From 71ebf7348ca3a2b0681441326187e437bf4a1e18 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Fri, 18 Mar 2022 13:22:25 +0800
Subject: [PATCH 01/19] implement first pass at using sd.greta_array method

tests currently fail
---
 NAMESPACE                       |  3 +++
 R/functions.R                   | 34 +++++++++++++++++++++++++++++----
 R/tf_functions.R                |  6 ++++++
 man/functions.Rd                |  5 +++--
 man/overloaded.Rd               |  3 +++
 tests/testthat/test_functions.R |  3 +++
 6 files changed, 48 insertions(+), 6 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 2a366cdf2..df8b1cfe3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -116,6 +116,8 @@ S3method(rowMeans,default)
 S3method(rowMeans,greta_array)
 S3method(rowSums,default)
 S3method(rowSums,greta_array)
+S3method(sd,default)
+S3method(sd,greta_array)
 S3method(sign,greta_array)
 S3method(simulate,greta_model)
 S3method(sin,greta_array)
@@ -232,6 +234,7 @@ export(rms_prop)
 export(rowMeans)
 export(rowSums)
 export(rwmh)
+export(sd)
 export(simplex_variable)
 export(slice)
 export(slsqp)
diff --git a/R/functions.R b/R/functions.R
index 6e75dcf61..2a9bdfbfb 100644
--- a/R/functions.R
+++ b/R/functions.R
@@ -62,6 +62,7 @@
 #'  prod(..., na.rm = TRUE)
 #'  min(..., na.rm = TRUE)
 #'  max(..., na.rm = TRUE)
+#'  sd(..., na.rm = TRUE)
 #'
 #'  # cumulative operations
 #'  cumsum(x)
@@ -77,10 +78,10 @@
 #'
 #'  # miscellaneous operations
 #'  aperm(x, perm)
-#'  apply(x, MARGIN, FUN = c("sum", "max", "mean", "min",
+#'  apply(x, MARGIN, FUN = c("sum", "max", "mean", "min", "sd,
 #'                           "prod", "cumsum", "cumprod"))
 #'  sweep(x, MARGIN, STATS, FUN = c('-', '+', '/', '*'))
-#'  tapply(X, INDEX, FUN = c("sum", "max", "mean", "min", "prod"), ...)
+#'  tapply(X, INDEX, FUN = c("sum", "max", "mean", "min", "sd, "prod"), ...)
 #'
 #' }
 #'
@@ -590,6 +591,31 @@ mean.greta_array <- function(x, trim = 0, na.rm = TRUE, ...) { # nolint
   )
 }
 
+# need to define sd as a generic since it isn't actually a generic
+#' @rdname overloaded
+#' @export
+sd <- function(x, ...) UseMethod("sd", x)
+
+# setting default and setting arguments for it so it passes package check
+#' @export
+sd.default <- function(x, na.rm = FALSE, ...) {
+  sd_result <- stats::sd(x = x,
+                         na.rm = na.rm)
+  formals(sd.default) <- c(formals(sd.default), alist(... =))
+
+  sd_result
+}
+
+#' @export
+sd.greta_array <- function(x, na.rm = TRUE, ...) { # nolint
+
+  # calculate SD on greta array
+  op("sd", x,
+    dim = c(1, 1),
+    tf_operation = "tf_sd"
+  )
+}
+
 #' @export
 max.greta_array <- function(..., na.rm = TRUE) { # nolint
 
@@ -1073,7 +1099,7 @@ apply.default <- function(X, MARGIN, FUN, ...) { # nolint
 #' @export
 apply.greta_array <- function(X, MARGIN,
                               FUN = c(
-                                "sum", "max", "mean", "min", "prod",
+                                "sum", "max", "mean", "min", "sd", "prod",
                                 "cumsum", "cumprod"
                               ),
                               ...) {
@@ -1169,7 +1195,7 @@ tapply.default <- function(X, INDEX, FUN = NULL, ...,
 # nolint start
 #' @export
 tapply.greta_array <- function(X, INDEX,
-                               FUN = c("sum", "max", "mean", "min", "prod"),
+                               FUN = c("sum", "max", "mean", "min", "prod", "sd"),
                                ...) {
   # nolint end
 
diff --git a/R/tf_functions.R b/R/tf_functions.R
index d58b48e5f..c97ab1cc1 100644
--- a/R/tf_functions.R
+++ b/R/tf_functions.R
@@ -80,6 +80,12 @@ tf_mean <- function(x, drop = FALSE) {
   skip_dim("reduce_mean", x, drop)
 }
 
+tf_sd <- function(x, drop = FALSE) {
+  n_dim <- length(dim(x))
+  reduction_dims <- seq_len(n_dim - 1)
+  tf$math$reduce_std(x, axis = reduction_dims, keepdims = !drop)
+}
+
 tf_max <- function(x, drop = FALSE) {
   skip_dim("reduce_max", x, drop)
 }
diff --git a/man/functions.Rd b/man/functions.Rd
index aa97c9494..b3d7c9500 100644
--- a/man/functions.Rd
+++ b/man/functions.Rd
@@ -87,6 +87,7 @@ precision than R's equivalent.
  prod(..., na.rm = TRUE)
  min(..., na.rm = TRUE)
  max(..., na.rm = TRUE)
+ sd(..., na.rm = TRUE)
 
