From 528bcedc4679f8423b95ffb7e9603e2522feb7e2 Mon Sep 17 00:00:00 2001
From: "Lin, Chanjuan {MDBJ~Shanghai}" <chanjuan.lin@roche.com>
Date: Mon, 27 Mar 2023 09:44:54 +0200
Subject: [PATCH 01/14] create prototype of bland altman analysis

---
 R/bland_altman.R | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 R/bland_altman.R

diff --git a/R/bland_altman.R b/R/bland_altman.R
new file mode 100644
index 0000000000..a6c1c49a4b
--- /dev/null
+++ b/R/bland_altman.R
@@ -0,0 +1,41 @@
+s_bland_altman_cj <- function(x, y, conf_level = 0.95, group = NULL){
+
+  alpha <- 1 - conf_level
+
+  ind <- complete.cases(x, y) # use only pairwise complete observations, and check if x and y have the same length
+  x <- x[ind]
+  y <- y[ind]
+  group <- group[ind]
+
+  difference <- x - y                                 # vector of differences
+  average <- (x + y) / 2                              # vector of means
+  difference_mean <- mean(difference)                 # mean difference
+  difference_sd <- sd(difference)                     # SD of differences
+  al <- qnorm(1 - alpha / 2) * difference_sd
+  upper_agreement_limit <- difference_mean + al       # agreement limits
+  lower_agreement_limit <- difference_mean - al
+  n <- length(difference)                             # number of 'observations'
+
+  difference_se <- difference_sd / sqrt(n)            # standard error of the mean
+  al_se <- difference_sd * sqrt(3) / sqrt(n)          # standard error of the agreement limit
+  tvalue <- qt(1 - alpha / 2, n - 1)                  # t value for 95% CI calculation
+  difference_mean_ci <- difference_se * tvalue
+  al_ci <- al_se * tvalue
+  upper_agreement_limit_ci <- c(upper_agreement_limit - al_ci, upper_agreement_limit + al_ci)
+  lower_agreement_limit_ci <- c(lower_agreement_limit - al_ci, lower_agreement_limit + al_ci)
+
+
+  list(
+    difference_mean = difference_mean,
+    ci_mean = difference_mean + c(-1, 1) * difference_mean_ci,
+    difference_sd = difference_sd,
+    difference_se = difference_se,
+    upper_agreement_limit = upper_agreement_limit,
+    lower_agreement_limit = lower_agreement_limit,
+    agreement_limit_se = al_se,
+    upper_agreement_limit_ci = upper_agreement_limit_ci,
+    lower_agreement_limit_ci = lower_agreement_limit_ci,
+    t_value = tvalue,
+    n = n
+  )
+}

From d776173e6175dfdfa8b8212bc3771550c851f2ca Mon Sep 17 00:00:00 2001
From: "Lin, Chanjuan {MDBJ~Shanghai}" <chanjuan.lin@roche.com>
Date: Mon, 27 Mar 2023 09:44:54 +0200
Subject: [PATCH 02/14] create prototype of bland altman analysis add the
 documentation

---
 R/bland_altman.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 R/bland_altman.R

diff --git a/R/bland_altman.R b/R/bland_altman.R
new file mode 100644
index 0000000000..5ac0ae220c
--- /dev/null
+++ b/R/bland_altman.R
@@ -0,0 +1,57 @@
+#' Bland Altman analysis
+#'
+#' @description 'r lifecycle::badge("stable")'
+#'
+#' @inheritParams argument_convention
+#' @param y ('numeric')\cr vector of numbers we want to analyze.
+#'
+#' @name s_bland_altman
+#'
+#' @examples
+#' x = seq(1, 60, 5)
+#' y = seq(5, 50, 4)
+#' conf_level = 0.9
+#' s_bland_altman(x, y, conf_level = conf_level)
+
+
+s_bland_altman_cj <- function(x, y, conf_level = 0.95, group = NULL){
+
+  alpha <- 1 - conf_level
+
+  ind <- complete.cases(x, y) # use only pairwise complete observations, and check if x and y have the same length
+  x <- x[ind]
+  y <- y[ind]
+  group <- group[ind]
+
+  difference <- x - y                                 # vector of differences
+  average <- (x + y) / 2                              # vector of means
+  difference_mean <- mean(difference)                 # mean difference
+  difference_sd <- sd(difference)                     # SD of differences
+  al <- qnorm(1 - alpha / 2) * difference_sd
+  upper_agreement_limit <- difference_mean + al       # agreement limits
+  lower_agreement_limit <- difference_mean - al
+  n <- length(difference)                             # number of 'observations'
+
+  difference_se <- difference_sd / sqrt(n)            # standard error of the mean
+  al_se <- difference_sd * sqrt(3) / sqrt(n)          # standard error of the agreement limit
+  tvalue <- qt(1 - alpha / 2, n - 1)                  # t value for 95% CI calculation
+  difference_mean_ci <- difference_se * tvalue
+  al_ci <- al_se * tvalue
+  upper_agreement_limit_ci <- c(upper_agreement_limit - al_ci, upper_agreement_limit + al_ci)
+  lower_agreement_limit_ci <- c(lower_agreement_limit - al_ci, lower_agreement_limit + al_ci)
+
+
+  list(
+    difference_mean = difference_mean,
+    ci_mean = difference_mean + c(-1, 1) * difference_mean_ci,
+    difference_sd = difference_sd,
+    difference_se = difference_se,
+    upper_agreement_limit = upper_agreement_limit,
+    lower_agreement_limit = lower_agreement_limit,
+    agreement_limit_se = al_se,
+    upper_agreement_limit_ci = upper_agreement_limit_ci,
+    lower_agreement_limit_ci = lower_agreement_limit_ci,
+    t_value = tvalue,
+    n = n
+  )
+}

