| Title: | Kidney-Related Functions for Clinical and Epidemiological Research |
| Version: | 1.4.0 |
| Maintainer: | Boris Bikbov <boris.bikbov@scientific-tools.org> |
| Description: | Contains kidney care oriented functions. Current version contains functions for calculation of: - Estimated glomerular filtration rate by CKD-EPI (2021 and 2009), MDRD, CKiD, FAS, EKFC, etc. - Kidney Donor Risk Index and Kidney Donor Profile Index for kidney transplant donors. - Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. <doi:10.32614/CRAN.package.kidney.epi>. |
| Depends: | R (≥ 3.4.0) |
| License: | LGPL-2 | LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2)] |
| URL: | https://Scientific-Tools.Org/, https://www.linkedin.com/in/boris-bikbov/, https://kidney.Scientific-Tools.Org/r/ |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.3.2 |
| Imports: | readxl, openxlsx, purrr |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2025-05-31 16:24:27 UTC; BB2 |
| Author: | Boris Bikbov 
[aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2025-05-31 17:00:03 UTC |
A synthetic dataset contains variables for eGFR calculation.
Description
A synthetic dataset contains variables for eGFR calculation for 1000 adults and 1000 children.
Usage
ckd.data
Format
A data frame with 2000 rows (1000 adults and 1000 children/young adults) and 12 variables:
- cr
Serum creatinine, micromol/L
- cys
Serum cystatin C, mg/L
- age
Age, years
- sex
Sex
- ethnicity
Ethnicity
- height
Height, cm
- category
Indication on whether the generated data refer to adults or children
Details
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Source
Synthetic dataset was generated based on two publications:
adults: Lamb EJ, Barratt J, Brettell EA et al. Accuracy of glomerular filtration rate estimation using creatinine and cystatin C for identifying and monitoring moderate chronic kidney disease: the eGFR-C study. Health Technol Assess 2024;28(35), doi:10.3310/HYHN1078.
children/young adults: Pierce CB, Muñoz A, Ng DK et al. 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.
Calculate KDIGO albuminuria categories
Description
Calculate KDIGO albuminuria categories
Usage
ckd.kdigo_category.albuminuria(
albuminuria,
albuminuria_units = "mg/g",
semiquantitative_values = "forbidden"
)
Arguments
albuminuria |
Numeric vector. Urine albumin, could be expressed in "mg/day" (24-hour urine collection), "mg/mmol" (UACR) or "mg/g" (UACR). Units of measurement should be defined in variable albuminuria_units (if not defined explicitly by user, the default value is "mg/g"). |
albuminuria_units |
Character string. Units in which urine albumin is measured. Could be one of the following: "mg/day", "mg/mmol" or "mg/g". |
semiquantitative_values |
Character string. Defines whether semiquantitative values are allowed in the data. If "any", all semiquantitative values ('<30', '30-300', '>300') and any numeric values (29, 30, 35, etc) will be classified into A categories (NB! both '30-300' and '30-299' will be classified as A2). If "only_limits", only limiting semiquantitative values ('<30', '>300') will be classified into A categories, but middle semiquantitative values ('30-300') will be omitted; but numeric values (29, 30, 35, etc) will be classified into A categories. If "forbidden", only numeric values will be classified into A categories. |
Details
Calculate albuminuria categories (A1, A2, A3) based on albuminuria values.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
string albuminuria category.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
ckd.kdigo_category.albuminuria(albuminuria = 25, albuminuria_units = "mg/g")
# for a dataset - see vignettes for details
# ckd.kdigo_category.albuminuria(albuminuria = dta$alb, albuminuria_units = "mg/g")
Calculate eGFR categories
Description
Calculate eGFR categories
Usage
ckd.kdigo_category.gfr(gfr)
Arguments
gfr |
Numeric vector. eGFR, expressed in "ml/min/1.73m2". |
Details
Calculate eGFR categories (G1, G2, G3a, G3b, G4, G5) based on eGFR values.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
string gfr category.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
ckd.kdigo_category.gfr(gfr = 25)
# for a dataset - see vignettes for details
# ckd.kdigo_category.gfr(gfr = dta$egfr)
Calculate proteinuria categories
Description
Calculate proteinuria categories
Usage
ckd.kdigo_category.proteinuria(
proteinuria,
proteinuria_units = "mg/g",
semiquantitative_values = "forbidden"
)
Arguments
proteinuria |
Numeric vector. Urine protein, could be expressed in "mg/day" (24-hour urine collection), "mg/mmol" (UPCR) or "mg/g" (UPCR). Units of measurement should be defined in variable proteinuria_units (if not defined explicitly by user, the default value is "mg/g"). |
proteinuria_units |
Character string. Units in which urine protein is measured. Could be one of the following: "mg/day", "mg/mmol" or "mg/g". |
semiquantitative_values |
Character string. Defines whether semiquantitative values are allowed in the data. If "any", all semiquantitative values ('<30', '30-300', '>300') and any numeric values (29, 30, 35, etc) will be classified into A categories (NB! both '30-300' and '30-299' will be classified as A2). If "only_limits", only limiting semiquantitative values ('<30', '>300') will be classified into A categories, but middle semiquantitative values ('30-300') will be omitted; but numeric values (29, 30, 35, etc) will be classified into A categories. If "forbidden", only numeric values will be classified into A categories. |
Details
Calculate albuminuria categories (A1, A2, A3) based on proteinuria values.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
string albuminuria category.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
ckd.kdigo_category.proteinuria(proteinuria = 25, proteinuria_units = "mg/g")