  # cumulative operations
  cumsum(x)
@@ -102,10 +103,10 @@ precision than R's equivalent.
 
  # miscellaneous operations
  aperm(x, perm)
- apply(x, MARGIN, FUN = c("sum", "max", "mean", "min",
+ apply(x, MARGIN, FUN = c("sum", "max", "mean", "min", "sd,
                           "prod", "cumsum", "cumprod"))
  sweep(x, MARGIN, STATS, FUN = c('-', '+', '/', '*'))
- tapply(X, INDEX, FUN = c("sum", "max", "mean", "min", "prod"), ...)
+ tapply(X, INDEX, FUN = c("sum", "max", "mean", "min", "sd, "prod"), ...)
 
 }
 }
diff --git a/man/overloaded.Rd b/man/overloaded.Rd
index 41f92950c..4062a0ecc 100644
--- a/man/overloaded.Rd
+++ b/man/overloaded.Rd
@@ -6,6 +6,7 @@
 \alias{\%*\%}
 \alias{chol2inv}
 \alias{cov2cor}
+\alias{sd}
 \alias{identity}
 \alias{colMeans}
 \alias{rowMeans}
@@ -28,6 +29,8 @@ chol2inv(x, size = NCOL(x), LINPACK = FALSE)
 
 cov2cor(V)
 
+sd(x, ...)
+
 identity(x)
 
 colMeans(x, na.rm = FALSE, dims = 1L)
diff --git a/tests/testthat/test_functions.R b/tests/testthat/test_functions.R
index a08df9c46..9eff87dfb 100644
--- a/tests/testthat/test_functions.R
+++ b/tests/testthat/test_functions.R
@@ -22,6 +22,7 @@ test_that("simple functions work as expected", {
   check_op(mean, x)
   check_op(sqrt, exp(x))
   check_op(sign, x)
+  check_op(sd, x)
 
   # rounding of numbers
   check_op(ceiling, x)
@@ -230,6 +231,7 @@ test_that("apply works as expected", {
     check_apply(a, margin, "prod")
     check_apply(a, margin, "cumsum")
     check_apply(a, margin, "cumprod")
+    check_apply(a, margin, "sd")
   }
 })
 
@@ -243,6 +245,7 @@ test_that("tapply works as expected", {
   check_expr(tapply(x, rep(1:5, each = 3), "mean"))
   check_expr(tapply(x, rep(1:5, each = 3), "min"))
   check_expr(tapply(x, rep(1:5, each = 3), "prod"))
+  check_expr(tapply(x, rep(1:5, each = 3), "sd"))
 })
 
 test_that("cumulative functions error as expected", {

From 1ccf56ba52c272e665be3fe218c87f1a0c7f52a9 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Mon, 21 Mar 2022 08:41:14 +0800
Subject: [PATCH 02/19] export `is_mac_arm64()`

---
 NAMESPACE           |  1 +
 R/utils.R           |  5 +++++
 man/is_mac_arm64.Rd | 11 +++++++++++
 3 files changed, 17 insertions(+)
 create mode 100644 man/is_mac_arm64.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 2a366cdf2..575f30f85 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -198,6 +198,7 @@ export(install_greta_deps)
 export(install_tensorflow)
 export(inverse_gamma)
 export(iprobit)
+export(is_mac_arm64)
 export(joint)
 export(l_bfgs_b)
 export(laplace)
diff --git a/R/utils.R b/R/utils.R
index 052d13209..c0108ef7a 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -930,6 +930,11 @@ greta_sitrep <- function(){
 }
 
 # adapted from https://github.com/rstudio/tensorflow/blob/main/R/utils.R
+#' Is the operating system M1?
+#'
+#' This is used to check if the operating system is M1 mac
+#'
+#' @export
 is_mac_arm64 <- function() {
   if (nzchar(Sys.getenv("GRETA_M1_MESSAGE_TESTING"))) {
     return(TRUE)
diff --git a/man/is_mac_arm64.Rd b/man/is_mac_arm64.Rd
new file mode 100644
index 000000000..3866c25d5
--- /dev/null
+++ b/man/is_mac_arm64.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{is_mac_arm64}
+\alias{is_mac_arm64}
+\title{Is the operating system M1?}
+\usage{
+is_mac_arm64()
+}
+\description{
+This is used to check if the operating system is M1 mac
+}

From 069043a527d055927562e04aead984ad014ce3a8 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Mon, 21 Mar 2022 08:42:41 +0800
Subject: [PATCH 03/19] downgrade check for M1 from an error to a message

---
 R/checkers.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/checkers.R b/R/checkers.R
index fdb1f7db2..399bfdd06 100644
--- a/R/checkers.R
+++ b/R/checkers.R
@@ -26,14 +26,14 @@ check_tf_version <- function(alert = c("none",
 
   if (is_mac_arm64()) {
 
-    msg <-  cli::format_error(
+    msg <-  cli::format_message(
       c(
         "{.pkg greta} does not currently work with Apple Silicon (M1)",
         "We are working on getting this resolved ASAP, see {.url https://github.com/greta-dev/greta/issues/458} for current progress."
       )
     )
 
