In JMLuther/tabletools: Helpful Tools to Make html Tables

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(tabletools)

Introduction

This package has evolved to include functions useful for metabolic studies in humans, in particular to assess insulin sensitivity.

Unit conversion functions

Convenience functions are provided to convert glucose, insulin and other units to the desired units.

Glucose and Insulin

Most functions default to using glucose (mg/dL) and insulin (uU/mL) as the input units because these are most commonly reported in the US.

To convert glucose from mg/dL to mmol/L, use the convert_glucose_to_mM function, indicating the original units of the glucose value.

convert_glucose_to_mM(100, glucose_units =  "mg/dL")

To convert insulin from uU/mL to pmol/L, use the convert_insulin_to_pM function, indicating the original units of the insulin value.

convert_insulin_to_pM(10, insulin_units = "uU/mL")

Weight and Height

Similar functions are available to convert weight and height to the desired units.

convert_weight_to_kg(150, weight_units = "lbs")

Height from inches to meters:

convert_height_to_m(70, height_units = "in")

Insulin sensitivity

Sample OGTT Data, to use for fasting and OGTT based calculations.

# handling data stored in a dataframe
ogtt1 <- data.frame(time=c(0, 30, 60, 90, 120),              # minutes
                    glucose=c(93, 129, 178, 164, 97),        # mg/dL
                    insulin=c(12.8, 30.7, 68.5, 74.1, 44.0)) # uU/mL

# example from Gutch et al 2015
ogtt2 <- data.frame(time=c(0, 30, 60, 90, 120),              # minutes
                    glucose=c(100, 160, 160, 160, 140),      # mg/dL
                    insulin=c(5, 10, 10, 10, 5))             # uU/mL

Fasting Glucose and insulin

The HOMA-IR and QUICKI indices are used to assess insulin sensitivity. There is an updated HOMA2 calculation that is preferable to the original HOMA-IR calculation, but it is based on a series of equations that are not accessible to incorporate into a function. There is an online and downloadable calculator for HOMA2 that is readily available here.

A1C estimated average glucose

The estimated average glucose can be calculated from A1C:

calculate_avg_glucose(5.5)

HOMA-IR:

Higher values indicate lower insulin sensitivity.

calculate_homair(ogtt1$glucose[1], ogtt1$insulin[1])

QUICKI:

Higher values indicate higher insulin sensitivity.

calculate_quicki(ogtt1$glucose[1], ogtt1$insulin[1])

OGTT based calculations

Matsuda Index

Matsuda index is the most often used OGTT-based estimate of insulin sensitivity. Calculations can be verified at an online calculator here.

calculate_matsuda_index(ogtt1$time, ogtt1$glucose, ogtt1$insulin)

Stumvoll Index

calculate_stumvoll_isi(ogtt1$time, ogtt1$glucose, ogtt1$insulin) #

Body Surface Area

The bsa command calculates Body Surface area (m²) using the most commonly available methods Yu et al.

The default method is the Mosteller formula. Functions will conduct unit conversions if the proper units are provided- defaults to kg and m.

calculate_bsa(weight = 70, height =  1.50, method = "Mosteller",
              weight_units = "kg", height_units = "m")

Available Methods and Formulas:

```{=tex} \begin{equation} \sqrt{\frac{Ht(cm) \cdot Wt(kg)}{3600}} \tag{Mosteller} \end{equation}

```{=tex}
\begin{equation}
Wt(kg)^{0.425} \cdot Ht(cm)^{0.725} \cdot 0.007184 \tag{DuBois and DuBois}
\end{equation}

```{=tex} \begin{equation} Wt(kg)^{0.51456} \cdot Ht(cm)^{0.42246} \cdot 0.0235 \tag{Gehan and George} \end{equation}

```{=tex}
\begin{equation}
Wt(kg)^{0.5378} \cdot Ht(cm)^{0.3964} \cdot 0.024265 \tag{Haycock}
\end{equation}

```{=tex} \begin{equation} 71.3989 \cdot Ht(cm)^{0.7437} \cdot Wt(kg)^{0.4040} \div 10000 \tag{Yu} \end{equation}

