data_modeling

Last updated: 2024-10-03

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File	Version	Author	Date	Message
Rmd	572131a	calliquire	2024-10-03	baby’s first data vis
html	572131a	calliquire	2024-10-03	baby’s first data vis
Rmd	e0261c4	calliquire	2024-10-03	Create data_modeling_1.Rmd

About This Analysis: This analysis markdown page is for fitting the initial multivariate model to the cleaned_screening_data.csv. Baby’s first data visualization.

Set Up

Load the cleaned data.

data <- read.csv("data/cleaned_screening_long.csv")

Load relevant libraries.

library(lme4)
library(car)
library(ggplot2)

Fit the Multivariate Mixed-Effects Model. Here’s a general structure for the multivariate model:

Dependent Variable: Reflectance
Fixed Effects: Reflectance Type, Body Site, Time Point
Random Effects: Individual participants (to account for variability across individuals)

model <- lmer(reflectance ~ body_site * reflectance_type * collection_period + (1|participant_centre_id), data = data)

Visualize the results.

ggplot(data, aes(x = body_site, y = reflectance, color = reflectance_type)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  facet_wrap(~ collection_period) +
  labs(title = "Reflectance by Body Site and Reflectance Type",
       x = "Body Site",
       y = "Reflectance",
       color = "Reflectance Type") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))  # Rotate x-axis labels for readability

`geom_smooth()` using formula = 'y ~ x'

Warning: Removed 319 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 319 rows containing missing values or values outside the scale range
(`geom_point()`).

Version	Author	Date
572131a	calliquire	2024-10-03

Save the plot.

# Save the last plot you made
ggsave("data/reflectance_plot.png", width = 8, height = 6)

`geom_smooth()` using formula = 'y ~ x'

Warning: Removed 319 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 319 rows containing missing values or values outside the scale range
(`geom_point()`).

# Or save it as a PDF
ggsave("data/reflectance_plot.pdf", width = 8, height = 6)

`geom_smooth()` using formula = 'y ~ x'

Warning: Removed 319 rows containing non-finite outside the scale range
(`stat_smooth()`).
Removed 319 rows containing missing values or values outside the scale range
(`geom_point()`).

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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] ggplot2_3.5.1 car_3.1-3     carData_3.0-5 lme4_1.1-35.5 Matrix_1.7-0 

loaded via a namespace (and not attached):
 [1] generics_0.1.3    sass_0.4.9        utf8_1.2.4        stringi_1.8.4    
 [5] lattice_0.22-6    digest_0.6.37     magrittr_2.0.3    evaluate_1.0.0   
 [9] grid_4.4.1        fastmap_1.2.0     rprojroot_2.0.4   workflowr_1.7.1  
[13] jsonlite_1.8.9    whisker_0.4.1     Formula_1.2-5     promises_1.3.0   
[17] fansi_1.0.6       scales_1.3.0      textshaping_0.4.0 jquerylib_0.1.4  
[21] abind_1.4-8       cli_3.6.3         rlang_1.1.4       munsell_0.5.1    
[25] splines_4.4.1     withr_3.0.1       cachem_1.1.0      yaml_2.3.10      
[29] tools_4.4.1       nloptr_2.1.1      dplyr_1.1.4       minqa_1.2.8      
[33] colorspace_2.1-1  httpuv_1.6.15     boot_1.3-30       vctrs_0.6.5      
[37] R6_2.5.1          lifecycle_1.0.4   git2r_0.33.0      stringr_1.5.1    
[41] fs_1.6.4          MASS_7.3-60.2     ragg_1.3.3        pkgconfig_2.0.3  
[45] pillar_1.9.0      bslib_0.8.0       later_1.3.2       gtable_0.3.5     
[49] glue_1.7.0        Rcpp_1.0.13       systemfonts_1.1.0 highr_0.11       
[53] tidyselect_1.2.1  xfun_0.47         tibble_3.2.1      rstudioapi_0.16.0
[57] knitr_1.48        farver_2.1.2      htmltools_0.5.8.1 nlme_3.1-164     
[61] labeling_0.4.3    rmarkdown_2.28    compiler_4.4.1

data_modeling_1

calliquire

2024-10-03

Set Up