From 49cff5ac9c17b36419a6706a8e0a8778eedc934a Mon Sep 17 00:00:00 2001
From: "Lin, Chanjuan {MDBJ~Shanghai}" <chanjuan.lin@roche.com>
Date: Wed, 26 Apr 2023 10:28:23 +0200
Subject: [PATCH 03/14] update

---
 DESCRIPTION                        |  1 +
 R/bland_altman.R                   | 28 +++++++++++----
 tests/testthat/test-bland-altman.R | 56 ++++++++++++++++++++++++++++++
 3 files changed, 79 insertions(+), 6 deletions(-)
 create mode 100644 tests/testthat/test-bland-altman.R

diff --git a/DESCRIPTION b/DESCRIPTION
index d031c7ce6a..93bb21bcb9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -76,6 +76,7 @@ Collate:
     'abnormal_by_worst_grade_worsen.R'
     'analyze_vars_in_cols.R'
     'argument_convention.R'
+    'bland_altman.R'
     'combination_function.R'
     'summarize_variables.R'
     'compare_variables.R'
diff --git a/R/bland_altman.R b/R/bland_altman.R
index 5ac0ae220c..692e3f034f 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -6,22 +6,38 @@
 #' @param y ('numeric')\cr vector of numbers we want to analyze.
 #'
 #' @name s_bland_altman
-#'
+#' @details
+#' https://doi.org/10.1016/S0140-6736(86)90837-8
+#' @references
+#' @article{bland1986statistical,
+# title={Statistical methods for assessing agreement between two methods of clinical measurement},
+# author={Bland, J Martin and Altman, DouglasG},
+# journal={The lancet},
+# volume={327},
+# number={8476},
+# pages={307--310},
+# year={1986},
+# publisher={Elsevier}
+# }
+# https://cran.r-project.org/web/packages/Rdpack/vignettes/Inserting_bibtex_references.pdf
+
 #' @examples
-#' x = seq(1, 60, 5)
-#' y = seq(5, 50, 4)
-#' conf_level = 0.9
+#' x <- seq(1, 60, 5)
+#' y <- seq(5, 50, 4)
+#' conf_level <- 0.9
 #' s_bland_altman(x, y, conf_level = conf_level)
 
 
-s_bland_altman_cj <- function(x, y, conf_level = 0.95, group = NULL){
+s_bland_altman <- function(x, y, conf_level = 0.95){
+  checkmate::assert_numeric(x, min.len = 1, any.missing = TRUE)
+  checkmate::assert_numeric(y, len = length(x), any.missing = TRUE)
+  checkmate::assert_numeric(conf_level, lower = 0, upper = 1, any.missing = TRUE)
 
   alpha <- 1 - conf_level
 
   ind <- complete.cases(x, y) # use only pairwise complete observations, and check if x and y have the same length
   x <- x[ind]
   y <- y[ind]
-  group <- group[ind]
 
   difference <- x - y                                 # vector of differences
   average <- (x + y) / 2                              # vector of means
diff --git a/tests/testthat/test-bland-altman.R b/tests/testthat/test-bland-altman.R
new file mode 100644
index 0000000000..6daea62b8f
--- /dev/null
+++ b/tests/testthat/test-bland-altman.R
@@ -0,0 +1,56 @@
+testthat::test_that("unequal length vector gives correct error", {
+  testthat::expect_error(s_bland_altman (x = 1:5, y = 1:6, 0.95))
+})
+
+testthat::test_that("infeasible input gives correct error", {
+  testthat::expect_error(s_bland_altman (x = c('a', 'b', 'c'), y = 1:3, 0.95))
+  testthat::expect_error(s_bland_altman (x = 1:3, y = 4:6, 2))
+})
+
+
+testthat::test_that("works correctly", {
+  set.seed(1)
+  x = rnorm(20)
+  y = rnorm(20)
+  res = s_bland_altman(x, y, 0.9)
+  expect = list(
+    difference_mean = mean(x) - mean(y),
+    ci_mean = c(-0.3414723, 0.7354631),
+    difference_sd = 1.392664,
+    difference_se = 0.3114091,
+    upper_agreement_limit = 2.487724,
+    lower_agreement_limit = -2.093733,
+    agreement_limit_se = 0.5393764,
+    upper_agreement_limit_ci = c(1.555070, 3.420377),
+    lower_agreement_limit_ci = c(-3.026386,-1.161079),
+    t_value = 1.729133,
+    n = 20L
+  )
+  expect_identical(res, expect, tolerance = 1e-5)
+
+
+})
+
+
+testthat::test_that("works correctly with NA element in either vectors", {
+  set.seed(1)
+  x = rnorm(20)
+  y = rnorm(20)
+  x = c(NA_real_, 2, x, NA_real_)
+  y = c(1, NA_real_, y, 2)
+  res = s_bland_altman(x, y, 0.9)
+  expect = list(
+    difference_mean = 0.1969954,
+    ci_mean = c(-0.3414723, 0.7354631),
+    difference_sd = 1.392664,
+    difference_se = 0.3114091,
+    upper_agreement_limit = 2.487724,
+    lower_agreement_limit = -2.093733,
+    agreement_limit_se = 0.5393764,
+    upper_agreement_limit_ci = c(1.555070, 3.420377),
+    lower_agreement_limit_ci = c(-3.026386,-1.161079),
+    t_value = 1.729133,
+    n = 20L
+  )
+  expect_identical(res, expect)
+})

