From 9e80eafa9d103358e2392ccab75ef23469b2f332 Mon Sep 17 00:00:00 2001
From: Xavier <33167618+xgaeta@users.noreply.github.com>
Date: Wed, 11 Sep 2024 15:32:09 -0700
Subject: [PATCH 1/8] Update nephro.R with CKiD u25 equations
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

I have added functions to calculate eGFR for children ages 1-25 using the CKiD U25 algorithms. These include calculations based on creatinine, based on cystatin C, and a composite based on both.

References:
Pierce CB, Muñoz A, Ng DK, Warady BA, Furth SL, Schwartz GJ. Age- and sex-dependent clinical equations to estimate glomerular filtration rates in children and young adults with chronic kidney disease. Kidney International. 2021;99(4):948–956. doi:10.1016/j.kint.2020.10.047

https://www.niddk.nih.gov/research-funding/research-programs/kidney-clinical-research-epidemiology/laboratory/glomerular-filtration-rate-equations/children-adolescents-young-adults#ckid-u25
---
 R/nephro.R | 128 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 128 insertions(+)

diff --git a/R/nephro.R b/R/nephro.R
index 94d437a..3eac8a1 100644
--- a/R/nephro.R
+++ b/R/nephro.R
@@ -769,3 +769,131 @@ Schwartz.Bedside <- function(creatinine, ht, age)
     } else
       stop ("Some variables are not defined") 
   }
+
+CKiD.U25.cystatin <- function(cystatin, age, sex)
+# CKiD U25 calculation for Cystatin C only
+# Requires Cystatin C level, age, sex
+{
+  if (!is.null(age) & !is.null(cystatin) & !is.null(sex))
+  {
+    cystatin <- as.numeric(cystatin)
+    age <- as.numeric(age)
+    sex <- as.numeric(sex) # 0 = male, 1 = female
+    n <- length(cystatin)
+
+    if (length(age) == n)
+    {
+      if ( (min(age)<1) | (max(age)>25)) cat("\nWarning: there are age values <1 or >25 years; for those children, eGFR values might be invalid\n")
+
+      # Identify missing data and store the index
+      idx <- c(1:n)[is.na(cystatin)]
+
+      # Replace missing data with fake data to avoid problems with formulas
+      cystatin[is.na(cystatin)] <- 10
+
+      coeff <- if(age < 12){
+        if(sex == 1) 79.9*1.004 ^ (age-12)
+        else 87.2*1.011 ^ (age-15)
+      } else if(age < 15) {
+        if(sex == 1) 79.9*0.974 ^ (age-12)
+        else 87.2*1.011 ^ (age-15)
+      } else if (age < 18) {
+        if(sex == 1) 79.9*0.974 ^ (age-12)
+        else 87.2*0.960 ^ (age-15)
+      } else {
+        if(sex == 1) 77.1
+        else 68.3
+      }
+
+      eGFR <- coeff / cystatin
+
+      # Restore missing data at the indexed positions
+      eGFR[idx] <- NA
+
+      # Output
+      round(eGFR, 1)
+
+    } else
+      stop ("Different number of observations between variables")
+  } else
+    stop ("Some variables are not defined")
+}
+
+CKiD.U25.creatinine <- function(creatinine, age, ht, sex)
+  # CKiD U25 calculation for creatinine only
+  # Requires creatinine, age, ht (in cm), sex
+{
+  if (!is.null(creatinine) & !is.null(ht) & !is.null(age) & !is.null(sex))
+  {
+    creatinine <- as.numeric(creatinine)
+    ht <- as.numeric(ht)
+    age <- as.numeric(age)
+    sex <- as.numeric(sex) # 0 = male, 1 = female
+    n <- length(creatinine)
+
+    if (length(ht) == n)
+    {
+      if ( (min(age)<1) | (max(age)>25)) cat("\nWarning: there are age values <1 or >25 years; for those children, eGFR values might be invalid\n")
+
+      # Identify missing data and store the index
+      idx <- c(1:n)[is.na(creatinine) |  is.na(ht)]
+
+      # Replace missing data with fake data to avoid problems with formulas
+      creatinine[is.na(creatinine)] <- 10
+      ht[is.na(ht)] <- 10
+
+      coeff <- if(age < 12){
+        if(sex == 1) 36.1*1.008 ^ (age - 12)
+        else 39*1.008 ^ (age - 12)
+      } else if (age < 18) {
+        if(sex == 1) 36.1*1.023 ^ (age - 12)
+        else 39*1.045 ^ (age - 12)
+      } else {
+        if(sex == 1) 41.4
+        else 50.8
+      }
+
+      eGFR <- coeff * (ht / 100) / creatinine
+
+      # Restore missing data at the indexed positions
+      eGFR[idx] <- NA
+
+      # Output
+      round(eGFR, 1)
+
+    } else
+      stop ("Different number of observations between variables")
+  } else
+    stop ("Some variables are not defined")
+}
+
+CKiD.U25.combined <- function(creatinine, cystatin, age, ht, sex, verbose = FALSE)
+  # CKiD U25 calculation for both creatinine and Cystatin C
+  # Requires serum Cr, Cystatin C level, age, ht (in cm), sex
+{
+  if (!is.null(creatinine) & !is.null(ht) & !is.null(age) &
+      !is.null(cystatin) & !is.null(sex))
+  {
+    creatinine <- as.numeric(creatinine)
+    cystatin <- as.numeric(cystatin)
+    ht <- as.numeric(ht)
+    age <- as.numeric(age)
+    sex <- as.numeric(sex) # 0 = male, 1 = female
+
+    # Return the average of the two other calculations
+    eGFRU25.cr <- CKiD.U25.creatinine(creatinine = creatinine, age = age,
+                                      ht = ht, sex = sex)
+    eGFRU25.cys <-  CKiD.U25.cystatin(cystatin = cystatin, age = age, sex = sex)
+    sGFRU25.avg <- (eGFRU25.cys + eGFRU25.cr) / 2
+
+    ## Determine if we should return all the component parts or just the result
+    ## of the combined calculation
+    if(verbose) {
+      return(round(cbind(eGFRU25.cr, eGFRU25.cys, sGFRU25.avg),1))
+    } else {
+      return(round(sGFRU25.avg, 1))
+    }
+
+  } else
+    stop ("Some variables are not defined")
+}