-    stop(
+    message(
       msg,
       call. = FALSE
     )

From d57b83e97feba19d9e411e4036eb9ee86e15eeed Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Mon, 21 Mar 2022 08:44:04 +0800
Subject: [PATCH 04/19] only evaluate if not an M1 mac

---
 vignettes/example_models.Rmd | 2 +-
 vignettes/get_started.Rmd    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/vignettes/example_models.Rmd b/vignettes/example_models.Rmd
index e9d98fc69..54f654d58 100644
--- a/vignettes/example_models.Rmd
+++ b/vignettes/example_models.Rmd
@@ -9,7 +9,7 @@ vignette: >
 
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(comment = NA,
-                      eval = greta:::check_tf_version("message"),
+                      eval = !greta::is_mac_arm64(),
                       cache = TRUE)
 library (greta)
 ```
diff --git a/vignettes/get_started.Rmd b/vignettes/get_started.Rmd
index 38f7f643a..e473622c8 100644
--- a/vignettes/get_started.Rmd
+++ b/vignettes/get_started.Rmd
@@ -10,7 +10,7 @@ vignette: >
 ```{r setup, include = FALSE}
 
 knitr::opts_chunk$set(echo = TRUE,
-                      eval = greta:::check_tf_version("message"),
+                      eval = !greta::is_mac_arm64(),
                       cache = TRUE,
                       comment = NA,
                       progress = FALSE)

From 65095c46fca6b13c07d3c38778713c7c9106280d Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Mon, 21 Mar 2022 12:19:21 +0800
Subject: [PATCH 05/19] change back to error not message

---
 R/checkers.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/checkers.R b/R/checkers.R
index 399bfdd06..fdb1f7db2 100644
--- a/R/checkers.R
+++ b/R/checkers.R
@@ -26,14 +26,14 @@ check_tf_version <- function(alert = c("none",
 
   if (is_mac_arm64()) {
 
-    msg <-  cli::format_message(
+    msg <-  cli::format_error(
       c(
         "{.pkg greta} does not currently work with Apple Silicon (M1)",
         "We are working on getting this resolved ASAP, see {.url https://github.com/greta-dev/greta/issues/458} for current progress."
       )
     )
 
-    message(
+    stop(
       msg,
       call. = FALSE
     )

From 83140c2d245d7c64bf6c29b14684155082bc6ce3 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Mon, 21 Mar 2022 14:17:59 +0800
Subject: [PATCH 06/19] remove documentation for is_mac_arm64; add
 `is_not_cran()` function

---
 NAMESPACE           |  1 -
 R/utils.R           |  9 ++++-----
 man/is_mac_arm64.Rd | 11 -----------
 3 files changed, 4 insertions(+), 17 deletions(-)
 delete mode 100644 man/is_mac_arm64.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 575f30f85..2a366cdf2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -198,7 +198,6 @@ export(install_greta_deps)
 export(install_tensorflow)
 export(inverse_gamma)
 export(iprobit)
-export(is_mac_arm64)
 export(joint)
 export(l_bfgs_b)
 export(laplace)
diff --git a/R/utils.R b/R/utils.R
index c0108ef7a..ac23c7f0d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -930,11 +930,6 @@ greta_sitrep <- function(){
 }
 
 # adapted from https://github.com/rstudio/tensorflow/blob/main/R/utils.R
-#' Is the operating system M1?
-#'
-#' This is used to check if the operating system is M1 mac
-#'
-#' @export
 is_mac_arm64 <- function() {
   if (nzchar(Sys.getenv("GRETA_M1_MESSAGE_TESTING"))) {
     return(TRUE)
@@ -954,3 +949,7 @@ create_temp_file <- function(path){
   file.create(file_path)
   return(file_path)
 }
+
+is_not_cran <- function(){
+  identical(Sys.getenv("NOT_CRAN", unset = "true"), "true")
+}
diff --git a/man/is_mac_arm64.Rd b/man/is_mac_arm64.Rd
deleted file mode 100644
index 3866c25d5..000000000
--- a/man/is_mac_arm64.Rd
+++ /dev/null
@@ -1,11 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{is_mac_arm64}
-\alias{is_mac_arm64}
-\title{Is the operating system M1?}
-\usage{
-is_mac_arm64()
-}
-\description{
-This is used to check if the operating system is M1 mac
-}

From 981abca8723a7d1ef1ec28c5a49c46369377b543 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Mon, 21 Mar 2022 14:18:21 +0800
Subject: [PATCH 07/19] evaluate code depending on whether this is being
 assessed on CRAN

---
 vignettes/example_models.Rmd | 2 +-
 vignettes/get_started.Rmd    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/vignettes/example_models.Rmd b/vignettes/example_models.Rmd
index 54f654d58..e4ddd8909 100644
--- a/vignettes/example_models.Rmd
+++ b/vignettes/example_models.Rmd
@@ -9,7 +9,7 @@ vignette: >
 
