Last updated: 2024-10-03
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Knit directory: SAPPHIRE/
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About: This is the second iteration of data cleaning that must be done after data_cleaning_1. Here, I clean the screening_long long-form dataset to have columns for body_site and reflectance_type (as well as collection_period, which was done in data_cleaning_1).
library(tidyr)data <- read.csv("data/screening_long.csv")head(data) participant_centre_id interviewer_name today_date age_years date_of_birth
1 VDKH001 Betty 2013-02-11 20 1993-08-07
2 VDKH002 Betty 2013-02-11 23 1990-01-20
3 VDKH003 Betty 2013-02-11 23 1989-05-05
4 VDKH004 Betty 2013-02-12 20 1992-08-10
5 VDKH005 Betty 2013-02-12 19 1993-05-06
6 VDKH006 Betty 2013-02-12 21 1992-04-14
gender ethnicity_coloured ethnicity_white ethnicity_african_black
1 1 FALSE FALSE TRUE
2 1 FALSE FALSE TRUE
3 2 FALSE FALSE TRUE
4 2 FALSE FALSE TRUE
5 1 FALSE FALSE TRUE
6 1 FALSE FALSE TRUE
ethnicity_indian_asian ethnicity_other ethnicity_specify_other ethnicity
1 FALSE FALSE NA NA
2 FALSE FALSE NA NA
3 FALSE FALSE NA NA
4 FALSE FALSE NA NA
5 FALSE FALSE NA NA
6 FALSE FALSE NA NA
refuse_to_answer weight_measure1 weight_measure2 avg_weight height_measure1
1 FALSE 60.6 60.6 60.6 1.728
2 FALSE 60.5 60.5 60.5 1.678
3 FALSE 63.5 63.5 63.5 1.588
4 FALSE 64.4 64.4 64.4 1.595
5 FALSE 53.7 53.7 53.7 1.632
6 FALSE 53.3 53.3 53.3 1.523
height_measure2 avg_height bmi sore_throat_yes sore_throat_no
1 1.728 1.728 20.29482 FALSE TRUE
2 1.678 1.678 21.48679 FALSE TRUE
3 1.588 1.588 25.18098 FALSE TRUE
4 1.595 1.595 25.31421 FALSE TRUE
5 1.632 1.632 20.16202 FALSE TRUE
6 1.523 1.523 22.97880 FALSE TRUE
runny_nose_yes runny_nose_no cough_yes cough_no fever_yes fever_no
1 FALSE TRUE FALSE TRUE FALSE TRUE
2 FALSE TRUE FALSE TRUE FALSE TRUE
3 FALSE TRUE FALSE TRUE FALSE TRUE
4 FALSE TRUE FALSE TRUE FALSE TRUE
5 FALSE TRUE FALSE TRUE FALSE TRUE
6 FALSE TRUE FALSE TRUE FALSE TRUE
night_sweats_yes night_sweats_no unexplained_weight_loss_yes
1 FALSE TRUE FALSE
2 FALSE TRUE FALSE
3 FALSE TRUE FALSE
4 FALSE TRUE FALSE
5 FALSE TRUE FALSE
6 FALSE TRUE FALSE
unexplained_weight_loss_no currently_taking_supplements_yes
1 TRUE FALSE
2 TRUE FALSE
3 TRUE FALSE
4 TRUE FALSE
5 TRUE FALSE
6 TRUE FALSE
currently_taking_supplements_no supplements currently_taking_medications_yes
1 TRUE <NA> FALSE
2 TRUE <NA> FALSE
3 TRUE <NA> FALSE
4 TRUE <NA> FALSE
5 TRUE <NA> FALSE
6 TRUE <NA> FALSE
currently_taking_medications_no medications participant_included_yes
1 TRUE <NA> TRUE
2 TRUE <NA> TRUE
3 TRUE <NA> TRUE
4 TRUE <NA> TRUE
5 TRUE <NA> TRUE
6 TRUE <NA> TRUE
participant_included_no if_no_reason_for_exclusion
1 FALSE <NA>
2 FALSE <NA>
3 FALSE <NA>
4 FALSE <NA>
5 FALSE <NA>
6 FALSE <NA>
smoking_do_you_regularly_smoke_at_least1cigarette5daysa_week smoking_comments
1 FALSE <NA>
2 FALSE <NA>
3 FALSE <NA>
4 FALSE <NA>
5 FALSE <NA>
6 FALSE <NA>
skin_reflectance_forehead_e1 skin_reflectance_forehead_e2
1 17.01 18.73
2 17.22 19.82
3 14.33 16.13
4 22.46 21.45
5 18.57 19.73