From 3f7ef78394ae80896d7e4b3681679df448434bfb Mon Sep 17 00:00:00 2001
From: Xavier <33167618+xgaeta@users.noreply.github.com>
Date: Mon, 11 Nov 2024 12:07:16 -0800
Subject: [PATCH 2/8] Create README.md

---
 README.md | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 README.md

diff --git a/README.md b/README.md
new file mode 100644
index 0000000..fc641d2
--- /dev/null
+++ b/README.md
@@ -0,0 +1,57 @@
+# Nephro with CKiD U25 equations
+Xavier Gaeta MD, PhD
+
+## Nephro - CKiD U25
+
+This is fork of the R **nephro** package that’s hosted on CRAN.org which
+includes functions to calculate pediatric eGFR based on the following
+publication:
+
+Pierce CB, Muñoz A, Ng DK, Warady BA, Furth SL, Schwartz GJ. **Age- and
+sex-dependent clinical equations to estimate glomerular filtration rates
+in children and young adults with chronic kidney disease.** *Kidney
+International*. 2021;99(4):948–956.
+[doi:10.1016/j.kint.2020.10.047](https://doi.org/10.1016/j.kint.2020.10.047 "Persistent DOI link for Pierce et al. paper")
+
+## Installation
+
+You can install the package from Github
+
+``` r
+devtools::install_github("xgaeta/nephro-CKiD")
+```
+
+then include the package in your script:
+
+``` r
+library(nephro)
+```
+
+## Using the functions
+
+These new equations follow the same style as the rest of the package,
+including sex as a binary variable with 0 for female and 1 for male.
+Height is provided in cm. They currently use US based equations. Outputs
+are in mL/min/1.73m<sup>2</sup>.
+
+``` r
+CKiD.U25.cystatin(cystatin = 1.2, age = 9.5, sex = 0)
+```
+
+    [1] 68.4
+
+``` r
+CKiD.U25.creatinine(creatinine = 0.8, age = 9.5, sex = 0, ht = 132)
+```
+
+    [1] 63.1
+
+``` r
+CKiD.U25.combined(creatinine = 0.8, cystatin = 1.2, age = 9.5, sex = 0, ht = 132, verbose = TRUE)
+```
+
+         eGFRU25.cr eGFRU25.cys sGFRU25.avg
+    [1,]       63.1        68.4        65.8
+
+Pull requests have been filed to merge these equations into the main
+**nephro** package