# for a dataset - see vignettes for details
# ckd.kdigo_category.proteinuria(proteinuria = dta$alb, proteinuria_units = "mg/g")
Calculate KDIGO risk categories
Description
Calculate KDIGO risk categories
Usage
ckd.kdigo_category.risk(gfr_cat, alb_cat)
Arguments
gfr_cat |
Character vector. eGFR categories coded as G1, G2, G3a, G3b, G4, G5. |
alb_cat |
Character vector. Albuminuria categories coded as A1, A2, A3. |
Details
Calculate KDIGO risk of complications categories (Low, Moderate, High, Very high) based on eGFR and albuminuria grades.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
string risk category.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
ckd.kdigo_category.risk(gfr_cat = "G2", alb_cat = "A3")
# for a dataset - see vignettes for details
# ckd.kdigo_category.risk(gfr_cat = dta$gfr_cat, alb_cat = dta$alb_cat)
Calculate eGFR by all creatinine-based equations for adults
Description
Calculate eGFR by all creatinine-based equations for adults
Usage
egfr.all_adults.cr(
creatinine,
age,
sex,
ethnicity = NA,
creatinine_units = "micromol/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
label_african = c("Afroamerican"),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
ethnicity |
Vector. Ethnicity. If no ethnicity will be defined, the calculation will use coefficients for Caucasian subjects. Specify ethnicity labels in the function parameter label_african. |
creatinine_units |
Character string. Units in which serum creatinine is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
label_african |
List. Label(s) for African ethnicity. Required only by race-specific equations. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate eGFR by all creatinine-based equations for adults available in the kidney.epi package.
References to the equations are available in single functions of the kidney.epi package.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.all_adults.cr (creatinine = 1.4, age = 60, sex = "Male",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.all_adults.cr (creatinine = dta$scr, age = dta$age, sex = dta$sex,
# creatinine_units = "mg/dl")
Calculate eGFR by all creatinine-cystatin-based equations for adults
Description
Calculate eGFR by all creatinine-cystatin-based equations for adults
Usage
egfr.all_adults.cr_cys(
creatinine,
cystatin,
age,
sex,
creatinine_units = "micromol/l",
cystatin_units = "mg/L",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
creatinine_units |
Character string. Units in which serum creatinine is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate eGFR by all creatinine-cystatin-based equations for adults available in the kidney.epi package.
References to the equations are available in single functions of the kidney.epi package.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Calculate eGFR by all cystatin-based equations for adults
Description
Calculate eGFR by all cystatin-based equations for adults
Usage
egfr.all_adults.cys(cystatin, age, cystatin_units = "mg/L", max_age = 100)
Arguments
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
age |
Numeric vector. Age, in years. |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate eGFR by all cystatin-based equations for adults available in the kidney.epi package.
References to the equations are available in single functions of the kidney.epi package.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.all_adults.cys (cystatin = 1.4, age = 60,
cystatin_units = "mg/L")
# for a dataset - see vignettes for details
# egfr.all_adults.cys (cystatin = dta$cys, age = dta$age,
# cystatin_units = "mg/L")
Calculate eGFR by the Berlin Initiative Study (BIS1) creatinine-based equation
Description
Calculate eGFR by the Berlin Initiative Study (BIS1) creatinine-based equation
Usage
egfr.bis.cr(
creatinine,
age,
sex,
creatinine_units = "micromol/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the Berlin Initiative Study (BIS1) creatinine-based equation.
Reference to the equation: Schaeffner ES, Ebert N, Delanaye P et al. Two novel equations to estimate kidney function in persons aged 70 years or older. Ann Intern Med 2012; 157: 471–481 doi: 10.7326/0003-4819-157-7-201210020-00003.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.bis.cr (creatinine = 1.4, age = 80, sex = "Male",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.bis.cr (creatinine = dta$scr, age = dta$age, sex = dta$sex,
# creatinine_units = "mg/dl")
Calculate eGFR by the Berlin Initiative Study (BIS2) creatinine-cystatin C-based equation
Description
Calculate eGFR by the Berlin Initiative Study (BIS2) creatinine-cystatin C-based equation
Usage
egfr.bis.cr_cys(
creatinine,
cystatin,
age,
sex,
creatinine_units = "micromol/l",
cystatin_units = "mg/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the Berlin Initiative Study (BIS2) creatinine-cystatin C-based equation.
Reference to the equation: Schaeffner ES, Ebert N, Delanaye P et al. Two novel equations to estimate kidney function in persons aged 70 years or older. Ann Intern Med 2012; 157: 471–481 doi: 10.7326/0003-4819-157-7-201210020-00003.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.bis.cr_cys (creatinine = 1.4, cystatin = 1.0, age = 80,
sex = "Male", creatinine_units = "mg/dl",
cystatin_units = "mg/L")
# for a dataset - see vignettes for details
# egfr.bis.cr_cys (creatinine = dta$scr, cystatin = dta$cys,
# age = dta$age, sex = dta$sex,
# creatinine_units = "mg/dl", cystatin_units = "mg/l")
Calculate creatinine clearance by the Cockcroft-Gault equation
Description
Calculate creatinine clearance by the Cockcroft-Gault equation
Usage
egfr.cg.cr(
creatinine,
age,
sex,
weight,
creatinine_units = "micromol/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
weight |
Numeric vector. Weight, kg. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate Cockcroft-Gault by the Cockcroft-Gault equation.
