fri, 13 Oct 2023 10:33:12 -0500
Subject: [PATCH 18/18] Install torch in chapter 1.

So if earlier chapters use it in later clubs, it's set to go.
---
 .github/workflows/deploy_bookdown.yml       |  6 +-----
 .github/workflows/pr_check.yml              | 15 +--------------
 01_overview-getting-familiar-with-torch.Rmd |  7 +++++++
 3 files changed, 9 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/deploy_bookdown.yml b/.github/workflows/deploy_bookdown.yml
index 7705a17..eaa103f 100644
--- a/.github/workflows/deploy_bookdown.yml
+++ b/.github/workflows/deploy_bookdown.yml
@@ -7,8 +7,4 @@ on:
 
 jobs:
   bookdown:
-    runs-on: ubuntu-latest
-    env:
-      TORCH_INSTALL: 1
-    steps:
-      - uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
+    uses: r4ds/r4dsactions/.github/workflows/render_pages.yml@main
diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index d5b3a72..b7b9756 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -7,17 +7,4 @@ on:
 
 jobs:
   pr_check:
-    runs-on: ubuntu-latest
-    env:
-      TORCH_INSTALL: 1
-    steps:
-      - uses: actions/checkout@v3
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: '4.2.2'
-      - uses: r-lib/actions/setup-pandoc@v2
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          cache-version: 1
-      - name: Render Book
-        run: Rscript -e 'bookdown::render_book("index.Rmd")'
+    uses: r4ds/r4dsactions/.github/workflows/render_check.yml@main
diff --git a/01_overview-getting-familiar-with-torch.Rmd b/01_overview-getting-familiar-with-torch.Rmd
index d155f29..a19a892 100644
--- a/01_overview-getting-familiar-with-torch.Rmd
+++ b/01_overview-getting-familiar-with-torch.Rmd
@@ -4,6 +4,13 @@
 
 - THESE ARE NICE TO HAVE BUT NOT ABSOLUTELY NECESSARY
 
+## Setup {-}
+
+```{r install-torch}
+Sys.setenv(TORCH_INSTALL = 1)
+library(torch)
+```
+
 ## SLIDE 1 {-}
 
 - ADD SLIDES AS SECTIONS (`##`).