From 7ad3a101ba9722e98274afbe026ea8dee838e017 Mon Sep 17 00:00:00 2001
From: "Lin, Chanjuan {MDBJ~Shanghai}" <chanjuan.lin@roche.com>
Date: Tue, 5 Dec 2023 07:41:43 +0100
Subject: [PATCH 04/14] use <- to replace =

---
 R/bland_altman.R                   |  8 +++++++-
 man/s_bland_altman.Rd              | 30 ++++++++++++++++++++++++++++++
 tests/testthat/test-bland-altman.R | 20 ++++++++++----------
 3 files changed, 47 insertions(+), 11 deletions(-)
 create mode 100644 man/s_bland_altman.Rd

diff --git a/R/bland_altman.R b/R/bland_altman.R
index c3972675f3..6b419c7a20 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -39,6 +39,12 @@ s_bland_altman <- function(x, y, conf_level = 0.95){
   ind <- complete.cases(x, y) # use only pairwise complete observations, and check if x and y have the same length
   x <- x[ind]
   y <- y[ind]
+  n <- length(n)                                      # number of 'observations'
+
+  if(n ==0){
+    stop("there is no valid paired data")
+  }
+
   difference <- x - y                                 # vector of differences
   average <- (x + y) / 2                              # vector of means
   difference_mean <- mean(difference)                 # mean difference
@@ -46,7 +52,7 @@ s_bland_altman <- function(x, y, conf_level = 0.95){
   al <- qnorm(1 - alpha / 2) * difference_sd
   upper_agreement_limit <- difference_mean + al       # agreement limits
   lower_agreement_limit <- difference_mean - al
-  n <- length(difference)                             # number of 'observations'
+
 
   difference_se <- difference_sd / sqrt(n)            # standard error of the mean
   al_se <- difference_sd * sqrt(3) / sqrt(n)          # standard error of the agreement limit
diff --git a/man/s_bland_altman.Rd b/man/s_bland_altman.Rd
new file mode 100644
index 0000000000..71db46adb9
--- /dev/null
+++ b/man/s_bland_altman.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bland_altman.R
+\name{s_bland_altman}
+\alias{s_bland_altman}
+\title{Bland Altman analysis}
+\usage{
+s_bland_altman(x, y, conf_level = 0.95)
+}
+\arguments{
+\item{x}{(\code{numeric})\cr vector of numbers we want to analyze.}
+
+\item{y}{('numeric')\cr vector of numbers we want to analyze.}
+
+\item{conf_level}{(\code{proportion})\cr confidence level of the interval.}
+}
+\description{
+'r lifecycle::badge("stable")'
+}
+\details{
+https://doi.org/10.1016/S0140-6736(86)90837-8
+}
+\examples{
+x <- seq(1, 60, 5)
+y <- seq(5, 50, 4)
+conf_level <- 0.9
+s_bland_altman(x, y, conf_level = conf_level)
+}
+\references{
+
+}
diff --git a/tests/testthat/test-bland-altman.R b/tests/testthat/test-bland-altman.R
index 6daea62b8f..5eb4e0c446 100644
--- a/tests/testthat/test-bland-altman.R
+++ b/tests/testthat/test-bland-altman.R
@@ -10,10 +10,10 @@ testthat::test_that("infeasible input gives correct error", {
 
 testthat::test_that("works correctly", {
   set.seed(1)
-  x = rnorm(20)
-  y = rnorm(20)
-  res = s_bland_altman(x, y, 0.9)
-  expect = list(
+  x <- rnorm(20)
+  y <- rnorm(20)
+  res <- s_bland_altman(x, y, 0.9)
+  expect <- list(
     difference_mean = mean(x) - mean(y),
     ci_mean = c(-0.3414723, 0.7354631),
     difference_sd = 1.392664,
@@ -34,12 +34,12 @@ testthat::test_that("works correctly", {
 
 testthat::test_that("works correctly with NA element in either vectors", {
   set.seed(1)
-  x = rnorm(20)
-  y = rnorm(20)
-  x = c(NA_real_, 2, x, NA_real_)
-  y = c(1, NA_real_, y, 2)
-  res = s_bland_altman(x, y, 0.9)
-  expect = list(
+  x <- rnorm(20)
+  y <- rnorm(20)
+  x <- c(NA_real_, 2, x, NA_real_)
+  y <- c(1, NA_real_, y, 2)
+  res <- s_bland_altman(x, y, 0.9)
+  expect <- list(
     difference_mean = 0.1969954,
     ci_mean = c(-0.3414723, 0.7354631),
     difference_sd = 1.392664,

From 736ed010aeea678a6e39e6f9d547a41f5d01735e Mon Sep 17 00:00:00 2001
From: "Lin, Chanjuan {MDBJ~Shanghai}" <chanjuan.lin@roche.com>
Date: Tue, 5 Dec 2023 09:07:55 +0100
Subject: [PATCH 05/14] modified a little bit per received comment: 1. use <-
 instead of = 2. remove redundant line break 3. add more clarity for parameter
 description 4. add more details for @description 5. move the bib information
 to REFERENCES.bib under tern

---
 NEWS.md                            |  1 +
 R/bland_altman.R                   | 20 +++-----------------
 inst/REFERENCES.bib                | 20 ++++++++++++++++++++
 tests/testthat/test-bland-altman.R |  2 --
 4 files changed, 24 insertions(+), 19 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index c74a03bd37..38d1ebdae0 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,6 +12,7 @@
 * Added summarize function version of `count_occurrences` analyze function, `summarize_occurrences`.
 * Added referential footnotes to `surv_time` for censored range observations, controlled via the `ref_fn_censor` parameter.
 * Added helper function `h_adlb_abnormal_by_worst_grade` to prepare `ADLB` data to use as input in `count_abnormal_by_worst_grade`.
+* Added `s_bland_altman` function to assess agreement between two numerical vectors. 
 