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(comment = NA,
-                      eval = !greta::is_mac_arm64(),
+                      eval = greta:::is_not_cran(),
                       cache = TRUE)
 library (greta)
 ```
diff --git a/vignettes/get_started.Rmd b/vignettes/get_started.Rmd
index e473622c8..48930b6d1 100644
--- a/vignettes/get_started.Rmd
+++ b/vignettes/get_started.Rmd
@@ -10,7 +10,7 @@ vignette: >
 ```{r setup, include = FALSE}
 
 knitr::opts_chunk$set(echo = TRUE,
-                      eval = !greta::is_mac_arm64(),
+                      eval = greta:::is_not_cran(),
                       cache = TRUE,
                       comment = NA,
                       progress = FALSE)

From 76f54757694d605aefbf630cf77f02e0c14f35b9 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Mon, 21 Mar 2022 15:50:44 +0800
Subject: [PATCH 08/19] use message instead of stop

---
 R/checkers.R                      | 4 ++--
 tests/testthat/_snaps/check-m1.md | 7 +++++--
 tests/testthat/test-check-m1.R    | 5 +++--
 vignettes/example_models.Rmd      | 2 +-
 vignettes/get_started.Rmd         | 2 +-
 5 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/R/checkers.R b/R/checkers.R
index fdb1f7db2..399bfdd06 100644
--- a/R/checkers.R
+++ b/R/checkers.R
@@ -26,14 +26,14 @@ check_tf_version <- function(alert = c("none",
 
   if (is_mac_arm64()) {
 
-    msg <-  cli::format_error(
+    msg <-  cli::format_message(
       c(
         "{.pkg greta} does not currently work with Apple Silicon (M1)",
         "We are working on getting this resolved ASAP, see {.url https://github.com/greta-dev/greta/issues/458} for current progress."
       )
     )
 
-    stop(
+    message(
       msg,
       call. = FALSE
     )
diff --git a/tests/testthat/_snaps/check-m1.md b/tests/testthat/_snaps/check-m1.md
index 791639442..f50cd8164 100644
--- a/tests/testthat/_snaps/check-m1.md
+++ b/tests/testthat/_snaps/check-m1.md
@@ -1,5 +1,8 @@
 # check_tf_version fails when M1 mac detected
 
-    greta does not currently work with Apple Silicon (M1)
-    We are working on getting this resolved ASAP, see <https://github.com/greta-dev/greta/issues/458> for current progress.
+    Code
+      check_tf_version("error")
+    Message <simpleMessage>
+      greta does not currently work with Apple Silicon (M1)
+      We are working on getting this resolved ASAP, see <https://github.com/greta-dev/greta/issues/458> for current progress.FALSE
 
diff --git a/tests/testthat/test-check-m1.R b/tests/testthat/test-check-m1.R
index 9aff18c31..26b97a013 100644
--- a/tests/testthat/test-check-m1.R
+++ b/tests/testthat/test-check-m1.R
@@ -1,7 +1,8 @@
 test_that("check_tf_version fails when M1 mac detected", {
   skip_if_not(check_tf_version())
   withr::local_envvar("GRETA_M1_MESSAGE_TESTING" = "on")
-  expect_snapshot_error(
-    check_tf_version("error")
+  expect_snapshot(
+    x = check_tf_version("error"),
+    cnd_class = FALSE
   )
 })
diff --git a/vignettes/example_models.Rmd b/vignettes/example_models.Rmd
index e4ddd8909..e9d98fc69 100644
--- a/vignettes/example_models.Rmd
+++ b/vignettes/example_models.Rmd
@@ -9,7 +9,7 @@ vignette: >
 
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(comment = NA,
-                      eval = greta:::is_not_cran(),
+                      eval = greta:::check_tf_version("message"),
                       cache = TRUE)
 library (greta)
 ```
diff --git a/vignettes/get_started.Rmd b/vignettes/get_started.Rmd
index 48930b6d1..38f7f643a 100644
--- a/vignettes/get_started.Rmd
+++ b/vignettes/get_started.Rmd
@@ -10,7 +10,7 @@ vignette: >
 ```{r setup, include = FALSE}
 
 knitr::opts_chunk$set(echo = TRUE,
-                      eval = greta:::is_not_cran(),
+                      eval = greta:::check_tf_version("message"),
                       cache = TRUE,
                       comment = NA,
                       progress = FALSE)

From c1fbc4f2885cc132c1a3ecd28eaf25250eb09475 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Tue, 22 Mar 2022 07:56:40 +0800
Subject: [PATCH 09/19] change to 0.4.2

---
 DESCRIPTION      | 4 ++--
 NEWS.md          | 6 +++++-
 cran-comments.md | 5 +++--
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 829dc60ff..cc5d0dfc8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: greta
 Title: Simple and Scalable Statistical Modelling in R
-Version: 0.4.1.9000
-Date: 2022-03-14
+Version: 0.4.2
+Date: 2022-03-22
 Authors@R: c(
     person("Nick", "Golding", , "nick.golding.research@gmail.com", role = "aut",
            comment = c(ORCID = "0000-0001-8916-5570")),
diff --git a/NEWS.md b/NEWS.md
index 76e701a5b..972e65a78 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,8 @@
-# greta 0.4.1.9000 (development version)
+# greta 0.4.2
+
+## Fixes
+
+* workaround for M1 issues (#507)
 