Reference to the equation: Cockcroft, DW, Gault MH. Prediction of creatinine clearance from serum creatinine. Nephron. 1976. 16(1):31-41.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric creatinine clearance expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.cg.cr (creatinine = 1.4, age = 60, sex = "Male",
weight = 80, creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
Alias to the latest eGFR CKD-EPI creatinine-based equation
Description
Alias to the latest eGFR CKD-EPI creatinine-based equation
Usage
egfr.ckdepi.cr(...)
Arguments
... |
all arguments for the egfr.ckdepi.cr.2021 function. |
Details
The function is just an alias to the latest eGFR CKD-EPI creatinine-based equation.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Calculate eGFR based on CKD-EPI 2009 creatinine-based equation
Description
Calculate eGFR based on CKD-EPI 2009 creatinine-based equation
Usage
egfr.ckdepi.cr.2009(
creatinine,
age,
sex,
ethnicity = NA,
creatinine_units = "micromol/l",
label_afroamerican = c("Afroamerican"),
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
ethnicity |
Vector. Ethnicity. If no ethnicity will be defined, the calculation will use coefficients for White subjects. Specify ethnicity if a study includes African-American subjects, and define the the values of variable in the parameter label_afroamerican. |
creatinine_units |
Character string. Units in which serum creatinine is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_afroamerican |
List. Label(s) for Afroamerican ethnicity. |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by CKD-EPI 2009 creatinine-based equation.
Reference to the equation: Levey AS, Stevens LA, Schmid CH et al. A New Equation to Estimate Glomerular Filtration Rate. Ann Intern Med 2009;150:604–12.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.ckdepi.cr.2009 (creatinine = 1.4, age = 60, sex = "Male", ethnicity = "White",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.ckdepi.cr.2009 (creatinine = dta$scr, age = dta$age, sex = dta$sex,
# ethnicity = dta$race, creatinine_units = "mg/dl")
Calculate eGFR by the CKD-EPI 2021 creatinine-based equation
Description
Calculate eGFR by the CKD-EPI 2021 creatinine-based equation
Usage
egfr.ckdepi.cr.2021(
creatinine,
age,
sex,
creatinine_units = "micromol/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the CKD-EPI 2021 creatinine-based equation.
Reference to the equation: Inker LA, Eneanya ND, Coresh J, et al. New creatinine- and cystatin C–based equations to estimate GFR without race. N Engl J Med. 2021;385:1737-1749.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.ckdepi.cr.2021(creatinine = 1.4, age = 60, sex = "Male",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.ckdepi.cr.2021(creatinine = dta$scr, age = dta$age, sex = dta$sex,
# creatinine_units = "mg/dl")
Calculate eGFR by the CKD-EPI 2021 creatinine-cystatin-based equation
Description
Calculate eGFR by the CKD-EPI 2021 creatinine-cystatin-based equation
Usage
egfr.ckdepi.cr_cys.2021(
creatinine,
cystatin,
age,
sex,
creatinine_units = "micromol/l",
cystatin_units = "mg/L",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the CKD-EPI 2021 creatinine-cystatin-based equation.
Reference to the equation: Inker LA, Eneanya ND, Coresh J, et al. New creatinine- and cystatin C–based equations to estimate GFR without race. N Engl J Med. 2021;385:1737-1749.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.ckdepi.cr_cys.2021 (creatinine = 1.4, cystatin = 0.8, age = 60,
sex = "Male", creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.ckdepi.cr_cys.2021 (creatinine = dta$scr, cystatin = dta$cys,
# age = dta$age, sex = dta$sex, creatinine_units = "mg/dl")
Calculate eGFR by CKiD U25 creatinine-based equation (for children and young adults less then 25 years old)
Description
Calculate eGFR by CKiD U25 creatinine-based equation (for children and young adults less then 25 years old)
Usage
egfr.ckid_u25.cr(
creatinine,
age,
sex,
height_cm = 0,
height_ft = 0,
height_inch = 0,
creatinine_units = "micromol/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0)
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
height_cm |
Numeric vector. Could be defined either as height_cm if is measured in cm, or as height_ft and height_inch if is measured in feet and inches. If the parameter height_cm is greater than 0, the function uses cm, otherwise - feet and inches. |
height_ft |
see height_cm |
height_inch |
see height_cm |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
Details
Calculate estimated glomerular filtration rate (eGFR) by creatinine-based CKiD U25 equation.