 ### Enhancements
 * Added `ref_group_coxph` parameter to `g_km` to specify the reference group used for pairwise Cox-PH calculations when `annot_coxph = TRUE`.
diff --git a/R/bland_altman.R b/R/bland_altman.R
index 6b419c7a20..18cb2d181d 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -1,26 +1,12 @@
-
 #' Bland Altman analysis
 #'
-#' @description 'r lifecycle::badge("stable")'
+#' @description 'r lifecycle::badge("experimental")'
+#' This function uses bland altman method to assess the agreement between two numerical vectors.
 #'
 #' @inheritParams argument_convention
-#' @param y ('numeric')\cr vector of numbers we want to analyze.
+#' @param y ('numeric')\cr vector of numbers we want to analyze, which we want to compare with x.
 #'
 #' @name s_bland_altman
-#' @details
-#' https://doi.org/10.1016/S0140-6736(86)90837-8
-#' @references
-#' @article{bland1986statistical,
-# title={Statistical methods for assessing agreement between two methods of clinical measurement},
-# author={Bland, J Martin and Altman, DouglasG},
-# journal={The lancet},
-# volume={327},
-# number={8476},
-# pages={307--310},
-# year={1986},
-# publisher={Elsevier}
-# }
-# https://cran.r-project.org/web/packages/Rdpack/vignettes/Inserting_bibtex_references.pdf
 
 #' @examples
 #' x <- seq(1, 60, 5)
diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib
index 879f39c540..2cfea6b9ae 100644
--- a/inst/REFERENCES.bib
+++ b/inst/REFERENCES.bib
@@ -51,3 +51,23 @@ @ARTICLE{Schouten1980-kd
   year      =  1980,
   language  = "en"
 }
+
+@ARTICLE{bland1986statistical,
+  title     = "Statistical methods for assessing agreement between two methods of clinical measurement",
+  author    = "Bland, J Martin and Altman, DouglasG",
+  abstract  = "In clinical measurement comparison of a new measurement technique
+              with an established one is often needed to see whether they agree
+              sufficiently for the new to replace the old. Such investigations
+              are often analysed inappropriately, notably by using correlation
+              coefficients. The use of correlation is misleading. An alternative
+              approach, based on graphical techniques and simple calculations,
+              is described, together with the relation between this analysis and
+              the assessment of repeatability.",
+  journal   = "The lancet",
+  publisher = "Elsevier",
+  volume    ="327",
+  number    ="8476",
+  pages     ="307--310",
+  year      ="1986",
+  language  = "en"
+}
diff --git a/tests/testthat/test-bland-altman.R b/tests/testthat/test-bland-altman.R
index 5eb4e0c446..7f9ddec0dd 100644
--- a/tests/testthat/test-bland-altman.R
+++ b/tests/testthat/test-bland-altman.R
@@ -27,8 +27,6 @@ testthat::test_that("works correctly", {
     n = 20L
   )
   expect_identical(res, expect, tolerance = 1e-5)
-
-
 })
 
 

From 09c3319b6b4667fe9753cdeadf80dafbf71b199a Mon Sep 17 00:00:00 2001
From: shajoezhu <sha.joe.zhu@gmail.com>
Date: Fri, 12 Jan 2024 11:31:19 +0800
Subject: [PATCH 06/14] restyle files

---
 R/bland_altman.R                   | 24 +++++++++++-------------
 tests/testthat/test-bland-altman.R | 10 +++++-----
 2 files changed, 16 insertions(+), 18 deletions(-)

diff --git a/R/bland_altman.R b/R/bland_altman.R
index 18cb2d181d..fb775076a0 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -13,9 +13,7 @@
 #' y <- seq(5, 50, 4)
 #' conf_level <- 0.9
 #' s_bland_altman(x, y, conf_level = conf_level)
-
-
-s_bland_altman <- function(x, y, conf_level = 0.95){
+s_bland_altman <- function(x, y, conf_level = 0.95) {
   checkmate::assert_numeric(x, min.len = 1, any.missing = TRUE)
   checkmate::assert_numeric(y, len = length(x), any.missing = TRUE)
   checkmate::assert_numeric(conf_level, lower = 0, upper = 1, any.missing = TRUE)
@@ -25,24 +23,24 @@ s_bland_altman <- function(x, y, conf_level = 0.95){
   ind <- complete.cases(x, y) # use only pairwise complete observations, and check if x and y have the same length
   x <- x[ind]
   y <- y[ind]
-  n <- length(n)                                      # number of 'observations'
+  n <- length(n) # number of 'observations'
 
-  if(n ==0){
+  if (n == 0) {
     stop("there is no valid paired data")
   }
 
-  difference <- x - y                                 # vector of differences
-  average <- (x + y) / 2                              # vector of means
-  difference_mean <- mean(difference)                 # mean difference
-  difference_sd <- sd(difference)                     # SD of differences
+  difference <- x - y # vector of differences
+  average <- (x + y) / 2 # vector of means
+  difference_mean <- mean(difference) # mean difference
+  difference_sd <- sd(difference) # SD of differences
   al <- qnorm(1 - alpha / 2) * difference_sd
-  upper_agreement_limit <- difference_mean + al       # agreement limits
+  upper_agreement_limit <- difference_mean + al # agreement limits
   lower_agreement_limit <- difference_mean - al
 