 # greta 0.4.1 (2022-03-14)
 
diff --git a/cran-comments.md b/cran-comments.md
index c9fb85763..d5fd6506c 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,5 +1,5 @@
 ## Test environments
-* local R installation, R 4.1.3
+* Mac OSX (Intel) local R installation, R 4.1.3
 * ubuntu 16.04 (on travis-ci), R 4.1.3
 * win-builder (devel)
 
@@ -7,7 +7,8 @@
 
 0 errors | 0 warnings | 1 notes
 
-* Maintainer has changed from Nick Golding to Nicholas Tierney.
+* Days since last update: 6
+* Package has been resubmitted based on request to fix error on install of M1. This has now been resolved
 
 ## revdepcheck results
 

From 924c6ea34e759f1eb77122f86bf15c4643a7ace2 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Tue, 22 Mar 2022 08:10:45 +0800
Subject: [PATCH 10/19] update codemeta

---
 codemeta.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/codemeta.json b/codemeta.json
index c5dfa3ecd..ec223d517 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,8 +6,8 @@
   "name": "greta: Simple and Scalable Statistical Modelling in R",
   "codeRepository": "https://github.com/njtierney/greta",
   "issueTracker": "https://github.com/greta-dev/greta/issues",
-  "license": "Apache License 2",
-  "version": "0.4.1",
+  "license": "https://spdx.org/licenses/Apache-2.0",
+  "version": "0.4.2",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -515,7 +515,7 @@
     },
     "SystemRequirements": "Python (>= 2.7.0) with header files and shared\n    library; TensorFlow (v1.14; https://www.tensorflow.org/); TensorFlow\n    Probability (v0.7.0; https://www.tensorflow.org/probability/)"
   },
-  "fileSize": "1326.582KB",
+  "fileSize": "1320.891KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

From afaef4ede116ebc7c256bf3a85eb3a0c86a88212 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Tue, 22 Mar 2022 08:11:20 +0800
Subject: [PATCH 11/19] update cran-comments

---
 cran-comments.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index d5fd6506c..504e71b0c 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -5,9 +5,9 @@
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 notes
+0 errors | 0 warnings | 0 notes
 
-* Days since last update: 6
+* Days since last update: 7
 * Package has been resubmitted based on request to fix error on install of M1. This has now been resolved
 
 ## revdepcheck results

From 6426e2f0c3961499601e1b93dd3b44b721b4c92a Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Tue, 22 Mar 2022 08:13:42 +0800
Subject: [PATCH 12/19] remove `is_not_cran()` function

---
 R/utils.R        | 4 ----
 cran-comments.md | 2 +-
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index ac23c7f0d..052d13209 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -949,7 +949,3 @@ create_temp_file <- function(path){
   file.create(file_path)
   return(file_path)
 }
-
-is_not_cran <- function(){
-  identical(Sys.getenv("NOT_CRAN", unset = "true"), "true")
-}
diff --git a/cran-comments.md b/cran-comments.md
index 504e71b0c..9c79e71d4 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,5 +1,5 @@
 ## Test environments
-* Mac OSX (Intel) local R installation, R 4.1.3
+* local R installation, R 4.1.3
 * ubuntu 16.04 (on travis-ci), R 4.1.3
 * win-builder (devel)
 

From 45657cd0c1978defdd1e6ba54ba79047c866baff Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Wed, 23 Mar 2022 16:41:05 +0800
Subject: [PATCH 13/19] Increment version number to 0.4.2.9000

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cc5d0dfc8..f143707de 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: greta
 Title: Simple and Scalable Statistical Modelling in R
-Version: 0.4.2
+Version: 0.4.2.9000
 Date: 2022-03-22
 Authors@R: c(
     person("Nick", "Golding", , "nick.golding.research@gmail.com", role = "aut",
diff --git a/NEWS.md b/NEWS.md
index 972e65a78..4d871b5d4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+# greta (development version)
+
 # greta 0.4.2
 
 ## Fixes

From ef1069d3ced553cf0d13a9faaf563f68d6fe048b Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Wed, 30 Mar 2022 10:53:25 +0800
Subject: [PATCH 14/19] first attempt at using tensorflow to make different
 calculations of standard deviation

---
 R/tf_functions.R | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/R/tf_functions.R b/R/tf_functions.R
index c97ab1cc1..24452af69 100644
--- a/R/tf_functions.R
+++ b/R/tf_functions.R
@@ -80,12 +80,25 @@ tf_mean <- function(x, drop = FALSE) {
   skip_dim("reduce_mean", x, drop)
 }
 
-tf_sd <- function(x, drop = FALSE) {
-  n_dim <- length(dim(x))
-  reduction_dims <- seq_len(n_dim - 1)
-  tf$math$reduce_std(x, axis = reduction_dims, keepdims = !drop)
+tf_sd <- function(x, n_minus_1 = TRUE){
+  if (n_minus_1){
+    # replace these parts with tf_sum and friends?
+    x_mean_sq <- tf_mean(x) * tf_mean(x)
+    total_ss <- tf_sum(x - x_mean_sq)
+    var <- total_ss / (length(x) - 1)
+    sd_result <- sqrt(var)
+    # total_ss <- sum((x - mean(x))^2)
+    # var <- (total_ss / (length(x) - 1))
+    # sd_result <- sqrt(var)
+  } else if (!n_minus_1) {
+    n_dim <- length(dim(x))
+    reduction_dims <- seq_len(n_dim - 1)
+    sd_result <- tf$math$reduce_std(x, axis = reduction_dims, keepdims = !drop)
+  }
+  return(sd_result)
 }
 
