Last updated: 2025-12-17

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Knit directory: SkinOptics/

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File	Version	Author	Date	Message
Rmd	a6f7dc4	Junhui He	2025-12-17	update JID_SkinOptics.Rmd
html	32c3e8f	Junhui He	2025-12-11	Rebuild site to apply navbar layout
html	b2cbe44	Junhui He	2025-12-11	Build site.
Rmd	df71367	Junhui He	2025-12-11	modify face site
html	d98f12d	Junhui He	2025-12-11	Build site.
Rmd	2fc3d03	Junhui He	2025-12-11	add correlation analysis
html	81580b5	Junhui He	2025-12-11	build workflowr
Rmd	e11deee	Junhui He	2025-12-11	calculate EI
html	e11deee	Junhui He	2025-12-11	calculate EI
Rmd	53d4f9c	Junhui He	2025-12-11	create SkinOptics
html	53d4f9c	Junhui He	2025-12-11	create SkinOptics

Clarifications

Melanin index (MI) is calculated based on skin reflectance at 680 nm. Specifically, MI = -100 * log10(R680 / 100), where R680 is the reflectance percentage at 680 nm.
Erythema index (EI) is calculated as EI = 100 * log10(R680 / ((R550 + R560)/2)), where R550 and R560 are the reflectance percentages at 550 nm and 560 nm, respectively.
EI variability is measured by the standard deviation of EIs within a sliding window of MI values. The window size is set to 20 MI units, and the step size is 1 MI unit.
- For each center MI value in the sequence, all EI values corresponding to MI values within the window (center MI ± 10) are collected, and their standard deviation is computed.
- The center MI values range from the 1st to the 99th percentile of observed MI values.
FACE site refers to Forehead or Cheek, while PALM site refers to the Palm of the hand.
Representative FACE MI:
- For each subject, the FACE MI is given by the Forehead MI if the Forehead MI is available; otherwise, it is the Cheek MI.
- For subjects with multiple measurements at the same FACE site, we randomly select one measurement.
- Each subject has only one representative FACE reflectance spectra.
First derivatives of skin spectra are estimated using local polynomial regression with bandwidth selected by the dpill function, scaled by a factor of 0.7.
Eumelanin classes are defined based on melanin index ranges as follows:
- Low: MI < 25
- Intermediate low: 25 ≤ MI < 50
- Intermediate: 50 ≤ MI < 75
- Intermediate high: 75 ≤ MI < 100
- High: MI ≥ 100
The pdf files generated in this analysis are saved in the “output” directory.

Visualizations

Distribution of melanin index by site

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
53d4f9c	Junhui He	2025-12-11

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Unique subjects per site across representative face melanin index bins (Heatmap)

Version	Author	Date
53d4f9c	Junhui He	2025-12-11

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Number of subjects in each eumelanin class (Forehead/Cheek)
Eumelanin class	Number of subjects
Low	77
Intermediate low	1800
Intermediate	191
Intermediate high	30
High	3

Number of subjects in each eumelanin class (Palm)
Eumelanin class	Number of subjects
Low	127
Intermediate low	621
Intermediate	27
Intermediate high	1

Reflectance by eumelanin classes

Face reflectance by face eumelanin class

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Palm reflectance by palm eumelanin class

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Palm reflectance by face eumelanin class

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First derivatives of reflectance by eumelanin classes

Face reflectance derivatives by face eumelanin class

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
53d4f9c	Junhui He	2025-12-11

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Palm reflectance derivatives by palm eumelanin class

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
53d4f9c	Junhui He	2025-12-11

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Palm reflectance derivatives by face eumelanin class

Version	Author	Date
b2cbe44	Junhui He	2025-12-11

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First derivatives of absorbance by eumelanin classes

Face absorbance derivatives by face eumelanin class

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
53d4f9c	Junhui He	2025-12-11

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Palm absorbance derivatives by palm eumelanin class

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
53d4f9c	Junhui He	2025-12-11

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Palm absorbance derivatives by face eumelanin class

Version	Author	Date
b2cbe44	Junhui He	2025-12-11

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Correlation between reflectance derivative sd and melanin index

