Package 'epocakir'

Title: Clinical Coding of Patients with Kidney Disease
Description: Clinical coding and diagnosis of patients with kidney using clinical practice guidelines. The guidelines used are the evidence-based KDIGO guidelines, see <https://kdigo.org/guidelines/> for more information. This package covers acute kidney injury (AKI), anemia, and chronic kidney disease (CKD).
Authors: Alwin Wang [aut, cre] , Lisa Toh [aut] , Davis Vaughan [ctb]
Maintainer: Alwin Wang <[email protected]>
License: MIT + file LICENSE
Version: 0.9.9
Built: 2025-02-15 05:25:31 UTC
Source: https://github.com/alwinw/epocakir

Help Index

AKI Staging based on Baseline Serum Creatinine

Description

Using KDIGO Clinical Practice Guideline for Acute Kidney Injury Volume 2 | Issue 1 | March 2012

Usage

aki_bCr(...)

## S3 method for class 'data.frame'
aki_bCr(.data, SCr, bCr, ...)

## S3 method for class 'units'
aki_bCr(SCr, bCr, ...)

## S3 method for class 'numeric'
aki_bCr(SCr, bCr, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCr

Serum creatinine column name, or vector of units or numeric if .data is not provided
bCr

Baseline creatinine column name, or vector of units or numeric if .data is not provided

Details

  • AKI Stage 1: 1.5-1.9 times baseline

  • AKI Stage 2: 2.0-2.9 times baseline

  • AKI Stage 3: 3.0 times baseline

See https://kdigo.org/guidelines/acute-kidney-injury/ for more details.

Value

(ordered factor) AKI stages

Examples

aki_bCr(aki_pt_data, SCr = "SCr_", bCr = "bCr_")

aki_pt_data %>%
  dplyr::mutate(aki = aki_bCr(SCr = SCr_, bCr = bCr_))

AKI Patient Data

Description

A sample dataset to demonstrate calculating AKI with epocakir

Usage

aki_pt_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 27 rows and 7 columns.

Examples

aki_pt_data

AKI Staging based on Changes in Serum Creatinine

Description

Using KDIGO Clinical Practice Guideline for Acute Kidney Injury Volume 2 | Issue 1 | March 2012

Usage

aki_SCr(...)

## S3 method for class 'data.frame'
aki_SCr(.data, SCr, dttm, pt_id, ...)

## S3 method for class 'units'
aki_SCr(SCr, dttm, pt_id, ...)

## S3 method for class 'numeric'
aki_SCr(SCr, dttm, pt_id, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCr

Serum creatinine column name, or vector of units or numeric if .data is not provided
dttm

DateTime column name, or vector of POSIXct if .data is not provided
pt_id

Patient ID column name, or vector of characters or factors if .data is not provided

Details

  • AKI Stage 1: ≥\ge0.3 mg/dl (≥\ge26.5 mmol/l) increase

  • AKI Stage 2: N/A

  • AKI Stage 3: ≥\ge4.0 mg/dl (≥\ge353.6 mmol/l)

See https://kdigo.org/guidelines/acute-kidney-injury/ for more details.

Value

(ordered factor) AKI stages

Examples

aki_SCr(aki_pt_data, SCr = "SCr_", dttm = "dttm_", pt_id = "pt_id_")

aki_pt_data %>%
  dplyr::mutate(aki = aki_SCr(SCr = SCr_, dttm = dttm_, pt_id = pt_id_))

AKI Stages

Description

Ordered factor of AKI stages

Usage

aki_stages

Format

An object of class ordered (inherits from factor) of length 4.

Details

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Examples

aki_stages

Codify AKI from Serum Creatinine and/or Urine Output

Description

Using KDIGO Clinical Practice Guideline for Acute Kidney Injury Volume 2 | Issue 1 | March 2012

Usage

aki_staging(...)