+
 tf_max <- function(x, drop = FALSE) {
   skip_dim("reduce_max", x, drop)
 }

From 7b9c5b934c2780770e56ec67487492eba3a2203a Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Thu, 31 Mar 2022 14:35:11 +0800
Subject: [PATCH 15/19] implement using correct tensorflow dimensions etc

---
 R/tf_functions.R | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/R/tf_functions.R b/R/tf_functions.R
index 24452af69..7a01e833f 100644
--- a/R/tf_functions.R
+++ b/R/tf_functions.R
@@ -80,22 +80,22 @@ tf_mean <- function(x, drop = FALSE) {
   skip_dim("reduce_mean", x, drop)
 }
 
-tf_sd <- function(x, n_minus_1 = TRUE){
-  if (n_minus_1){
-    # replace these parts with tf_sum and friends?
-    x_mean_sq <- tf_mean(x) * tf_mean(x)
-    total_ss <- tf_sum(x - x_mean_sq)
-    var <- total_ss / (length(x) - 1)
-    sd_result <- sqrt(var)
-    # total_ss <- sum((x - mean(x))^2)
-    # var <- (total_ss / (length(x) - 1))
-    # sd_result <- sqrt(var)
-  } else if (!n_minus_1) {
-    n_dim <- length(dim(x))
-    reduction_dims <- seq_len(n_dim - 1)
-    sd_result <- tf$math$reduce_std(x, axis = reduction_dims, keepdims = !drop)
-  }
-  return(sd_result)
+# need to create a "reduce_sd" function
+# which
+
+tf_sd <- function(x, drop = FALSE){
+
+  n_dim <- length(dim(x))
+  reduction_dims <- seq_len(n_dim - 1)
+
+  # replace these parts with tf_sum and friends?
+  x_mean_sq <- tf_mean(x, drop = drop) * tf_mean(x, drop = drop)
+  total_ss <- tf_sum(x - x_mean_sq, drop = drop)
+  n_denom <- prod(dim(x)[reduction_dims + 1])
+  var <- total_ss / fl(n_denom - 1)
+  sd_result <- tf$math$sqrt(var)
+
+  sd_result
 }
 
 

From 0ebf81dde43cb678b00902689e993803a3680c50 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Fri, 18 Mar 2022 13:22:25 +0800
Subject: [PATCH 16/19] implement first pass at using sd.greta_array method

tests currently fail
---
 NAMESPACE                       |  3 +++
 R/functions.R                   | 34 +++++++++++++++++++++++++++++----
 R/tf_functions.R                |  6 ++++++
 man/functions.Rd                |  5 +++--
 man/overloaded.Rd               |  3 +++
 tests/testthat/test_functions.R |  3 +++
 6 files changed, 48 insertions(+), 6 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 2a366cdf2..df8b1cfe3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -116,6 +116,8 @@ S3method(rowMeans,default)
 S3method(rowMeans,greta_array)
 S3method(rowSums,default)
 S3method(rowSums,greta_array)
+S3method(sd,default)
+S3method(sd,greta_array)
 S3method(sign,greta_array)
 S3method(simulate,greta_model)
 S3method(sin,greta_array)
@@ -232,6 +234,7 @@ export(rms_prop)
 export(rowMeans)
 export(rowSums)
 export(rwmh)
+export(sd)
 export(simplex_variable)
 export(slice)
 export(slsqp)
diff --git a/R/functions.R b/R/functions.R
index 6e75dcf61..2a9bdfbfb 100644
--- a/R/functions.R
+++ b/R/functions.R
@@ -62,6 +62,7 @@
 #'  prod(..., na.rm = TRUE)
 #'  min(..., na.rm = TRUE)
 #'  max(..., na.rm = TRUE)
+#'  sd(..., na.rm = TRUE)
 #'
 #'  # cumulative operations
 #'  cumsum(x)
@@ -77,10 +78,10 @@
 #'
 #'  # miscellaneous operations
 #'  aperm(x, perm)
-#'  apply(x, MARGIN, FUN = c("sum", "max", "mean", "min",
+#'  apply(x, MARGIN, FUN = c("sum", "max", "mean", "min", "sd,
 #'                           "prod", "cumsum", "cumprod"))
 #'  sweep(x, MARGIN, STATS, FUN = c('-', '+', '/', '*'))
-#'  tapply(X, INDEX, FUN = c("sum", "max", "mean", "min", "prod"), ...)
+#'  tapply(X, INDEX, FUN = c("sum", "max", "mean", "min", "sd, "prod"), ...)
 #'
 #' }
 #'
@@ -590,6 +591,31 @@ mean.greta_array <- function(x, trim = 0, na.rm = TRUE, ...) { # nolint
   )
 }
 
