Last updated: 2024-03-01

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Knit directory: PODFRIDGE/

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File Version Author Date Message
html 9e71347 Tina Lasisi 2024-01-22 Build site.
html 85d8cd5 Tina Lasisi 2024-01-16 Create manuscript_figures.html
Rmd 4fc6ed6 jakevc 2023-11-29 fill by population
Rmd 8ba0e34 jakevc 2023-11-21 fix
Rmd 0b61210 jakevc 2023-11-20 add number of matches plot
Rmd 836eb7a jakevc 2023-11-17 Variable configurations, draft separate plot
Rmd 9c4e31e Tina Lasisi 2023-11-13 Create manuscript_figures.Rmd 
# Load required packages
library(tidyverse)
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.4.4     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.0
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
library(patchwork)

knitr::opts_knit$set(root.dir = "..")
knitr::opts_chunk$set(eval = TRUE, echo = FALSE, fig.width = 7, fig.height = 6)

# CONFIGURE CONSTANTS

# Total US Population 1990: source?
US_POP_1990 = 2.5e8

# European American Population 1990: source?
EA_POP_1990 = 199686070
  
# African American Population 1990: source?
AA_POP_1990 = 29986060

# calculate proportion of us population each group
US_PROP_AA = AA_POP_1990 / US_POP_1990
US_PROP_EA = EA_POP_1990 / US_POP_1990

# CODIS SIZE 
CODIS_SIZE = 2.10e7

# DTC SIZE 
ANCESTRY_SIZE = 2.3e7
TWTY_THREE_ME_SIZE = 1.4e7
MY_HERATIGE_SIZE = 7e6
FTDNA = 1.8e6
GEDMATCH = 1.8e6

# calculate total DTC SIZE
DTC_SIZE = ANCESTRY_SIZE + TWTY_THREE_ME_SIZE + MY_HERATIGE_SIZE + FTDNA + GEDMATCH

# calculate searchable DTC size (FTDNA + GEDMATCH)
DTC_SEARCH = FTDNA + GEDMATCH

# Proportion AA in CODIS
PROP_AA_CODIS = 0.236

# Proportion EA in CODIS
PROP_EA_CODIS = 0.429

### TODO: UPDATE THESE WITH CORRECT VALUES
PROP_AA_DTC = 0.03 # TODO: need this value
PROP_EA_DTC = 0.60 # TODO: need this value

### TODO: UPDATE THESE NUMBERS WITH CORRECT VALUES
PROP_AA_DTC_S = 0.03
PROP_EA_DTC_S = 0.60

European American vs African American probability of match

IBD accounted

Version Author Date
85d8cd5 Tina Lasisi 2024-01-16

Version Author Date
85d8cd5 Tina Lasisi 2024-01-16

Version Author Date
85d8cd5 Tina Lasisi 2024-01-16

Version Author Date
9e71347 Tina Lasisi 2024-01-22
85d8cd5 Tina Lasisi 2024-01-16 

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3.1

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] ggrepel_0.9.5   patchwork_1.2.0 lubridate_1.9.3 forcats_1.0.0  
 [5] stringr_1.5.1   dplyr_1.1.4     purrr_1.0.2     readr_2.1.5    
 [9] tidyr_1.3.0     tibble_3.2.1    ggplot2_3.4.4   tidyverse_2.0.0
[13] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] sass_0.4.8        utf8_1.2.4        generics_0.1.3    stringi_1.8.3    
 [5] hms_1.1.3         digest_0.6.34     magrittr_2.0.3    timechange_0.2.0 
 [9] evaluate_0.23     grid_4.3.2        fastmap_1.1.1     rprojroot_2.0.4  
[13] jsonlite_1.8.8    processx_3.8.3    whisker_0.4.1     ps_1.7.5         
[17] promises_1.2.1    httr_1.4.7        fansi_1.0.6       scales_1.3.0     
[21] jquerylib_0.1.4   cli_3.6.2         rlang_1.1.3       munsell_0.5.0    
[25] withr_2.5.2       cachem_1.0.8      yaml_2.3.8        tools_4.3.2      
[29] tzdb_0.4.0        colorspace_2.1-0  httpuv_1.6.13     vctrs_0.6.5      
[33] R6_2.5.1          lifecycle_1.0.4   git2r_0.33.0      fs_1.6.3         
[37] pkgconfig_2.0.3   callr_3.7.3       pillar_1.9.0      bslib_0.6.1      
[41] later_1.3.2       gtable_0.3.4      glue_1.7.0        Rcpp_1.0.12      
[45] highr_0.10        xfun_0.41         tidyselect_1.2.0  rstudioapi_0.15.0
[49] knitr_1.45        farver_2.1.1      htmltools_0.5.7   labeling_0.4.3   
[53] rmarkdown_2.25    compiler_4.3.2    getPass_0.2-4