## S3 method for class 'data.frame'
aki_staging(
  .data,
  SCr = NULL,
  bCr = NULL,
  UO = NULL,
  dttm = NULL,
  pt_id = NULL,
  ...
)

## S3 method for class 'units'
aki_staging(SCr = NULL, bCr = NULL, UO = NULL, dttm = NULL, pt_id = NULL, ...)

## S3 method for class 'numeric'
aki_staging(SCr = NULL, bCr = NULL, UO = NULL, dttm = NULL, pt_id = NULL, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCr

Serum creatinine column name, or vector of units or numeric if .data is not provided
bCr

Baseline creatinine column name, or vector of units or numeric if .data is not provided
UO

Urine output column name, or vector of units or numeric if .data is not provided
dttm

DateTime column name, or vector of POSIXct if .data is not provided
pt_id

Patient ID column name, or vector of characters or factors if .data is not provided

Details

Provided a baseline creatinine, series of Serum Creatinine readings and/or Urine Output, aki_staging() calculates whether or not a patient has AKI. The staging (1, 2, 3) of AKI is returned.

When multiple columns are provided, aki_staging() will automatically calculate whether or not AKI has occurred using each KDIGO definition.

  • aki_bCr(): Staging of AKI based on baseline serum creatinine

  • aki_SCr(): Staging of AKI based on changes in serum creatinine

  • aki_UO(): Staging of AKI based on urine output

The most severe AKI stage is then returned.

See https://kdigo.org/guidelines/acute-kidney-injury/ for more details.

Value

(ordered factor) AKI stages

Examples

aki_staging(aki_pt_data, SCr = "SCr_", bCr = "bCr_", UO = "UO_", dttm = "dttm_", pt_id = "pt_id_")

aki_pt_data %>%
  dplyr::mutate(aki = aki_staging(SCr = SCr_, bCr = bCr_, UO = UO_, dttm = dttm_, pt_id = pt_id_))

AKI Staging based on Urine Output

Description

Using KDIGO Clinical Practice Guideline for Acute Kidney Injury Volume 2 | Issue 1 | March 2012

Usage

aki_UO(...)

## S3 method for class 'data.frame'
aki_UO(.data, UO, dttm, pt_id, ...)

## S3 method for class 'units'
aki_UO(UO, dttm, pt_id, ...)

## S3 method for class 'numeric'
aki_UO(UO, dttm, pt_id, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
UO

Urine output column name, or vector of units or numeric if .data is not provided
dttm

DateTime column name, or vector of POSIXct if .data is not provided
pt_id

Patient ID column name, or vector of characters or factors if .data is not provided

Details

  • AKI Stage 1: <0.5 ml/kg/h for 6–12 hours

  • AKI Stage 2: <0.5 ml/kg/h for ≥\ge12 hours

  • AKI Stage 3: <0.3 ml/kg/h for ≥\ge24 hours OR Anuria for ≥\ge12 hours

See https://kdigo.org/guidelines/acute-kidney-injury/ for more details.

Value

(ordered factor) AKI stages

Examples

aki_UO(aki_pt_data, UO = "UO_", dttm = "dttm_", pt_id = "pt_id_")

aki_pt_data %>%
  dplyr::mutate(aki = aki_UO(UO = UO_, dttm = dttm_, pt_id = pt_id_))

Albuminuria Stages

Description

Ordered factor of Albuminuria stages

Usage

Albuminuria_stages

Format

An object of class ordered (inherits from factor) of length 4.

Details

  • A1: Normal to mildly increased

  • A2: Moderately increased

  • A3: Severely increased

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Examples

Albuminuria_stages

Albuminuria Staging based on ACR

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

Albuminuria_staging_ACR(...)

## S3 method for class 'data.frame'
Albuminuria_staging_ACR(.data, ACR, ...)

## S3 method for class 'units'
Albuminuria_staging_ACR(ACR, ...)

## S3 method for class 'numeric'
Albuminuria_staging_ACR(ACR, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
ACR

Albumin-to-creatinine ratio column name, or vector of units or numeric if .data is not provided

Details

  • A1: Normal to mildly increased

  • A2: Moderately increased

  • A3: Severely increased

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

Albuminuria category

Examples

df <- tibble::tibble(
  ACR = units::set_units(c(-1, NA, 1, 10, 50), "mg/g")
)

Albuminuria_staging_ACR(df, "ACR")

df %>%
  dplyr::mutate(GFR_level = Albuminuria_staging_ACR(ACR))

Albuminuria Staging based on AER

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

Albuminuria_staging_AER(...)