 
-  difference_se <- difference_sd / sqrt(n)            # standard error of the mean
-  al_se <- difference_sd * sqrt(3) / sqrt(n)          # standard error of the agreement limit
-  tvalue <- qt(1 - alpha / 2, n - 1)                  # t value for 95% CI calculation
+  difference_se <- difference_sd / sqrt(n) # standard error of the mean
+  al_se <- difference_sd * sqrt(3) / sqrt(n) # standard error of the agreement limit
+  tvalue <- qt(1 - alpha / 2, n - 1) # t value for 95% CI calculation
   difference_mean_ci <- difference_se * tvalue
   al_ci <- al_se * tvalue
   upper_agreement_limit_ci <- c(upper_agreement_limit - al_ci, upper_agreement_limit + al_ci)
diff --git a/tests/testthat/test-bland-altman.R b/tests/testthat/test-bland-altman.R
index 7f9ddec0dd..02ada24512 100644
--- a/tests/testthat/test-bland-altman.R
+++ b/tests/testthat/test-bland-altman.R
@@ -1,10 +1,10 @@
 testthat::test_that("unequal length vector gives correct error", {
-  testthat::expect_error(s_bland_altman (x = 1:5, y = 1:6, 0.95))
+  testthat::expect_error(s_bland_altman(x = 1:5, y = 1:6, 0.95))
 })
 
 testthat::test_that("infeasible input gives correct error", {
-  testthat::expect_error(s_bland_altman (x = c('a', 'b', 'c'), y = 1:3, 0.95))
-  testthat::expect_error(s_bland_altman (x = 1:3, y = 4:6, 2))
+  testthat::expect_error(s_bland_altman(x = c("a", "b", "c"), y = 1:3, 0.95))
+  testthat::expect_error(s_bland_altman(x = 1:3, y = 4:6, 2))
 })
 
 
@@ -22,7 +22,7 @@ testthat::test_that("works correctly", {
     lower_agreement_limit = -2.093733,
     agreement_limit_se = 0.5393764,
     upper_agreement_limit_ci = c(1.555070, 3.420377),
-    lower_agreement_limit_ci = c(-3.026386,-1.161079),
+    lower_agreement_limit_ci = c(-3.026386, -1.161079),
     t_value = 1.729133,
     n = 20L
   )
@@ -46,7 +46,7 @@ testthat::test_that("works correctly with NA element in either vectors", {
     lower_agreement_limit = -2.093733,
     agreement_limit_se = 0.5393764,
     upper_agreement_limit_ci = c(1.555070, 3.420377),
-    lower_agreement_limit_ci = c(-3.026386,-1.161079),
+    lower_agreement_limit_ci = c(-3.026386, -1.161079),
     t_value = 1.729133,
     n = 20L
   )

From dccef420c2ceea2d6511958de368a57e7a6cf05b Mon Sep 17 00:00:00 2001
From: "Lin, Chanjuan {MDBJ~Shanghai}" <chanjuan.lin@roche.com>
Date: Thu, 18 Jan 2024 06:17:16 +0100
Subject: [PATCH 07/14] add bland altman plot

---
 R/bland_altman.R | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/R/bland_altman.R b/R/bland_altman.R
index fb775076a0..c32c2732db 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -23,7 +23,7 @@ s_bland_altman <- function(x, y, conf_level = 0.95) {
   ind <- complete.cases(x, y) # use only pairwise complete observations, and check if x and y have the same length
   x <- x[ind]
   y <- y[ind]
-  n <- length(n) # number of 'observations'
+  n <- length(ind) # number of 'observations'
 
   if (n == 0) {
     stop("there is no valid paired data")
@@ -61,3 +61,36 @@ s_bland_altman <- function(x, y, conf_level = 0.95) {
     n = n
   )
 }
+
+
+#' @inheritParams s_bland_altman
+#' @rdname s_bland_altman
+#' @examples
+#' x <- seq(1, 60, 5)
+#' y <- seq(5, 50, 4)
+#' conf_level <- 0.9
+#' g_bland_altman(x, y, conf_level = conf_level)
+#'
+g_bland_altman <- function(x, y, conf_level = 0.95){
+  result_tem <- s_bland_altman(x,y,conf_level = conf_level)
+  xpos <- max(result_tem$df$average) * 0.9 + min(result_tem$df$average) * 0.1
+  yrange <- diff(range(result_tem$df$difference))
+
+  p <- ggplot(result_tem$df) +
+    geom_point(aes(x = average, y = difference), color = "blue") +
+    geom_hline(yintercept = result_tem$difference_mean, color = "blue", linetype = 1) +
+    geom_hline(yintercept = 0, color = "blue", linetype = 2) +
+    geom_hline(yintercept = result_tem$lower_agreement_limit, color = "red", linetype = 2) +
+    geom_hline(yintercept = result_tem$upper_agreement_limit, color = "red", linetype = 2) +
+    annotate("text", x = xpos, y = result_tem$lower_agreement_limit + 0.03 * yrange, label = "lower limits of agreement", color = "red") +
+    annotate("text", x = xpos, y = result_tem$upper_agreement_limit + 0.03 * yrange, label = "upper limits of agreement", color = "red") +
+    annotate("text", x = xpos, y = result_tem$difference_mean + 0.03 * yrange, label = "mean of difference between two measures", color = "blue") +
+    annotate("text", x = xpos, y = result_tem$lower_agreement_limit - 0.03 * yrange, label = sprintf("%.2f", result_tem$lower_agreement_limit), color = "red") +
+    annotate("text", x = xpos, y = result_tem$upper_agreement_limit - 0.03 * yrange, label = sprintf("%.2f", result_tem$upper_agreement_limit), color = "red") +
+    annotate("text", x = xpos, y = result_tem$difference_mean - 0.03 * yrange, label = sprintf("%.2f", result_tem$difference_meanm), color = "blue") +
+    xlab("average of two measures") +
+    ylab("difference between two measures")
+
+  return(p)
+}
+