+# need to define sd as a generic since it isn't actually a generic
+#' @rdname overloaded
+#' @export
+sd <- function(x, ...) UseMethod("sd", x)
+
+# setting default and setting arguments for it so it passes package check
+#' @export
+sd.default <- function(x, na.rm = FALSE, ...) {
+  sd_result <- stats::sd(x = x,
+                         na.rm = na.rm)
+  formals(sd.default) <- c(formals(sd.default), alist(... =))
+
+  sd_result
+}
+
+#' @export
+sd.greta_array <- function(x, na.rm = TRUE, ...) { # nolint
+
+  # calculate SD on greta array
+  op("sd", x,
+    dim = c(1, 1),
+    tf_operation = "tf_sd"
+  )
+}
+
 #' @export
 max.greta_array <- function(..., na.rm = TRUE) { # nolint
 
@@ -1073,7 +1099,7 @@ apply.default <- function(X, MARGIN, FUN, ...) { # nolint
 #' @export
 apply.greta_array <- function(X, MARGIN,
                               FUN = c(
-                                "sum", "max", "mean", "min", "prod",
+                                "sum", "max", "mean", "min", "sd", "prod",
                                 "cumsum", "cumprod"
                               ),
                               ...) {
@@ -1169,7 +1195,7 @@ tapply.default <- function(X, INDEX, FUN = NULL, ...,
 # nolint start
 #' @export
 tapply.greta_array <- function(X, INDEX,
-                               FUN = c("sum", "max", "mean", "min", "prod"),
+                               FUN = c("sum", "max", "mean", "min", "prod", "sd"),
                                ...) {
   # nolint end
 
diff --git a/R/tf_functions.R b/R/tf_functions.R
index d58b48e5f..c97ab1cc1 100644
--- a/R/tf_functions.R
+++ b/R/tf_functions.R
@@ -80,6 +80,12 @@ tf_mean <- function(x, drop = FALSE) {
   skip_dim("reduce_mean", x, drop)
 }
 
+tf_sd <- function(x, drop = FALSE) {
+  n_dim <- length(dim(x))
+  reduction_dims <- seq_len(n_dim - 1)
+  tf$math$reduce_std(x, axis = reduction_dims, keepdims = !drop)
+}
+
 tf_max <- function(x, drop = FALSE) {
   skip_dim("reduce_max", x, drop)
 }
diff --git a/man/functions.Rd b/man/functions.Rd
index aa97c9494..b3d7c9500 100644
--- a/man/functions.Rd
+++ b/man/functions.Rd
@@ -87,6 +87,7 @@ precision than R's equivalent.
  prod(..., na.rm = TRUE)
  min(..., na.rm = TRUE)
  max(..., na.rm = TRUE)
+ sd(..., na.rm = TRUE)
 
  # cumulative operations
  cumsum(x)
@@ -102,10 +103,10 @@ precision than R's equivalent.
 
  # miscellaneous operations
  aperm(x, perm)
- apply(x, MARGIN, FUN = c("sum", "max", "mean", "min",
+ apply(x, MARGIN, FUN = c("sum", "max", "mean", "min", "sd,
                           "prod", "cumsum", "cumprod"))
  sweep(x, MARGIN, STATS, FUN = c('-', '+', '/', '*'))
- tapply(X, INDEX, FUN = c("sum", "max", "mean", "min", "prod"), ...)
+ tapply(X, INDEX, FUN = c("sum", "max", "mean", "min", "sd, "prod"), ...)
 
 }
 }
diff --git a/man/overloaded.Rd b/man/overloaded.Rd
index 41f92950c..4062a0ecc 100644
--- a/man/overloaded.Rd
+++ b/man/overloaded.Rd
@@ -6,6 +6,7 @@
 \alias{\%*\%}
 \alias{chol2inv}
 \alias{cov2cor}
+\alias{sd}
 \alias{identity}
 \alias{colMeans}
 \alias{rowMeans}
@@ -28,6 +29,8 @@ chol2inv(x, size = NCOL(x), LINPACK = FALSE)
 
 cov2cor(V)
 
+sd(x, ...)
+
 identity(x)
 
 colMeans(x, na.rm = FALSE, dims = 1L)
diff --git a/tests/testthat/test_functions.R b/tests/testthat/test_functions.R
index a08df9c46..9eff87dfb 100644
--- a/tests/testthat/test_functions.R
+++ b/tests/testthat/test_functions.R
@@ -22,6 +22,7 @@ test_that("simple functions work as expected", {
   check_op(mean, x)
   check_op(sqrt, exp(x))
   check_op(sign, x)
+  check_op(sd, x)
 
   # rounding of numbers
   check_op(ceiling, x)
@@ -230,6 +231,7 @@ test_that("apply works as expected", {
     check_apply(a, margin, "prod")
     check_apply(a, margin, "cumsum")
     check_apply(a, margin, "cumprod")
+    check_apply(a, margin, "sd")
   }
 })
 