Reference to the equation: 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.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.ckid_u25.cr (creatinine = 1.4, age = 10, height_cm = 90, sex = "Male",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.ckid_u25.cr (creatinine = dta$scr, age = dta$age, height_cm = dta$ht,
# sex = dta$sex, creatinine_units = "mg/dl")
Calculate eGFR by CKiD U25 cystatin-based equation (for children and young adults less then 25 years old)
Description
Calculate eGFR by CKiD U25 cystatin-based equation (for children and young adults less then 25 years old)
Usage
egfr.ckid_u25.cys(
cystatin,
age,
sex,
cystatin_units = "mg/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0)
)
Arguments
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
age |
Numeric vector. Age, in years. Age does not accounted in Schwartz equation, but used in the function to check whether Schwartz equation could be applied to a given patient. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
Details
Calculate estimated glomerular filtration rate (eGFR) by cystatin-based CKiD U25 equation.
Reference to the equation: 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.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.ckid_u25.cys (cystatin = 0.8, age = 10, sex = "Male",
cystatin_units = "mg/l")
# for a dataset - see vignettes for details
# egfr.ckid_u25.cys (cystatin = dta$cystatin, age = dta$age,
# sex = dta$sex, cystatin_units = "mg/l")
Calculate eGFR by the EKFC creatinine-based equation
Description
Calculate eGFR by the EKFC creatinine-based equation
Usage
egfr.ekfc.cr(
creatinine,
age,
sex,
ethnicity = NA,
creatinine_units = "micromol/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
label_african = c("African"),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
ethnicity |
Vector. Ethnicity. If no ethnicity will be defined, the calculation will use coefficients for White European subjects. Specify ethnicity if a study includes African and Black European subjects, and define the values of variable in the parameter label_african. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
label_african |
List. Label(s) for African ethnicity. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the EKFC creatinine-based equation.
References to the equation:
Initial creatinine-based equation was reported in Pottel H, Björk J, Courbebaisse M, et al. Development and validation of a modified full age spectrum creatinine-based equation to estimate glomerular filtration rate. a cross-sectional analysis of pooled data. Ann Int Med. 2021;174:183–192 doi:10.7326/M20-4366.
Subsequent definition of Q coefficients for African and Black European subjects was reported in Pottel H, Björk J, Rule AD, et al. Cystatin C–based equation to estimate GFR without the inclusion of race and sex. N Engl J Med. 2023;388:333-343 doi: 10.1056/NEJMoa22037.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.ekfc.cr (creatinine = 1.4, age = 60, sex = "Male",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.ekfc.cr (creatinine = dta$scr, age = dta$age, sex = dta$sex,
# creatinine_units = "mg/dl")
Calculate eGFR by the EKFC cystatin-based equation
Description
Calculate eGFR by the EKFC cystatin-based equation
Usage
egfr.ekfc.cys(cystatin, age, cystatin_units = "mg/L", max_age = 100)
Arguments
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
age |
Numeric vector. Age, in years. |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the EKFC cystatin-based equation.
Reference to the equation: Pottel H, Björk J, Rule AD, et al. Cystatin C–based equation to estimate GFR without the inclusion of race and sex. N Engl J Med. 2023;388:333-343 doi: 10.1056/NEJMoa22037.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.ekfc.cys (cystatin = 0.8, age = 60)
# for a dataset - see vignettes for details
# egfr.ekfc.cys (cystatin = dta$cys, age = dta$age)
Calculate eGFR by the Full age spectrum (FAS) creatinine-based equation
Description
Calculate eGFR by the Full age spectrum (FAS) creatinine-based equation
Usage
egfr.fas.cr(
creatinine,
age,
sex,
creatinine_units = "micromol/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the Full age spectrum (FAS) creatinine-based equation.
Reference to the equation: Pottel H, Hoste L, Dubourg L et al. An estimating glomerular filtration rate equation for the full age spectrum. Nephrol Dial Transplant 2016; 31:798–806 doi:10.1093/ndt/gfv454.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.fas.cr (creatinine = 1.4, age = 60, sex = "Male",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.fas.cr (creatinine = dta$scr, age = dta$age, sex = dta$sex,
# creatinine_units = "mg/dl")
Calculate eGFR by the Full age spectrum (FAS) creatinine-cystatin-based equation
Description
Calculate eGFR by the Full age spectrum (FAS) creatinine-cystatin-based equation
Usage
egfr.fas.cr_cys(
creatinine,
cystatin,
age,
sex,
alpha = 0.5,
creatinine_units = "micromol/l",
cystatin_units = "mg/L",
equation_type = "precise",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
alpha |
Numeric vector. Alpha coefficient for the combined creatinine-cystatin equation. By default is equal to 0.5. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
equation_type |
Character string. Whether to use "precise" or "simplified" equation. |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the Full age spectrum (FAS) creatinine-cystatin-based equation.
Reference to the equation: Pottel H, Delanaye P, Schaeffner E et al. Estimating glomerular filtration rate for the full age spectrum from serum creatinine and cystatin C. Nephrol Dial Transplant 2017; 32:497–507 doi:10.1093/ndt/gfw425.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.fas.cr_cys (creatinine = 1.4, cystatin = 0.8, age = 60,
sex = "Male", creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.fas.cr_cys (creatinine = dta$scr, cystatin = dta$cys,
# age = dta$age, sex = dta$sex, creatinine_units = "mg/dl")
Calculate eGFR by the Full age spectrum (FAS) cystatin-based equation
Description
Calculate eGFR by the Full age spectrum (FAS) cystatin-based equation
Usage
egfr.fas.cys(
cystatin,
age,
cystatin_units = "mg/L",
equation_type = "precise",
max_age = 100
)
Arguments
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
age |
Numeric vector. Age, in years. |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
equation_type |
Character string. Whether to use "precise" or "simplified" equation. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the Full age spectrum (FAS) cystatin-based equation.
