Last updated: 2024-02-01
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Knit directory: LocksofLineage/
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# Read the CSV file
data <- read_csv("~/Desktop/Primates/Full_Hair_Traits_Updated_Names.csv")New names:
Rows: 238 Columns: 17
── Column specification
──────────────────────────────────────────────────────── Delimiter: "," chr
(16): family, Genus, species, subspecies, Sexual_dimorphism, Sexual_Dimo... lgl
(1): ...7
ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
Specify the column types or set `show_col_types = FALSE` to quiet this message.
• `` -> `...7`# Binarize the data
data_test_multiple <- data %>%
mutate(across(c(Sexual_dimorphism, Natal_coat, Sexual_dichromatism), ~if_else(. == "Yes", 1, 0)))#data_multiple_options <- data_test_SC_NA %>%
#mutate(Darker = match(Darker, unique(Darker)))
data_multiple_multiple <- data_test_multiple %>%
mutate(across(c(Darker, Direction, Natal_Coat_Type), ~match(., unique(.)) - 1))
write.csv(data_multiple_multiple, "~/Github/LocksofLineage/data/data_multiple_multiple.csv", row.names = FALSE)
#data_multiple_options <- data %>%
#mutate(Darker = if_else(is.na(Darker), NA_integer_, match(Darker, unique(Darker))))#Create the legend function
create_legend <- function(column) {
unique_values <- unique(column)
encoded_values <- match(unique_values, unique_values) - 1
legend <- tibble(Original = unique_values, Code = encoded_values)
return(legend)
}
#Create the legends for the columns
legend_Sexual_Dimorphism <- create_legend(data$Sexual_dimorphism)
legend_SD_Direction <- create_legend(data$Direction)
legend_Natal_coat <- create_legend(data$Natal_coat)
legend_Natal_coat_type <- create_legend(data$Natal_Coat_Type)
legend_Sexual_Dichrom <- create_legend(data$Sexual_dichromatism)
legend_Sexual_Dichrom_type <- create_legend(data$Sexual_dichromatism_type)
legend_Darker <- create_legend(data$Darker)
#Add column names
legend_Sexual_Dimorphism <- legend_Sexual_Dimorphism %>% mutate(Column = 'Sexual_Dimorphism')
legend_SD_Direction <- legend_SD_Direction %>% mutate(Column = 'SD_Direction')
legend_Natal_coat <- legend_Natal_coat %>% mutate(Column = 'Natal_Coat')
legend_Natal_coat_type <- legend_Natal_coat_type %>% mutate(Column = 'Natal_Coat_Type')
legend_Sexual_Dichrom <- legend_Sexual_Dichrom %>% mutate(Column = 'Sexual_Dichromatism')
legend_Sexual_Dichrom_type <- legend_Sexual_Dichrom %>% mutate(Column = 'Sexual_Dichrom_Type')
legend_Darker <- legend_Darker %>% mutate(Column = 'Darker')
#Combine the legends
combined_legends <- bind_rows(legend_Sexual_Dimorphism, legend_SD_Direction, legend_Natal_coat, legend_Natal_coat_type, legend_Sexual_Dichrom, legend_Sexual_Dichrom_type, legend_Darker)
#Create a csv for the legend
write.csv(combined_legends, "~/Github/LocksofLineage/data/combined_legends.csv", row.names = FALSE)
sessionInfo()R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.0
[5] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.1.8
[9] ggplot2_3.4.1 tidyverse_2.0.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 xfun_0.41 bslib_0.4.2 colorspace_2.0-3
[5] vctrs_0.5.2 generics_0.1.3 htmltools_0.5.4 yaml_2.3.7
[9] utf8_1.2.2 rlang_1.0.6 jquerylib_0.1.4 later_1.3.1
[13] pillar_1.8.1 glue_1.6.2 withr_2.5.0 bit64_4.0.5
[17] lifecycle_1.0.3 munsell_0.5.0 gtable_0.3.1 evaluate_0.20
[21] knitr_1.42 tzdb_0.3.0 callr_3.7.3 fastmap_1.1.0
[25] httpuv_1.6.11 ps_1.7.2 parallel_4.2.1 fansi_1.0.3
[29] highr_0.10 Rcpp_1.0.11 promises_1.2.1 scales_1.2.1
[33] cachem_1.0.6 vroom_1.6.1 jsonlite_1.8.4 bit_4.0.5
[37] fs_1.6.1 hms_1.1.2 digest_0.6.30 stringi_1.7.8
[41] processx_3.8.0 getPass_0.2-2 rprojroot_2.0.4 grid_4.2.1
[45] cli_3.6.0 tools_4.2.1 magrittr_2.0.3 sass_0.4.5
[49] crayon_1.5.2 whisker_0.4.1 pkgconfig_2.0.3 ellipsis_0.3.2
[53] timechange_0.2.0 rmarkdown_2.20 httr_1.4.4 rstudioapi_0.14
[57] R6_2.5.1 git2r_0.32.0 compiler_4.2.1