From 994c6fbe14da17f79946ff818cc39a0567a1a7d0 Mon Sep 17 00:00:00 2001
From: Xavier <33167618+xgaeta@users.noreply.github.com>
Date: Mon, 11 Nov 2024 12:08:00 -0800
Subject: [PATCH 3/8] Update nephro.R

small improvement to labeling
---
 R/nephro.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/nephro.R b/R/nephro.R
index 3eac8a1..da587d7 100644
--- a/R/nephro.R
+++ b/R/nephro.R
@@ -884,14 +884,14 @@ CKiD.U25.combined <- function(creatinine, cystatin, age, ht, sex, verbose = FALS
     eGFRU25.cr <- CKiD.U25.creatinine(creatinine = creatinine, age = age,
                                       ht = ht, sex = sex)
     eGFRU25.cys <-  CKiD.U25.cystatin(cystatin = cystatin, age = age, sex = sex)
-    sGFRU25.avg <- (eGFRU25.cys + eGFRU25.cr) / 2
+    eGFRU25.avg <- (eGFRU25.cys + eGFRU25.cr) / 2
 
     ## Determine if we should return all the component parts or just the result
     ## of the combined calculation
     if(verbose) {
-      return(round(cbind(eGFRU25.cr, eGFRU25.cys, sGFRU25.avg),1))
+      return(round(cbind(eGFRU25.cr, eGFRU25.cys, eGFRU25.avg),1))
     } else {
-      return(round(sGFRU25.avg, 1))
+      return(round(eGFRU25.avg, 1))
     }
 
   } else

From dad064f84d6a8dd2eabbb926ea805074aafadd61 Mon Sep 17 00:00:00 2001
From: Xavier <33167618+xgaeta@users.noreply.github.com>
Date: Mon, 11 Nov 2024 12:11:44 -0800
Subject: [PATCH 4/8] Added Readme.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index fc641d2..222643b 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,7 @@ CKiD.U25.creatinine(creatinine = 0.8, age = 9.5, sex = 0, ht = 132)
 CKiD.U25.combined(creatinine = 0.8, cystatin = 1.2, age = 9.5, sex = 0, ht = 132, verbose = TRUE)
 ```
 
-         eGFRU25.cr eGFRU25.cys sGFRU25.avg
+         eGFRU25.cr eGFRU25.cys eGFRU25.avg
     [1,]       63.1        68.4        65.8
 
 Pull requests have been filed to merge these equations into the main

From b0f219e913aa8a56e0f6a14206192f9ec63930e2 Mon Sep 17 00:00:00 2001
From: Xavier <33167618+xgaeta@users.noreply.github.com>
Date: Mon, 11 Nov 2024 12:18:17 -0800
Subject: [PATCH 5/8] Update README.md

---
 README.md | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 222643b..727d36b 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,12 @@
 # Nephro with CKiD U25 equations
-Xavier Gaeta MD, PhD
+**Xavier Gaeta MD, PhD**
 
 ## Nephro - CKiD U25
 
-This is fork of the R **nephro** package that’s hosted on CRAN.org which
-includes functions to calculate pediatric eGFR based on the following
-publication:
+This is a fork of the R
+[**nephro**](https://cran.r-project.org/web/packages/nephro/index.html "CRAN repository for original nephro package, currently v1.4")
+package that’s hosted on CRAN.org which includes functions to calculate
+pediatric eGFR based on the following publication:
 
 Pierce CB, Muñoz A, Ng DK, Warady BA, Furth SL, Schwartz GJ. **Age- and
 sex-dependent clinical equations to estimate glomerular filtration rates
@@ -53,5 +54,8 @@ CKiD.U25.combined(creatinine = 0.8, cystatin = 1.2, age = 9.5, sex = 0, ht = 132
          eGFRU25.cr eGFRU25.cys eGFRU25.avg
     [1,]       63.1        68.4        65.8
 
-Pull requests have been filed to merge these equations into the main
-**nephro** package
+[Pull requests have been
+filed](https://github.com/cran/nephro/pulls "Current status of CKiD U25 pull request")
+to merge these equations into the main
+[**nephro**](https://cran.r-project.org/web/packages/nephro/index.html "CRAN repository for original nephro package, currently v1.4")
+package

From a69f5fc6efdf6ecc25148980e4a406345c58ccef Mon Sep 17 00:00:00 2001
From: Xavier <33167618+xgaeta@users.noreply.github.com>
Date: Mon, 11 Nov 2024 12:20:50 -0800
Subject: [PATCH 6/8] Create LICENSE

---
 LICENSE | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 LICENSE

diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..41fe07d
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Xavier Gaeta MD PhD
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

From 562a557b4d042dbe6cdfc2ab8c4b3d59f2ddb721 Mon Sep 17 00:00:00 2001
From: Xavier <33167618+xgaeta@users.noreply.github.com>
Date: Mon, 11 Nov 2024 13:40:35 -0800
Subject: [PATCH 7/8] Update README.md

Mixed up sex coding variable, now fixed. No change to the actual functions.
---
 README.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 727d36b..d84c27d 100644
--- a/README.md
+++ b/README.md
@@ -31,28 +31,28 @@ library(nephro)
 ## Using the functions
 
 These new equations follow the same style as the rest of the package,
-including sex as a binary variable with 0 for female and 1 for male.
+including sex as a binary variable with 0 for male and 1 for female.
 Height is provided in cm. They currently use US based equations. Outputs
 are in mL/min/1.73m<sup>2</sup>.
 