Reference to the equation: Pottel H, Delanaye P, Schaeffner E et al. Estimating glomerular filtration rate for the full age spectrum from serum creatinine and cystatin C. Nephrol Dial Transplant 2017; 32:497–507 doi:10.1093/ndt/gfw425.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.fas.cys (cystatin = 0.8, age = 60)
# for a dataset - see vignettes for details
# egfr.fas.cys (cystatin = dta$cys, age = dta$age)
Calculate eGFR by the revised Lund-Malmö creatinine-based equation
Description
Calculate eGFR by the revised Lund-Malmö creatinine-based equation
Usage
egfr.lm.cr(
creatinine,
age,
sex,
creatinine_units = "micromol/l",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by the revised Lund-Malmö creatinine-based equation.
Reference to the equation: Björk J, Grubb A, Sterner G, Nyman U. Revised equations for estimating glomerular filtration rate based on the Lund-Malmö Study cohort. Scand J Clin Lab Invest. 2011;71: 232-239.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.lm.cr (creatinine = 1.4, age = 60, sex = "Male",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.lm.cr (creatinine = dta$scr, age = dta$age, sex = dta$sex,
# creatinine_units = "mg/dl")
Calculate estimated glomerular filtration rate (eGFR) by MDRD equation
Description
Calculate estimated glomerular filtration rate (eGFR) by MDRD equation
Usage
egfr.mdrd4(
creatinine,
age,
sex,
ethnicity = NA,
creatinine_units = "micromol/l",
creatinine_method = "non-IDMS",
label_afroamerican = c("Afroamerican"),
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0),
max_age = 100
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
ethnicity |
Vector. Ethnicity, specify in case of African-American patients. The value of variable refers to the parameter label_afroamerican. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
creatinine_method |
Character string. Creatinine standartisation method in a laboratory. Could be either "IDMS" or "non-IDMS". If not explicitly defined by user, the default assumption is "non-IDMS". |
label_afroamerican |
List. Label(s) for Afroamerican ethnicity. |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
max_age |
Numeric. Maximal age suitable for the equation application, in years. By default is 100 years, but change this value in case you would like to apply equation to older persons. |
Details
Calculate estimated glomerular filtration rate (eGFR) by MDRD equation.
Reference to the equation: Levey AS, Coresh J, Greene T, et al. Using standardized serum creatinine values in the modification of diet in renal disease study equation for estimating glomerular filtration rate. Annals of Internal Medicine 2006;145:247–54.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.mdrd4 (creatinine = 1.4, age = 60, sex = "Male", ethnicity = "White",
creatinine_units = "mg/dl")
# for a dataset - see vignettes for details
# egfr.mdrd4 (creatinine = dta$scr, age = dta$age, sex = dta$sex,
# ethnicity = dta$race, creatinine_units = "mg/dl")
Deprecated function name. Use specific functions egfr.schwartz.cr(), egfr.schwartz.cys(), egfr.schwartz.cr_cys().
Description
Deprecated function name. Use specific functions egfr.schwartz.cr(), egfr.schwartz.cys(), egfr.schwartz.cr_cys().
Usage
egfr.schwartz(...)
Arguments
... |
used for legacy only. |
Details
Deprecated function name.
Calculate eGFR by Schwartz creatinine-based equation (for children only, both "classic" bedside and "quadratic")
Description
Calculate eGFR by Schwartz creatinine-based equation (for children only, both "classic" bedside and "quadratic")
Usage
egfr.schwartz.cr(
creatinine,
age,
sex,
height_cm = 0,
height_ft = 0,
height_inch = 0,
creatinine_units = "micromol/l",
equation_type = "classic",
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0)
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
age |
Numeric vector. Age, in years. Age does not accounted in Schwartz equation, but used in the function to check whether Schwartz equation could be applied to a given patient. |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. Required only in case of quadratic Schwartz equation. |
height_cm |
Numeric vector. Could be defined either as height_cm if is measured in cm, or as height_ft and height_inch if is measured in feet and inches. If the parameter height_cm is greater than 0, the function uses cm, otherwise - feet and inches. |
height_ft |
see height_cm |
height_inch |
see height_cm |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
equation_type |
Character string. Define whether to calculate eGFR either by classic Schwartz or quadratic Schwartz equation. Could be one of the following: "classic", "quadratic". If not explicitly defined by user, the default assumption is "classic". |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
Details
Calculate estimated glomerular filtration rate (eGFR) by Schwartz creatinine-based equation.