From 6bf39fa7525104fbc179c2ae1adbf0ba2bcd28bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Chanjuan=20Lin=20=EF=BC=88=E6=9E=97=E5=A9=B5=E5=A8=9F?=
 =?UTF-8?q?=EF=BC=89?= <chanjuan.lin@roche.com>
Date: Thu, 18 Jan 2024 05:38:56 +0000
Subject: [PATCH 08/14] add data.frame, which is lost by accident

---
 R/bland_altman.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/bland_altman.R b/R/bland_altman.R
index c32c2732db..31ab1ade20 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -48,6 +48,7 @@ s_bland_altman <- function(x, y, conf_level = 0.95) {
 
 
   list(
+    df= data.frame(average, difference),
     difference_mean = difference_mean,
     ci_mean = difference_mean + c(-1, 1) * difference_mean_ci,
     difference_sd = difference_sd,

From cd6dc468d8c55e5157db849ded317cadcfd64733 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Chanjuan=20Lin=20=EF=BC=88=E6=9E=97=E5=A9=B5=E5=A8=9F?=
 =?UTF-8?q?=EF=BC=89?= <chanjuan.lin@roche.com>
Date: Thu, 18 Jan 2024 05:42:42 +0000
Subject: [PATCH 09/14] render docs

---
 man/s_bland_altman.Rd | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/man/s_bland_altman.Rd b/man/s_bland_altman.Rd
index 71db46adb9..5eba2ae478 100644
--- a/man/s_bland_altman.Rd
+++ b/man/s_bland_altman.Rd
@@ -2,29 +2,32 @@
 % Please edit documentation in R/bland_altman.R
 \name{s_bland_altman}
 \alias{s_bland_altman}
+\alias{g_bland_altman}
 \title{Bland Altman analysis}
 \usage{
 s_bland_altman(x, y, conf_level = 0.95)
+
+g_bland_altman(x, y, conf_level = 0.95)
 }
 \arguments{
 \item{x}{(\code{numeric})\cr vector of numbers we want to analyze.}
 
-\item{y}{('numeric')\cr vector of numbers we want to analyze.}
+\item{y}{('numeric')\cr vector of numbers we want to analyze, which we want to compare with x.}
 
 \item{conf_level}{(\code{proportion})\cr confidence level of the interval.}
 }
 \description{
-'r lifecycle::badge("stable")'
-}
-\details{
-https://doi.org/10.1016/S0140-6736(86)90837-8
+'r lifecycle::badge("experimental")'
+This function uses bland altman method to assess the agreement between two numerical vectors.
 }
 \examples{
 x <- seq(1, 60, 5)
 y <- seq(5, 50, 4)
 conf_level <- 0.9
 s_bland_altman(x, y, conf_level = conf_level)
-}
-\references{
+x <- seq(1, 60, 5)
+y <- seq(5, 50, 4)
+conf_level <- 0.9
+g_bland_altman(x, y, conf_level = conf_level)
 
 }

From 7b37dab236025d6a0dffdbc218f5c3a6fe7c2372 Mon Sep 17 00:00:00 2001
From: shajoezhu <sha.joe.zhu@gmail.com>
Date: Thu, 18 Jan 2024 17:31:01 +0800
Subject: [PATCH 10/14] update style

---
 R/bland_altman.R | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/R/bland_altman.R b/R/bland_altman.R
index 31ab1ade20..92ef25357d 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -48,7 +48,7 @@ s_bland_altman <- function(x, y, conf_level = 0.95) {
 
 
   list(
-    df= data.frame(average, difference),
+    df = data.frame(average, difference),
     difference_mean = difference_mean,
     ci_mean = difference_mean + c(-1, 1) * difference_mean_ci,
     difference_sd = difference_sd,
@@ -72,8 +72,8 @@ s_bland_altman <- function(x, y, conf_level = 0.95) {
 #' conf_level <- 0.9
 #' g_bland_altman(x, y, conf_level = conf_level)
 #'
-g_bland_altman <- function(x, y, conf_level = 0.95){
-  result_tem <- s_bland_altman(x,y,conf_level = conf_level)
+g_bland_altman <- function(x, y, conf_level = 0.95) {
+  result_tem <- s_bland_altman(x, y, conf_level = conf_level)
   xpos <- max(result_tem$df$average) * 0.9 + min(result_tem$df$average) * 0.1
   yrange <- diff(range(result_tem$df$difference))
 
@@ -94,4 +94,3 @@ g_bland_altman <- function(x, y, conf_level = 0.95){
 
   return(p)
 }
-

From d92a35fd00a54bc1835f8a03cc41c03926eaf711 Mon Sep 17 00:00:00 2001
From: shajoezhu <sha.joe.zhu@gmail.com>
Date: Fri, 19 Jan 2024 00:04:08 +0800
Subject: [PATCH 11/14] rename help file

---
 NAMESPACE                                  |  2 +
 R/bland_altman.R                           | 48 +++++++++++++---------
 man/{s_bland_altman.Rd => bland_altman.Rd} | 21 ++++++----
 3 files changed, 44 insertions(+), 27 deletions(-)
 rename man/{s_bland_altman.Rd => bland_altman.Rd} (58%)