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
53d4f9c	Junhui He	2025-12-11

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Regression analysis


Call:
lm(formula = sd_ref ~ log_mi + I(log_mi^2), data = sd_face)

Residuals:
      Min        1Q    Median        3Q       Max 
-0.069041 -0.014131 -0.001693  0.011082  0.100521 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept)  1.560287   0.066388   23.50   <2e-16 ***
log_mi      -0.682188   0.035856  -19.03   <2e-16 ***
I(log_mi^2)  0.076287   0.004825   15.81   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.02265 on 2098 degrees of freedom
Multiple R-squared:  0.6498,    Adjusted R-squared:  0.6495 
F-statistic:  1947 on 2 and 2098 DF,  p-value: < 2.2e-16


Call:
lm(formula = sd_ref ~ log_mi, data = sd_palm)

Residuals:
      Min        1Q    Median        3Q       Max 
-0.066053 -0.016370  0.000337  0.015371  0.071971 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept)  0.560165   0.013160   42.56   <2e-16 ***
log_mi      -0.120567   0.003789  -31.82   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0238 on 774 degrees of freedom
Multiple R-squared:  0.5668,    Adjusted R-squared:  0.5662 
F-statistic:  1013 on 1 and 774 DF,  p-value: < 2.2e-16

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
53d4f9c	Junhui He	2025-12-11

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Correlation between absorbance derivative sd and melanin index

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
53d4f9c	Junhui He	2025-12-11

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Correlation between erythema index and melanin index by site

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
e11deee	Junhui He	2025-12-11

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Correlation between erythema index variability and melanin index by site

EI variability is measured by the standard deviation of EIs within a sliding window of MI values. The window size is set to 20 MI units, and the step size is 1 MI unit.
- For each center MI value in the sequence, all EI values corresponding to MI values within the window (center MI ± 10) are collected, and their standard deviation is computed.
- The center MI values range from the 1st to the 99th percentile of observed MI values.

Version	Author	Date
b2cbe44	Junhui He	2025-12-11
d98f12d	Junhui He	2025-12-11

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R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Detroit
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] KernSmooth_2.23-26 openxlsx_4.2.8.1   scales_1.4.0       lubridate_1.9.4   
 [5] forcats_1.0.1      stringr_1.6.0      dplyr_1.1.4        purrr_1.2.0       
 [9] readr_2.1.6        tidyr_1.3.1        tibble_3.3.0       ggplot2_4.0.1     
[13] tidyverse_2.0.0    patchwork_1.3.2    knitr_1.50        

loaded via a namespace (and not attached):
 [1] sass_0.4.10        generics_0.1.4     lattice_0.22-7     stringi_1.8.7     
 [5] hms_1.1.4          digest_0.6.39      magrittr_2.0.4     timechange_0.3.0  
 [9] evaluate_1.0.5     grid_4.3.1         RColorBrewer_1.1-3 fastmap_1.2.0     
[13] Matrix_1.5-4.1     rprojroot_2.1.1    workflowr_1.7.2    jsonlite_2.0.0    
[17] zip_2.3.3          whisker_0.4.1      promises_1.5.0     mgcv_1.8-42       
[21] viridisLite_0.4.2  jquerylib_0.1.4    cli_3.6.5          rlang_1.1.6       
[25] splines_4.3.1      withr_3.0.2        cachem_1.1.0       yaml_2.3.11       
[29] otel_0.2.0         tools_4.3.1        tzdb_0.5.0         httpuv_1.6.16     
[33] vctrs_0.6.5        R6_2.6.1           lifecycle_1.0.4    git2r_0.36.2      
[37] fs_1.6.6           pkgconfig_2.0.3    pillar_1.11.1      bslib_0.9.0       
[41] later_1.4.4        gtable_0.3.6       glue_1.8.0         Rcpp_1.1.0        
[45] xfun_0.54          tidyselect_1.2.1   farver_2.1.2       nlme_3.1-168      
[49] htmltools_0.5.9    labeling_0.4.3     rmarkdown_2.30     compiler_4.3.1    
[53] S7_0.2.1

Skin Optics Analysis based on ISSA Data

Junhui He

2025-12-17