References to the equation: Gao A, Cachat F, Faouzi M et al. Comparison of the glomerular filtration rate in children by the new revised Schwartz formula and a new generalized formula. Kidney International 2013;83:524–30.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.schwartz.cr (creatinine = 1.4, age = 10, height_cm = 90, sex = "Male",
creatinine_units = "mg/dl")
egfr.schwartz.cr (creatinine = 1.4, age = 10, height_cm = 90, sex = "Male",
creatinine_units = "mg/dl", equation_type = "quadratic")
# for a dataset - see vignettes for details
# egfr.schwartz.cr (creatinine = dta$scr, age = dta$age, height_cm = dta$ht,
# sex = dta$sex, creatinine_units = "mg/dl")
Calculate eGFR by Schwartz multivariate equation with cystatin C, ht/Scr, and BUN(for children only)
Description
Calculate eGFR by Schwartz multivariate equation with cystatin C, ht/Scr, and BUN(for children only)
Usage
egfr.schwartz.cr_cys(
creatinine,
creatinine_units = "mg/dL",
cystatin,
cystatin_units = "mg/L",
bun,
bun_units = "mg/dL",
sex,
height_cm = 0,
height_ft = 0,
height_inch = 0,
label_sex_male = c("Male", 1),
label_sex_female = c("Female", 0)
)
Arguments
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
creatinine_units |
Character string. Units in which serum creatinine is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L". |
bun |
Numeric vector. Blood urea nitrogen, could be expressed in "mg/dL" or "mmol/L". Units of measurement should be defined in variable bun_units (if not defined explicitly by user, the default value is "mg/dL"). |
bun_units |
Character string. Units in which blood urea nitrogen is expressed. Could be one of the following: "mg/dL" or "mmol/L". |
sex |
Vector. The value of variable refers to the parameters label_sex_male and label_sex_female. |
height_cm |
Numeric vector. Could be defined either as height_cm if is measured in cm, or as height_ft and height_inch if is measured in feet and inches. If the parameter height_cm is greater than 0, the function uses cm, otherwise - feet and inches. |
height_ft |
see height_cm |
height_inch |
see height_cm |
label_sex_male |
List. Label(s) for definition(s) of male sex. |
label_sex_female |
List. Label(s) for definition(s) of female sex. |
Details
Calculate estimated glomerular filtration rate (eGFR) by Schwartz multivariate equation with cystatin C, ht/Scr, and BUN.
Reference to the equation: Schwartz GJ, Schneider MF, Maier PS et al. Improved equations estimating GFR in children with chronic kidney disease using an immunonephelometric determination of cystatin C. Kidney Int 2012; 82: 445–453.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Calculate eGFR by Schwartz cystatin C-based equation (for children only)
Description
Calculate eGFR by Schwartz cystatin C-based equation (for children only)
Usage
egfr.schwartz.cys(cystatin, cystatin_units = "mg/L")
Arguments
cystatin |
Numeric vector. Serum cystatin, could be expressed in "mg/L" or "nanomol/L". Units of measurement should be defined in variable cystatin_units (if not defined explicitly by user, the default value is "mg/L"). |
cystatin_units |
Character string. Units in which serum cystatin is expressed. Could be one of the following: "mg/L" or "nanomol/L" |
Details
Calculate estimated glomerular filtration rate (eGFR) by Schwartz cystatin C-based equation.
Reference to the equation: Schwartz GJ, Schneider MF, Maier PS et al. Improved equations estimating GFR in children with chronic kidney disease using an immunonephelometric determination of cystatin C. Kidney Int 2012; 82: 445–453.
Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, https://Scientific-Tools.Org. DOI: 10.32614/CRAN.package.kidney.epi
Value
numeric eGFR expressed in ml/min/1.73m2.
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
egfr.schwartz.cys(cystatin = 1.4)
# for a dataset - see vignettes for details
A sample dataset with kidney transplant patients.
Description
A dataset contains 10 records for kidney transplant patients, including information about deceased donors.
Usage
ktx.data
Format
A data frame with 10 rows and 12 variables:
- ptid
patient identifier
- rec.age
age of the recipient, in years
- don.age
age of the donor, in years
- don.height
height of the donor, in cm
- don.weight
weight of the donor, in kg
- don.ethnicity
ethnicity of the donor
- don.hypertension
history of hypertension for the donor
- don.diabetes
history of diabetes for the donor
- don.causeofdeath
cause of death for the donor
- don.creatinine
serum creatinine of the donor, in mg/dL
- don.hcv
hepatitis c virus status of the donor
- don.dcdstatus
donation after circulatory death status of the donor
- don.sex
sex of the donor
Source
Generation from different patients' records
Calculate KDRI and KDPI for deceased kidney donor
Description
Calculate KDRI and KDPI for deceased kidney donor
Usage
ktx.kdpi.optn(
age,
height_cm = 0,
height_ft = 0,
height_inch = 0,
weight_kg = 0,
weight_lb = 0,
ethnicity = NA,
hypertension,
diabetes,
causeofdeath,
creatinine,
hcv,
dcdstatus,
creatinine_units = "micromol/l",
return_output_type = "KDPI",
mapping_values_year = "latest",
label_afroamerican = c("Afroamerican"),
label_hypertension_positive = c("yes"),
label_hypertension_unknown = "NA",
label_diabetes_positive = c("yes"),
label_diabetes_unknown = "NA",
label_causeofdeath = c("cva"),
label_hcv_positive = c("positive"),
label_hcv_unknown = "NA",
label_dcdstatus = c("yes")
)
Arguments
age |