```{=tex}
\begin{equation}
0.1173 \cdot Wt(kg)^{0.6466} \tag{Livingston}
\end{equation}

```{=tex} \begin{equation} 128.1 \cdot Ht(cm)^{0.60} \cdot Wt(kg)^{0.44} \tag{Tikuisis} \end{equation}

# Kidney function equations

## eGFR

Creatinine clearance is the historical standard to estimate glomerular filtration rate (GFR). The Cockcroft-Gault formula was used in the past, but has been superceded by the MDRD and more recently CKD-EPI equations. Newer methods incorporating Cystatin C are also available, and may increase accuracy when using race-free equations [@Inker2021].

Formulas for multiple methods of eGFR are provided- not meant to be comprehensive, but up to date. The ASN and NKF task force panels now recommend using equations that do not incorporate a race coefficient. Details on the formulas can be found in Supplemental Table S10 of [@Inker2021].

Online calculators to verify the results are available:

-   New CKD-EPI equations at [Kidney.org](https://www.kidney.org/professionals/kdoqi/gfr_calculator)\
-   Old 2009 CKD-EPI (race-based) calculator is maintained at [NIH/NIDDK](https://www.niddk.nih.gov/health-information/professionals/clinical-tools-patient-management/kidney-disease/laboratory-evaluation/glomerular-filtration-rate-calculators/historical) for comparison.
-   MDRD

### Cockcroft-Gault

This formula estimates Creatinine Clearance, whereas others estimate GFR.
The Cockcroft-Gault Creatinine Clearance estimating equation was used for decades in clinical practice before the MDRD and CKD-EPI equations were developed. 

$$Creatinine~CL_{CG}= \frac{(140-Age) \cdot Weight \cdot 0.85[Female]}{72 \cdot Creatinine}$$

where units are Weight (kg), Age (years), and Creatinine (mg/dL).


```r
calculate_creatclearance_cg(age=70, sex="Male", weight=70, creatinine=1.0) # 68

CKD-EPI

Note: When comparing results using this function against Inker Table S11 there are minor differences amounting to no more than 0.5-1.0 ml/min/1.73m2.

The 2021 CKD-EPI equation is: $$eGFR_{cr}= 142\cdot min(Cr/\kappa, 1)^\alpha \cdot max(Cr/\kappa, 1)^{-1.200} \cdot 0.9938^{Age} \cdot 1.102[Female] $$

where:

* $\kappa$ = 0.7 (Female) or 0.9 (Male)\ * $\alpha$ = -0.241 (Female) or -0.302 (Male)\ * Age is in years * Cr = serum Creatinine in mg/dL

Note that the 2021 CKD-EPI formula also has a version which was derived using Race, and produces slightly different results.

$$eGFR_{cr}= 141\cdot min(Cr/\kappa, 1)^\alpha \cdot max(Cr/\kappa, 1)^{-1.209} \cdot 0.9929^{Age} \cdot 1.018[Female] \cdot 1.159[Black] $$

where:

* $\kappa$ = 0.7 (Female) or 0.9 (Male)\ * $\alpha$ = -0.329 (Female) or -0.411 (Male)\

calculate_egfr_ckdepi(age=70, sex="Male", creatinine=0.8) # 95.2

MDRD

The MDRD equation was the first GFR estimating equation incorporated into widespread clinical practice.[@Levey2006] It has fallen out of use in favor of the newer CKD-EPI equations. Limitations include use of racial adjustments that are biased, and overestimation of GFR especially at higher values.

The best accepted MDRD version is the 4-variable equation incorporating age, sex, race, and creatinine.

$$eGFR_{MDRD}= 175 \cdot Cr^{-1.154} \cdot Age^{-0.203} \cdot 1.212[Black] \cdot 0.742[Female]$$ Where the race and sex adjustment is included if Black or Female.

CKD-EPI Cr-Cystatin-C

not yet incorporated

Bibliography

JMLuther/tabletools documentation built on July 1, 2024, 2:01 p.m.