## S3 method for class 'data.frame'
Albuminuria_staging_AER(.data, AER, ...)

## S3 method for class 'units'
Albuminuria_staging_AER(AER, ...)

## S3 method for class 'numeric'
Albuminuria_staging_AER(AER, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
AER

Albumin excretion rate column name, or vector of units or numeric if .data is not provided

Details

  • A1: Normal to mildly increased

  • A2: Moderately increased

  • A3: Severely increased

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

Albuminuria category

Examples

df <- tibble::tibble(
  AER = units::set_units(c(-1, NA, 15, 100, 500), "mg/day")
)

Albuminuria_staging_AER(df, "AER")

df %>%
  dplyr::mutate(GFR_level = Albuminuria_staging_AER(AER))

Diagnosis of anemia from Hb concentration

Description

KDIGO Clinical Practice Guideline for Anemia in Chronic Kidney Disease Volume 2 | Issue 4 | August (2) 2012

Usage

anemia(...)

## S3 method for class 'data.frame'
anemia(.data, Hb, age, male, ...)

## S3 method for class 'units'
anemia(Hb, age, male, ...)

## S3 method for class 'numeric'
anemia(Hb, age, male, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
Hb

Hemoglobin concentration column name, or vector of units or numeric if .data is not provided
age

Age of patient column name, or vector of units or numeric if .data is not provided
male

Male or not column name, or vector of logical (TRUE/FALSE) if .data is not provided

Details

  • Adults and children >15 years with CKD when the Hb concentration is <13.0 g/dl (<130 g/l) in males and <12.0 g/dl (<120 g/l) in females.

  • Children with CKD if Hb concentration is <11.0 g/dl (<110 g/l) in children 0.5-5 years, <11.5 g/dl (115 g/l) in children 5-12 years, and <12.0 g/dl (120 g/l) in children 12-15 years.

See https://kdigo.org/guidelines/anemia-in-ckd/ for more details.

Value

Anemia as logical TRUE or FALSE

Examples

anemia(anemia_pt_data, Hb = "Hb", age = "age", male = "male")

anemia_pt_data %>%
  dplyr::mutate(anemia = anemia(Hb = Hb, age = age, male = male))

Anemia Patient Data

Description

A sample dataset to demonstrate calculating anemia with epocakir

Usage

anemia_pt_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 10 rows and 3 columns.

Examples

anemia_pt_data

Convert a measured value to metric units

Description

Refer to conversion_factors for a full list of available conversions

Usage

as_metric(param = NULL, meas = NULL, ..., value_only = FALSE)

Arguments

param

(character) Name of measurement, e.g. param = "SCr"
meas

(units) Measurement or vector of measurements
...

(units) One of conversion_factors$parameter, e.g. SCr = units::set_units(88.4, "umol/l"). Case insensitive.
value_only

(logical) Return as value only without units

Value

(units) Converted measured value or vector of measured values, unless value_only = TRUE

Examples

as_metric(param = "scr", meas = units::set_units(88.4, "umol/l"))
as_metric("scr", units::set_units(88.4, "umol/l"))

values <- units::set_units(c(60, 70, 80), "umol/l")
as_metric(SCr = values)

Convert binary data to factors based on column name

Description

Convert binary data to factors based on column name

Usage

binary2factor(.data, ...)

Arguments

.data

(data.frame) A data frame or data frame extension (e.g. a tibble)
...

Name-value pairs. The names of columns to be transformed

Value

(data.frame) An object of the same type as .data

Examples

df <- data.frame(
  a = c(1, 0, NA, 1, 0),
  b = c("y", "n", NA, "Y", "n"),
  c = c("yes", "no", NA, "Yes", "No"),
  d = c(TRUE, FALSE, NA, TRUE, FALSE),
  e = c(1, 2, 3, 4, 5)
)
binary2factor(df, a, b:d)
df %>%
  binary2factor(-e)

Clinical Patient Data

Description

A sample dataset to demonstrate utility functions in epocakir

Usage

clinical_obvs

Format

An object of class tbl_df (inherits from tbl, data.frame) with 3 rows and 9 columns.