diff --git a/NAMESPACE b/NAMESPACE
index 9780039cdd..0f88aa7207 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -124,6 +124,7 @@ export(format_fraction_fixed_dp)
 export(format_fraction_threshold)
 export(format_sigfig)
 export(format_xx)
+export(g_bland_altman)
 export(g_forest)
 export(g_ipp)
 export(g_km)
@@ -243,6 +244,7 @@ export(prop_wilson)
 export(reapply_varlabels)
 export(ref_group_position)
 export(rtable2gg)
+export(s_bland_altman)
 export(s_compare)
 export(s_count_occurrences)
 export(s_count_occurrences_by_grade)
diff --git a/R/bland_altman.R b/R/bland_altman.R
index 92ef25357d..92373a6d78 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -1,18 +1,26 @@
 #' Bland Altman analysis
 #'
-#' @description 'r lifecycle::badge("experimental")'
-#' This function uses bland altman method to assess the agreement between two numerical vectors.
+#' @description `r lifecycle::badge("experimental")`
+#'
+#' Functions of bland altman method to assess the agreement between two numerical vectors.
 #'
 #' @inheritParams argument_convention
 #' @param y ('numeric')\cr vector of numbers we want to analyze, which we want to compare with x.
 #'
-#' @name s_bland_altman
-
+#' @name bland_altman
 #' @examples
 #' x <- seq(1, 60, 5)
 #' y <- seq(5, 50, 4)
 #' conf_level <- 0.9
+#' # Derive statistics that are needed for Bland Altman plot
 #' s_bland_altman(x, y, conf_level = conf_level)
+#' # Create a Bland Altman plot
+#' g_bland_altman(x, y, conf_level = conf_level)
+NULL
+
+#' @describeIn bland_altman
+#'
+#' @export
 s_bland_altman <- function(x, y, conf_level = 0.95) {
   checkmate::assert_numeric(x, min.len = 1, any.missing = TRUE)
   checkmate::assert_numeric(y, len = length(x), any.missing = TRUE)
@@ -63,15 +71,9 @@ s_bland_altman <- function(x, y, conf_level = 0.95) {
   )
 }
 
-
-#' @inheritParams s_bland_altman
-#' @rdname s_bland_altman
-#' @examples
-#' x <- seq(1, 60, 5)
-#' y <- seq(5, 50, 4)
-#' conf_level <- 0.9
-#' g_bland_altman(x, y, conf_level = conf_level)
+#' @describeIn bland_altman
 #'
+#' @export
 g_bland_altman <- function(x, y, conf_level = 0.95) {
   result_tem <- s_bland_altman(x, y, conf_level = conf_level)
   xpos <- max(result_tem$df$average) * 0.9 + min(result_tem$df$average) * 0.1
@@ -83,14 +85,20 @@ g_bland_altman <- function(x, y, conf_level = 0.95) {
     geom_hline(yintercept = 0, color = "blue", linetype = 2) +
     geom_hline(yintercept = result_tem$lower_agreement_limit, color = "red", linetype = 2) +
     geom_hline(yintercept = result_tem$upper_agreement_limit, color = "red", linetype = 2) +
-    annotate("text", x = xpos, y = result_tem$lower_agreement_limit + 0.03 * yrange, label = "lower limits of agreement", color = "red") +
-    annotate("text", x = xpos, y = result_tem$upper_agreement_limit + 0.03 * yrange, label = "upper limits of agreement", color = "red") +
-    annotate("text", x = xpos, y = result_tem$difference_mean + 0.03 * yrange, label = "mean of difference between two measures", color = "blue") +
-    annotate("text", x = xpos, y = result_tem$lower_agreement_limit - 0.03 * yrange, label = sprintf("%.2f", result_tem$lower_agreement_limit), color = "red") +
-    annotate("text", x = xpos, y = result_tem$upper_agreement_limit - 0.03 * yrange, label = sprintf("%.2f", result_tem$upper_agreement_limit), color = "red") +
-    annotate("text", x = xpos, y = result_tem$difference_mean - 0.03 * yrange, label = sprintf("%.2f", result_tem$difference_meanm), color = "blue") +
-    xlab("average of two measures") +
-    ylab("difference between two measures")
+    annotate("text", x = xpos, y = result_tem$lower_agreement_limit + 0.03 * yrange,
+             label = "lower limits of agreement", color = "red") +
+    annotate("text", x = xpos, y = result_tem$upper_agreement_limit + 0.03 * yrange,
+             label = "upper limits of agreement", color = "red") +
+    annotate("text", x = xpos, y = result_tem$difference_mean + 0.03 * yrange,
+             label = "mean of difference between two measures", color = "blue") +
+    annotate("text", x = xpos, y = result_tem$lower_agreement_limit - 0.03 * yrange,
+             label = sprintf("%.2f", result_tem$lower_agreement_limit), color = "red") +
+    annotate("text", x = xpos, y = result_tem$upper_agreement_limit - 0.03 * yrange,
+             label = sprintf("%.2f", result_tem$upper_agreement_limit), color = "red") +
+    annotate("text", x = xpos, y = result_tem$difference_mean - 0.03 * yrange,
+             label = sprintf("%.2f", result_tem$difference_meanm), color = "blue") +
+    xlab("Average of two measures") +
+    ylab("Difference between two measures")
 
   return(p)
 }
diff --git a/man/s_bland_altman.Rd b/man/bland_altman.Rd
similarity index 58%
rename from man/s_bland_altman.Rd
rename to man/bland_altman.Rd
index 5eba2ae478..a763b4b202 100644
--- a/man/s_bland_altman.Rd
+++ b/man/bland_altman.Rd
@@ -1,6 +1,7 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/bland_altman.R
-\name{s_bland_altman}
+\name{bland_altman}
+\alias{bland_altman}
 \alias{s_bland_altman}
 \alias{g_bland_altman}
 \title{Bland Altman analysis}
@@ -17,17 +18,23 @@ g_bland_altman(x, y, conf_level = 0.95)
 \item{conf_level}{(\code{proportion})\cr confidence level of the interval.}
 }
 \description{
-'r lifecycle::badge("experimental")'
-This function uses bland altman method to assess the agreement between two numerical vectors.
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
+
+Functions of bland altman method to assess the agreement between two numerical vectors.
 }
+\section{Functions}{
+\itemize{
+\item \code{s_bland_altman()}: 
+
+\item \code{g_bland_altman()}: 
+
+}}
 \examples{
 x <- seq(1, 60, 5)
 y <- seq(5, 50, 4)
 conf_level <- 0.9
+# Derive statistics that are needed for Bland Altman plot
 s_bland_altman(x, y, conf_level = conf_level)
-x <- seq(1, 60, 5)
-y <- seq(5, 50, 4)
-conf_level <- 0.9
+# Create a Bland Altman plot
 g_bland_altman(x, y, conf_level = conf_level)
-
 }