Numeric vector. Age, in years. |
height_cm |
Numeric vector. Could be defined either as height_cm if is measured in cm, or as height_ft and height_inch if is measured in feet and inches. If the parameter height_cm is greater than 0, the function uses cm, otherwise - feet and inches. |
height_ft |
see height_cm |
height_inch |
see height_cm |
weight_kg |
Numeric vector. Could be defined either as weight_kg if measured in kg, or as weight_lb if is measured in pounds. If the parameter weight_kg is greater than 0, the function uses kg, otherwise - pounds. |
weight_lb |
see weight_kg |
ethnicity |
Vector. Ethnicity, specify in case of African-American donors which have special coefficient in the regression equation. The value of variable refers to the parameter label_afroamerican. |
hypertension |
Vector. History of hypertension, specify in case of hypertensive donors which have special coefficient in the regression equation. The value of variable refers to the parameters label_hypertension_positive and label_hypertension_unknown. |
diabetes |
Vector. History of diabetes, specify in case of donors with diabetes which have special coefficient in the regression equation. The value of variable refers to the parameters label_diabetes_positive and label_diabetes_unknown. |
causeofdeath |
Vector. Cause of death, specify whether death was due to cerebrovascular disease, or other reasons. |
creatinine |
Numeric vector. Serum creatinine, could be expressed in "micromol/L", "mmol/L" or "mg/dL". Units of measurement should be defined in variable creatinine_units (if not defined explicitly by user, the default value is "micromol/L"). |
hcv |
Vector. Hepatitis C virus status. The value of variable refers to the parameters label_hcv_positive and label_hcv_unknown. |
dcdstatus |
Vector. Donation after circulatory death status. Specify whether organ was from a donor after circulatory death or not. The value of variable refers to the parameter label_dcdstatus. |
creatinine_units |
Character string. Units in which serum creatinne is expressed. Could be one of the following: "micromol/L", "mmol/L" or "mg/dL". |
return_output_type |
Character string. Specify which calculated parameter to return from the function: "KDRI_Rao" - Raw Kidney Donor Risk Index, "KDRI_median" - scaled to the median Kidney Donor Risk Index, or "KDPI" - Kidney Donor Profile Index. |
mapping_values_year |
Numeric value or character string. Specify which year to take for the OPTN mapping table, as well as KDRI scaling factor and chances of hypertension and diabetes in case if they were unknown for donor. By default the value is "latest", and the function takes the latest available OPTN mapping table and coefficients from the internal dataframes ktx.kdpi_mapping_table and ktx.kdpi_coefficients_table. But if necessary, a user could define the exact year (i.e. mapping_values_year = 2015). For a list of available years run the following: ktx.kdpi.optn.show.years(). |
label_afroamerican |
List. Label(s) for Afroamerican ethnicity. |
label_hypertension_positive |
List. Label(s) for a positive history of hypertension. |
label_hypertension_unknown |
List. Label(s) for donors with unknown history of hypertension. |
label_diabetes_positive |
List. Label(s) for a positive history of diabetes. |
label_diabetes_unknown |
List. Label(s) for donors with unknown history of diabetes. |
label_causeofdeath |
List. Label(s) for a cause of death due to cerebrovascular/stroke. |
label_hcv_positive |
List. Label(s) for a positive HCV status. |
label_hcv_unknown |
List. Label(s) for an unknown, not done, indeterminate, or pending HCV status. |
label_dcdstatus |
List. Label(s) for a donor after circulatory death status. |
Details
Calculate Kidney Donor Risk Index (KDRI) and Kidney Donor Profile Index (KDPI) based on the algorithm of US Organ Procurement and Transplantation Network. The Kidney Donor Profile Index (KDPI) is a numerical measure that combines ten donor factors to summarize into a single number the quality of deceased donor kidneys relative to other recovered kidneys. KDRI could be calculated only for a deceased donor!
More reading:
Citation: Bikbov B. R open source programming code for calculation of the Kidney Donor Profile Index and Kidney Donor Risk Index. Kidney Diseases, 2018; 4:269–272. DOI: 10.1159/000492427
Value
numeric One of the following values based on the return_output_type argument: Raw Kidney Donor Risk Index (KDRI), Scaled to the median Kidney Donor Risk Index (KDRI), or Kidney Donor Profile Index (KDPI).
Author(s)
Programming: Boris Bikbov https://www.linkedin.com/in/boris-bikbov.
Examples
# for a single patient
ktx.kdpi.optn (age = 60, height_cm = 168, weight_kg = 93, ethnicity = "White",
hypertension = "yes", diabetes = "no", causeofdeath = "roadinjury",
creatinine = 1.4, hcv = "negative", dcdstatus = "no",
creatinine_units = "mg/dl", return_output_type = "KDRI_Rao")
ktx.kdpi.optn (age = 30, height_cm = 176, weight_kg = 82, ethnicity = "White",
hypertension = "NA", diabetes = "no", causeofdeath = "roadinjury", # note that NA is in the quotes
creatinine = 150, hcv = "negative", dcdstatus = "no", return_output_type = "KDPI")
# for a dataset - see vignettes for details
Shows which years are available in the R package for the OPTN mapping table, KDRI scaling factor, etc.
Description
Shows which years are available in the R package for the OPTN mapping table, KDRI scaling factor, etc.