Examples

clinical_obvs

Combine date and time columns into a single DateTime column

Description

Combine date and time columns into a single DateTime column

Usage

combine_date_time_cols(.data, tz = NULL)

Arguments

.data

(data.frame) A data frame or data frame extension (e.g. a tibble)
tz

(character) a time zone name (default: time zone of the POSIXt object x)

Value

(data.frame) An object of the same type as .data

Examples

df <- data.frame(
  date_a = as.Date(c("2020-01-01", "2020-01-02")),
  date_b = as.POSIXct(c("2020-02-01", "2020-02-02")),
  time_a = as.POSIXct(c("1900-01-01 01:01:01", "1900-01-01 02:02:02")),
  time_b = as.POSIXct(c("1900-01-01 01:01:01", "1900-01-01 02:02:02"))
)

combine_date_time_cols(df)

Combinatorics changes

Description

Compares a value with all previous values

Usage

combn_changes(...)

## S3 method for class 'data.frame'
combn_changes(.data, dttm, val, pt_id, ...)

## S3 method for class 'POSIXct'
combn_changes(dttm, val, pt_id, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
dttm

DateTime column name, or vector of POSIXct if .data is not provided
val

Variable column name, or vector of units or numeric if .data is not provided
pt_id

Patient ID column name, or vector of characters or factors if .data is not provided

Value

Combinatorics changes of the same type provided (numeric or units)

Examples

combn_changes(aki_pt_data, dttm = "dttm_", val = "SCr_", pt_id = "pt_id_")

aki_pt_data %>%
  combn_changes(dttm_, SCr_, pt_id_)

Conversion Factors

Description

List of conversion factors based on tables in KDIGO Clinical Practice Guidelines.

Usage

conversion_factors

Format

An object of class tbl_df (inherits from tbl, data.frame) with 21 rows and 4 columns.

Details

parameter

Name of the measurement

metric_units

Metric units for the parameter

mol_weight

Molecular weight (where required)

description

Full name

Examples

conversion_factors

Calculate age from DOB

Description

Calculate age from DOB

Usage

dob2age(dob, age_on = lubridate::today(), fun = NULL, units = "years", ...)

Arguments

dob

The date or vector of dates representing date(s) of birth.
age_on

(Date) The date on which age is to be calculated. Defaults to today.
fun

(function) The function to be applied to the age, e.g. floor. Defaults to NULL.
units

(character) The units to measure age in, e.g. "years". Only used if fun is specified. Defaults to "years".
...

Further optional arguments that will be passed to fun

Value

(duration) The age as a duration.

Examples

dob2age(lubridate::as_date("1990-01-01"))
dob2age(
  dob = c(
    lubridate::as_date("1990-01-01"),
    lubridate::as_date("1994-01-01"),
    lubridate::as_date("1998-01-01")
  ),
  age_on = lubridate::as_date("2002-12-31"),
  fun = floor
)

GFR Estimation

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

eGFR(...)

## S3 method for class 'data.frame'
eGFR(
  .data,
  SCr = NULL,
  SCysC = NULL,
  Age = NULL,
  height = NULL,
  BUN = NULL,
  male = NULL,
  black = NULL,
  pediatric = NULL,
  ...
)

## S3 method for class 'units'
eGFR(
  SCr = NULL,
  SCysC = NULL,
  Age = NULL,
  height = NULL,
  BUN = NULL,
  male = NULL,
  black = NULL,
  pediatric = NULL,
  ...
)

## S3 method for class 'numeric'
eGFR(
  SCr = NULL,
  SCysC = NULL,
  Age = NULL,
  height = NULL,
  BUN = NULL,
  male = NULL,
  black = NULL,
  pediatric = NULL,
  ...
)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCr

Serum creatinine column name, or vector of units or numeric if .data is not provided
SCysC

Serum Cystatin C column name, or vector of units or numeric if .data is not provided
Age

Age of patient column name, or vector of units or numeric if .data is not provided
height

Height of patient column name, or vector of units or numeric if .data is not provided
BUN

Blood urea nitrogen column name, or vector of units or numeric if .data is not provided
male

Male or not column name, or vector of logical (TRUE/FALSE) if .data is not provided
black

Black race or not column name, or vector of logical (TRUE/FALSE) if .data is not provided
pediatric

(logical) Pediatric or not column name, or vector of logical (TRUE/FALSE) if .data is not provided

Details

Automatic selection of equation to estimation the Glomerular Filtration Rate (eGFR), based on input data