 ``` r
-CKiD.U25.cystatin(cystatin = 1.2, age = 9.5, sex = 0)
+CKiD.U25.cystatin(cystatin = 1.2, age = 9.5, sex = 1)
 ```
 
-    [1] 68.4
+    [1] 65.9
 
 ``` r
-CKiD.U25.creatinine(creatinine = 0.8, age = 9.5, sex = 0, ht = 132)
+CKiD.U25.creatinine(creatinine = 0.8, age = 9.5, sex = 1, ht = 132)
 ```
 
-    [1] 63.1
+    [1] 58.4
 
 ``` r
-CKiD.U25.combined(creatinine = 0.8, cystatin = 1.2, age = 9.5, sex = 0, ht = 132, verbose = TRUE)
+CKiD.U25.combined(creatinine = 0.8, cystatin = 1.2, age = 9.5, sex = 1, ht = 132, verbose = TRUE)
 ```
 
          eGFRU25.cr eGFRU25.cys eGFRU25.avg
-    [1,]       63.1        68.4        65.8
+    [1,]       58.4        65.9        62.2
 
 [Pull requests have been
 filed](https://github.com/cran/nephro/pulls "Current status of CKiD U25 pull request")

From 55e8af1dd1887d39bc8162aa5c59d86ad6c48524 Mon Sep 17 00:00:00 2001
From: Xavier <33167618+xgaeta@users.noreply.github.com>
Date: Mon, 11 Nov 2024 14:26:50 -0800
Subject: [PATCH 8/8] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d84c27d..ffe53fd 100644
--- a/README.md
+++ b/README.md
@@ -55,7 +55,7 @@ CKiD.U25.combined(creatinine = 0.8, cystatin = 1.2, age = 9.5, sex = 1, ht = 132
     [1,]       58.4        65.9        62.2
 
 [Pull requests have been
-filed](https://github.com/cran/nephro/pulls "Current status of CKiD U25 pull request")
+filed](https://github.com/cran/nephro/pull/1 "Current status of CKiD U25 pull request")
 to merge these equations into the main
 [**nephro**](https://cran.r-project.org/web/packages/nephro/index.html "CRAN repository for original nephro package, currently v1.4")
 package