From 242e298568ff001bceb249574636ae334359809d Mon Sep 17 00:00:00 2001
From: shajoezhu <sha.joe.zhu@gmail.com>
Date: Fri, 19 Jan 2024 00:41:17 +0800
Subject: [PATCH 12/14] update tests

---
 R/bland_altman.R                   |  2 +-
 tests/testthat/test-bland-altman.R | 13 ++++++++++---
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/R/bland_altman.R b/R/bland_altman.R
index 92373a6d78..a57356e6cc 100644
--- a/R/bland_altman.R
+++ b/R/bland_altman.R
@@ -31,7 +31,7 @@ s_bland_altman <- function(x, y, conf_level = 0.95) {
   ind <- complete.cases(x, y) # use only pairwise complete observations, and check if x and y have the same length
   x <- x[ind]
   y <- y[ind]
-  n <- length(ind) # number of 'observations'
+  n <- sum(ind) # number of 'observations'
 
   if (n == 0) {
     stop("there is no valid paired data")
diff --git a/tests/testthat/test-bland-altman.R b/tests/testthat/test-bland-altman.R
index 02ada24512..18cdb856bf 100644
--- a/tests/testthat/test-bland-altman.R
+++ b/tests/testthat/test-bland-altman.R
@@ -8,12 +8,15 @@ testthat::test_that("infeasible input gives correct error", {
 })
 
 
-testthat::test_that("works correctly", {
+testthat::test_that("s_bland_altman works with two vectors", {
   set.seed(1)
   x <- rnorm(20)
   y <- rnorm(20)
   res <- s_bland_altman(x, y, 0.9)
+  average <- (x + y) / 2
+  difference <- x - y
   expect <- list(
+    df = data.frame(average, difference),
     difference_mean = mean(x) - mean(y),
     ci_mean = c(-0.3414723, 0.7354631),
     difference_sd = 1.392664,
@@ -30,14 +33,18 @@ testthat::test_that("works correctly", {
 })
 
 
-testthat::test_that("works correctly with NA element in either vectors", {
+testthat::test_that("s_bland_altman works with two vectors with NA element in either vectors", {
   set.seed(1)
   x <- rnorm(20)
   y <- rnorm(20)
   x <- c(NA_real_, 2, x, NA_real_)
   y <- c(1, NA_real_, y, 2)
   res <- s_bland_altman(x, y, 0.9)
+  average <- (x + y) / 2
+  difference <- x - y
+  df <- data.frame(na.omit(data.frame(average, difference)), row.names = NULL)
   expect <- list(
+    df = df,
     difference_mean = 0.1969954,
     ci_mean = c(-0.3414723, 0.7354631),
     difference_sd = 1.392664,
@@ -50,5 +57,5 @@ testthat::test_that("works correctly with NA element in either vectors", {
     t_value = 1.729133,
     n = 20L
   )
-  expect_identical(res, expect)
+  expect_identical(res, expect, tolerance = 1e-5)
 })

From 8429c6ae8c8c0ca0d7fb5e19340793ee0e09ccf1 Mon Sep 17 00:00:00 2001
From: shajoezhu <sha.joe.zhu@gmail.com>
Date: Fri, 19 Jan 2024 00:46:25 +0800
Subject: [PATCH 13/14] update word list

---
 inst/WORDLIST | 1 +
 1 file changed, 1 insertion(+)

diff --git a/inst/WORDLIST b/inst/WORDLIST
index 5f67a2d233..3f22d828ef 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -37,3 +37,4 @@ subtables
 unformatted
 ungroup
 unstratified
+altman

From 678929a1f09905e75c2afb359944d7df616a3a03 Mon Sep 17 00:00:00 2001
From: shajoezhu <sha.joe.zhu@gmail.com>
Date: Fri, 19 Jan 2024 01:05:11 +0800
Subject: [PATCH 14/14] update namespace

---
 NAMESPACE   | 4 ++++
 R/package.R | 4 +++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/NAMESPACE b/NAMESPACE
index 0f88aa7207..61c8df366d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -318,7 +318,11 @@ importFrom(grid,widthDetails)
 importFrom(magrittr,"%>%")
 importFrom(methods,new)
 importFrom(rlang,.data)
+importFrom(stats,complete.cases)
 importFrom(stats,pchisq)
+importFrom(stats,qnorm)
+importFrom(stats,qt)
+importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(survival,Surv)
 importFrom(survival,coxph)
diff --git a/R/package.R b/R/package.R
index 141412fe23..9fc47540c7 100644
--- a/R/package.R
+++ b/R/package.R
@@ -12,13 +12,15 @@
 #' @importFrom Rdpack reprompt
 #' @importFrom rlang .data
 #' @importFrom survival coxph strata Surv
-#' @importFrom stats pchisq setNames
+#' @importFrom stats pchisq setNames complete.cases qnorm qt sd
 NULL
 
 # Resolve missing global definitions:
 utils::globalVariables(c(
   ".",
   "x",
+  "average",
+  "difference",
   "control_coxph",
   "control_incidence_rate",
   "control_analyze_vars",