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

(units) Estimated glomerular filtration rate (eGFR) of the same type provided (numeric or units in ml/min/1.73m2)

Examples

eGFR(eGFR_pt_data,
  SCr = "SCr_", SCysC = "SCysC_",
  Age = "Age_", height = "height_", BUN = "BUN_",
  male = "male_", black = "black_", pediatric = "pediatric_"
)

eGFR_pt_data %>%
  dplyr::mutate(eGFR = eGFR(
    SCr = SCr_, SCysC = SCysC_,
    Age = Age_, height = height_, BUN = BUN_,
    male = male_, black = black_, pediatric = pediatric_
  ))

eGFR 2009 CKD-EPI creatinine equation

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

eGFR_adult_SCr(...)

## S3 method for class 'data.frame'
eGFR_adult_SCr(.data, SCr, Age, male, black, ...)

## S3 method for class 'units'
eGFR_adult_SCr(SCr, Age, male, black, ...)

## S3 method for class 'numeric'
eGFR_adult_SCr(SCr, Age, male, black, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCr

Serum creatinine column name, or vector of units or numeric if .data is not provided
Age

Age of patient column name, or vector of units or numeric if .data is not provided
male

Male or not column name, or vector of logical (TRUE/FALSE) if .data is not provided
black

Black race or not column name, or vector of logical (TRUE/FALSE) if .data is not provided

Details

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

Estimated GFR of the same type provided (numeric or units)

Examples

eGFR_adult_SCr(eGFR_pt_data,
  SCr = "SCr_", Age = "Age_", male = "male_", black = "black_"
)

eGFR_pt_data %>%
  dplyr::mutate(eGFR = eGFR_adult_SCr(
    SCr = SCr_, Age = Age_, male = male_, black = black_
  ))

eGFR 2012 CKD-EPI creatinine-cystatin C equation

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

eGFR_adult_SCr_SCysC(...)

## S3 method for class 'data.frame'
eGFR_adult_SCr_SCysC(.data, SCr, SCysC, Age, male, black, ...)

## S3 method for class 'units'
eGFR_adult_SCr_SCysC(SCr, SCysC, Age, male, black, ...)

## S3 method for class 'numeric'
eGFR_adult_SCr_SCysC(SCr, SCysC, Age, male, black, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCr

Serum creatinine column name, or vector of units or numeric if .data is not provided
SCysC

Serum Cystatin C column name, or vector of units or numeric if .data is not provided
Age

Age of patient column name, or vector of units or numeric if .data is not provided
male

Male or not column name, or vector of logical (TRUE/FALSE) if .data is not provided
black

Black race or not column name, or vector of logical (TRUE/FALSE) if .data is not provided

Details

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

Estimated GFR of the same type provided (numeric or units)

Examples

eGFR_adult_SCr_SCysC(eGFR_pt_data,
  SCr = "SCr_", SCysC = "SCysC_",
  Age = "Age_", male = "male_", black = "black_"
)

eGFR_pt_data %>%
  dplyr::mutate(eGFR = eGFR_adult_SCr_SCysC(
    SCr = SCr_, SCysC = SCysC_,
    Age = Age_, male = male_, black = black_
  ))

eGFR 2012 CKD-EPI cystatin C equation

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

eGFR_adult_SCysC(...)

## S3 method for class 'data.frame'
eGFR_adult_SCysC(.data, SCysC, Age, male, ...)

## S3 method for class 'units'
eGFR_adult_SCysC(SCysC, Age, male, ...)

## S3 method for class 'numeric'
eGFR_adult_SCysC(SCysC, Age, male, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCysC

Serum Cystatin C column name, or vector of units or numeric if .data is not provided
Age

Age of patient column name, or vector of units or numeric if .data is not provided
male

Male or not column name, or vector of logical (TRUE/FALSE) if .data is not provided

Details

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

Estimated GFR of the same type provided (numeric or units)

Examples

eGFR_adult_SCysC(eGFR_pt_data,
  SCysC = "SCysC_", Age = "Age_", male = "male_"
)

eGFR_pt_data %>%
  dplyr::mutate(eGFR = eGFR_adult_SCysC(
    SCysC = SCysC_, Age = Age_, male = male_
  ))

eGFR Pediatric SCr and Height

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

eGFR_child_SCr(...)