@@ -243,6 +245,7 @@ test_that("tapply works as expected", {
   check_expr(tapply(x, rep(1:5, each = 3), "mean"))
   check_expr(tapply(x, rep(1:5, each = 3), "min"))
   check_expr(tapply(x, rep(1:5, each = 3), "prod"))
+  check_expr(tapply(x, rep(1:5, each = 3), "sd"))
 })
 
 test_that("cumulative functions error as expected", {

From da46fdd87d0d03141a4e731d611492d39baf26c7 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Wed, 30 Mar 2022 10:53:25 +0800
Subject: [PATCH 17/19] first attempt at using tensorflow to make different
 calculations of standard deviation

---
 R/tf_functions.R | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/R/tf_functions.R b/R/tf_functions.R
index c97ab1cc1..24452af69 100644
--- a/R/tf_functions.R
+++ b/R/tf_functions.R
@@ -80,12 +80,25 @@ tf_mean <- function(x, drop = FALSE) {
   skip_dim("reduce_mean", x, drop)
 }
 
-tf_sd <- function(x, drop = FALSE) {
-  n_dim <- length(dim(x))
-  reduction_dims <- seq_len(n_dim - 1)
-  tf$math$reduce_std(x, axis = reduction_dims, keepdims = !drop)
+tf_sd <- function(x, n_minus_1 = TRUE){
+  if (n_minus_1){
+    # replace these parts with tf_sum and friends?
+    x_mean_sq <- tf_mean(x) * tf_mean(x)
+    total_ss <- tf_sum(x - x_mean_sq)
+    var <- total_ss / (length(x) - 1)
+    sd_result <- sqrt(var)
+    # total_ss <- sum((x - mean(x))^2)
+    # var <- (total_ss / (length(x) - 1))
+    # sd_result <- sqrt(var)
+  } else if (!n_minus_1) {
+    n_dim <- length(dim(x))
+    reduction_dims <- seq_len(n_dim - 1)
+    sd_result <- tf$math$reduce_std(x, axis = reduction_dims, keepdims = !drop)
+  }
+  return(sd_result)
 }
 
+
 tf_max <- function(x, drop = FALSE) {
   skip_dim("reduce_max", x, drop)
 }

From 908be4833e34a2ac5418c0a65f9a19428aa3029e Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Thu, 31 Mar 2022 14:35:11 +0800
Subject: [PATCH 18/19] implement using correct tensorflow dimensions etc

---
 R/tf_functions.R | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/R/tf_functions.R b/R/tf_functions.R
index 24452af69..7a01e833f 100644
--- a/R/tf_functions.R
+++ b/R/tf_functions.R
@@ -80,22 +80,22 @@ tf_mean <- function(x, drop = FALSE) {
   skip_dim("reduce_mean", x, drop)
 }
 
-tf_sd <- function(x, n_minus_1 = TRUE){
-  if (n_minus_1){
-    # replace these parts with tf_sum and friends?
-    x_mean_sq <- tf_mean(x) * tf_mean(x)
-    total_ss <- tf_sum(x - x_mean_sq)
-    var <- total_ss / (length(x) - 1)
-    sd_result <- sqrt(var)
-    # total_ss <- sum((x - mean(x))^2)
-    # var <- (total_ss / (length(x) - 1))
-    # sd_result <- sqrt(var)
-  } else if (!n_minus_1) {
-    n_dim <- length(dim(x))
-    reduction_dims <- seq_len(n_dim - 1)
-    sd_result <- tf$math$reduce_std(x, axis = reduction_dims, keepdims = !drop)
-  }
-  return(sd_result)
+# need to create a "reduce_sd" function
+# which
+
+tf_sd <- function(x, drop = FALSE){
+
+  n_dim <- length(dim(x))
+  reduction_dims <- seq_len(n_dim - 1)
+
+  # replace these parts with tf_sum and friends?
+  x_mean_sq <- tf_mean(x, drop = drop) * tf_mean(x, drop = drop)
+  total_ss <- tf_sum(x - x_mean_sq, drop = drop)
+  n_denom <- prod(dim(x)[reduction_dims + 1])
+  var <- total_ss / fl(n_denom - 1)
+  sd_result <- tf$math$sqrt(var)
+
+  sd_result
 }
 
 

From 7321aa08f52bf5ca5450368d990f876ab4e23453 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Thu, 31 Mar 2022 14:53:40 +0800
Subject: [PATCH 19/19] might need to explore how things are happening with
 skip dim and the dimension that is being returned

---
 R/tf_functions.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/tf_functions.R b/R/tf_functions.R
index 7a01e833f..e02c33013 100644
--- a/R/tf_functions.R
+++ b/R/tf_functions.R
@@ -89,8 +89,10 @@ tf_sd <- function(x, drop = FALSE){
   reduction_dims <- seq_len(n_dim - 1)
 
   # replace these parts with tf_sum and friends?
-  x_mean_sq <- tf_mean(x, drop = drop) * tf_mean(x, drop = drop)
-  total_ss <- tf_sum(x - x_mean_sq, drop = drop)
+  x_mean <- tf_mean(x, drop = drop)
+  x_sub <- x - x_mean
+  x_mean_sq <- x_sub * x_sub
+  total_ss <- tf_sum(x_mean_sq, drop = drop)
   n_denom <- prod(dim(x)[reduction_dims + 1])
   var <- total_ss / fl(n_denom - 1)
   sd_result <- tf$math$sqrt(var)