Usage
ktx.kdpi.optn.show.years()
Details
Service function which shows for user for which year(s) the OPTN mapping table, as well as KDRI scaling factor and chances of hypertension and diabetes in case if they were unknown for donor in the ktx.kdpi_mapping_table and ktx.kdpi_coefficients_table. This years could be used for the argument mapping_values_year of the ktx.kdpi.optn function.
This function has no arguments.
Value
numeric List of years which could be used for the argument mapping_values_year of the ktx.kdpi.optn function.
Creates a named matrix from two variables.
Description
Creates a named matrix from two variables.
Usage
matrix.cross_table(var1, var2, predefined_levels = NA)
Arguments
var1 |
Character vector. Values representing first variable. |
var2 |
Character vector. Values representing second variable. |
predefined_levels |
Character vector. Levels for var1 and var2. If omitted, the variables just coded according to the levels they have. If contains vector, the variables are coded according to predefined_levels values, the latter could be useful if var1 and var2 contain not all levels of interest |
Details
Creates a named matrix from two variables.
Value
matrix with cross-tabulation of var1 and var2.
Access matrix cells by row and column names
Description
Access matrix cells by row and column names
Usage
matrix.get_named_matrix_value(matrix_data, row_name, col_name)
Arguments
matrix_data |
matrix. Matrix with data. |
row_name |
character. Row name in the matrix. |
col_name |
character. Column name in the matrix. |
Details
Access matrix cells by row and column names.
Value
vector. Matrix value.
Read Excel file and convert it to matrix with row and column names.
Description
Read Excel file and convert it to matrix with row and column names.
Usage
matrix.read_excel_to_named_matrix(file_path, sheet_name = NULL)
Arguments
file_path |
character. Path to Excel file. |
sheet_name |
character. Name of Excel sheet. Optional, if there is only one sheet with data, the function will read it with no need to specifying the sheet name. |
Details
Read Excel file and convert it to matrix with row and column names.
Value
Excel file saved to a specified folder.
Save a named matrix as an Excel file.
Description
Save a named matrix as an Excel file.
Usage
matrix.save_named_matrix_to_excel(
matrix_data,
file_path,
sheet_name = "Sheet1",
save_type = "new"
)
Arguments
matrix_data |
matrix. Matrix for saving. |
file_path |
character. Path to the Excel file. |
sheet_name |
character. Name of the Excel sheet. |
save_type |
character. Defines whether the Excel file should be created or overwritten (save_type = "new"), or new sheet should be added to the existing Excel file (save_type = "add"). |
Details
Save a named matrix as an Excel file.
Value
Excel file saved to a specified folder.
Legacy function to calculate albuminuria categories
Description
Legacy function to calculate albuminuria categories
Usage
nephro.albuminuria_category(...)
Arguments
... |
all arguments for the ckd.kdigo_category.albuminuria() function. |
Details
Legacy function to calculate albuminuria categories (A1, A2, A3) based on albuminuria values. Alias to the ckd.kdigo_category.albuminuria() function. This function is for legacy use only.
Legacy function to calculate KDIGO GFR categories
Description
Legacy function to calculate KDIGO GFR categories
Legacy function to calculate KDIGO risk categories
Usage
nephro.gfr_category(...)
nephro.kdigo_risk_category(...)
Arguments
... |
all arguments for the ckd.kdigo_category.risk() function. |
Details
Legacy function to calculate KDIGO GFR categories. Alias to the ckd.kdigo_category.gfr() function. This function is for legacy use only.
Legacy function to calculate KDIGO risk categories. Alias to the ckd.kdigo_category.risk() function. This function is for legacy use only.
Legacy function to calculate proteinuria categories
Description
Legacy function to calculate proteinuria categories
Usage
nephro.proteinuria_category(...)
Arguments
... |
all arguments for the ckd.kdigo_category.proteinuria() function. |
Details
Legacy function to calculate albuminuria categories (A1, A2, A3) based on proteinuria values. Alias to the ckd.kdigo_category.proteinuria() function. This function is for legacy use only.
Convert creatinine values between measurement units.
Description
Convert creatinine values between measurement units.
Usage
service.convert_creatinine(
creatinine,
creatinine_units,
creatinine_reference_units = "mg/dl"
)
Arguments
creatinine |
Numeric. The creatinine value from a data set. |
creatinine_units |
Character. Creatinine mesurement units in a data set. |
creatinine_reference_units |
Character. Creatinine measurement units as a desired output (mg/dl by default). |
Details
Service function which check measurement units and convert creatinine values to selected by user.
Value
numeric Creatinine values converted into reference measurement units.
Convert cystatin C values between measurement units.
Description
Convert cystatin C values between measurement units.
Convert blood urea nitrogen values between measurement units.
Usage
service.convert_cystatin(cystatin, cystatin_units)
service.convert_bun(bun, bun_units)
Arguments
cystatin |
Numeric. The cystatin C values from a data set. |
cystatin_units |
Character. Cystatin C measurement units in a data set. |
bun |
Numeric. The blood urea nitrogen values from a data set. |
bun_units |
Character. Blood urea nitrogen measurement units in a data set. |
Details
Service function which check measurement units and convert cystatin C values to mg/l.
Service function which check measurement units and convert blood urea nitrogen values.
Value
numeric Cystatin C values converted in mg/l.
numeric Blood urea nitrogen values converted in mg/dl.