## S3 method for class 'data.frame'
eGFR_child_SCr(.data, SCr, height, ...)

## S3 method for class 'units'
eGFR_child_SCr(SCr, height, ...)

## S3 method for class 'numeric'
eGFR_child_SCr(SCr, height, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCr

Serum creatinine column name, or vector of units or numeric if .data is not provided
height

Height of patient column name, or vector of units or numeric if .data is not provided

Details

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

Estimated GFR of the same type provided (numeric or units)

Examples

eGFR_child_SCr(eGFR_pt_data,
  SCr = "SCr_", height = "height_"
)

eGFR_pt_data %>%
  dplyr::mutate(eGFR = eGFR_child_SCr(
    SCr = SCr_, height = height_,
  ))

eGFR Pediatric SCr, Height and BUN

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

eGFR_child_SCr_BUN(...)

## S3 method for class 'data.frame'
eGFR_child_SCr_BUN(.data, SCr, height, BUN, ...)

## S3 method for class 'units'
eGFR_child_SCr_BUN(SCr, height, BUN, ...)

## S3 method for class 'numeric'
eGFR_child_SCr_BUN(SCr, height, BUN, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCr

Serum creatinine column name, or vector of units or numeric if .data is not provided
height

Height of patient column name, or vector of units or numeric if .data is not provided
BUN

Blood urea nitrogen column name, or vector of units or numeric if .data is not provided

Details

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

Estimated GFR of the same type provided (numeric or units)

Examples

eGFR_child_SCr_BUN(eGFR_pt_data,
  SCr = "SCr_", height = "height_", BUN = "BUN_",
)

eGFR_pt_data %>%
  dplyr::mutate(eGFR = eGFR_child_SCr_BUN(
    SCr = SCr_, height = height_, BUN = BUN_,
  ))

eGFR Pediatric SCysC

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

eGFR_child_SCysC(...)

## S3 method for class 'data.frame'
eGFR_child_SCysC(.data, SCysC, ...)

## S3 method for class 'units'
eGFR_child_SCysC(SCysC, ...)

## S3 method for class 'numeric'
eGFR_child_SCysC(SCysC, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
SCysC

Serum Cystatin C column name, or vector of units or numeric if .data is not provided

Details

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

Estimated GFR of the same type provided (numeric or units)

Examples

eGFR_child_SCysC(eGFR_pt_data,
  SCysC = "SCysC_"
)

eGFR_pt_data %>%
  dplyr::mutate(eGFR = eGFR_child_SCysC(
    SCysC = SCysC_
  ))

eGFR Patient Data

Description

A sample dataset to demonstrate calculating eGFR with epocakir

Usage

eGFR_pt_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 51 rows and 10 columns.

Examples

eGFR_pt_data

GFR Stages

Description

Ordered factor of GFR stages

Usage

GFR_stages

Format

An object of class ordered (inherits from factor) of length 6.

Details

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Examples

GFR_stages

GFR Staging

Description

Using KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Volume 3 | Issue 1 | January 2013

Usage

GFR_staging(...)

## S3 method for class 'data.frame'
GFR_staging(.data, GFR, ...)

## S3 method for class 'units'
GFR_staging(GFR, ...)

## S3 method for class 'numeric'
GFR_staging(GFR, ...)

Arguments

...

Further optional arguments
.data

(data.frame) A data.frame, optional
GFR

Glomerular filtration rate column name, or vector of units or numeric if .data is not provided

Details

  • G1: Normal or high GFR, ≥\ge90

  • G2: Mildly decreased, 60-89

  • G3a: Mildly to moderately decreased, 45-59

  • G3b: Moderately to severely decreased, 30-44

  • G4: Severely decreased, 15-29

  • G5: Kidney failure, <15

See https://kdigo.org/guidelines/ckd-evaluation-and-management/ for more details

Value

GFR category

Examples

df <- tibble::tibble(
  eGFR = units::set_units(c(-1, NA, 100, 70, 50, 35, 20, 10), "mL/min/1.73m2")
)

GFR_staging(df, "eGFR")

df %>%
  dplyr::mutate(GFR_level = GFR_staging(eGFR))