6 14.06 15.28
skin_reflectance_forehead_e3 skin_reflectance_forehead_m1
1 18.61 55.99
2 17.41 76.41
3 14.25 71.54
4 20.53 77.36
5 21.06 62.27
6 16.76 82.08
skin_reflectance_forehead_m2 skin_reflectance_forehead_m3
1 70.57 76.28
2 70.03 74.73
3 69.23 69.63
4 58.49 57.67
5 62.95 65.07
6 80.85 85.21
skin_reflectance_forehead_r1 skin_reflectance_forehead_r2
1 70 50
2 44 51
3 49 52
4 46 67
5 57 59
6 38 40
skin_reflectance_forehead_r3 skin_reflectance_forehead_g1
1 44 47
2 45 30
3 51 36
4 67 26
5 57 36
6 34 27
skin_reflectance_forehead_g2 skin_reflectance_forehead_g3
1 33 30
2 32 30
3 36 37
4 42 42
5 38 36
6 28 23
skin_reflectance_forehead_b1 skin_reflectance_forehead_b2
1 43 30
2 26 29
3 28 30
4 24 38
5 29 34
6 25 26
skin_reflectance_forehead_b3 skin_reflectance_forehead_l_1
1 27 19.93
2 26 11.93
3 32 13.88
4 37 8.59
5 32 15.02
6 22 9.24
skin_reflectance_forehead_l_2 skin_reflectance_forehead_l_3
1 13.10 11.45
2 12.82 12.02
3 14.54 13.98
4 16.59 17.97
5 15.19 14.38
6 10.28 7.74
skin_reflectance_foreheada_1 skin_reflectance_foreheada_2
1 14.37 11.16
2 8.13 12.65
3 7.69 9.87
4 10.58 16.24
5 13.25 13.04
6 7.36 7.99
skin_reflectance_foreheada_3 skin_reflectance_foreheadb_1
1 9.18 11.62
2 8.84 10.60
3 10.20 13.20
4 15.90 5.72
5 13.87 14.01
6 7.65 6.62
skin_reflectance_foreheadb_2 skin_reflectance_foreheadb_3
1 9.28 8.64
2 9.39 10.69
3 12.56 10.37
4 11.40 12.58
5 9.78 9.77
6 7.15 4.98
skin_reflectance_right_upper_inner_arm_e1
1 20.92
2 20.11
3 16.17
4 14.98
5 20.45
6 18.83
skin_reflectance_right_upper_inner_arm_e2
1 19.88
2 19.56
3 17.44
4 14.61
5 22.16
6 18.95
skin_reflectance_right_upper_inner_arm_e3
1 19.99
2 19.41
3 16.59
4 12.84
5 19.50
6 18.95
skin_reflectance_right_upper_inner_arm_m1
1 74.58
2 70.30
3 59.75
4 48.55
5 65.67
6 67.29
skin_reflectance_right_upper_inner_arm_m2
1 71.88
2 70.57
3 62.50
4 46.70
5 70.56
6 66.16
skin_reflectance_right_upper_inner_arm_m3
1 70.71
2 70.17
3 62.05
4 43.95
5 62.95
6 66.66
skin_reflectance_right_upper_inner_arm_r1
1 47
2 50
3 64
4 84
5 56
6 54
skin_reflectance_right_upper_inner_arm_r2
1 49
2 50
3 60
4 87
5 49
6 56
skin_reflectance_right_upper_inner_arm_r3
1 50
2 50
3 60
4 89
5 60
6 55
skin_reflectance_right_upper_inner_arm_g1
1 31
2 32
3 44
4 59
5 35
6 34
skin_reflectance_right_upper_inner_arm_g2
1 31
2 32
3 40
4 63
5 30
6 36
skin_reflectance_right_upper_inner_arm_g3
1 32
2 32
3 41
4 64
5 38
6 35
skin_reflectance_right_upper_inner_arm_b1
1 29
2 29
3 39
4 54
5 32
6 31
skin_reflectance_right_upper_inner_arm_b2
1 28
2 30
3 35
4 56
5 27
6 31
skin_reflectance_right_upper_inner_arm_b3
1 30
2 30
3 36
4 58
5 35
6 32
skin_reflectance_right_upper_inner_arm_l_1
1 12.03
2 12.73
3 18.41
4 25.68
5 14.38
6 13.83
skin_reflectance_right_upper_inner_arm_l_2
1 12.27
2 12.68
3 16.64
4 26.54
5 11.90
6 14.34
skin_reflectance_right_upper_inner_arm_l_3
1 12.68
2 12.68
3 16.95
4 27.43
5 16.23
6 14.28
skin_reflectance_right_upper_inner_arma_1
1 10.72
2 11.94
3 12.36
4 14.09
5 13.87
6 13.23
skin_reflectance_right_upper_inner_arma_2
1 12.00
2 12.09
3 12.58
4 14.51
5 12.78
6 13.02
skin_reflectance_right_upper_inner_arma_3
1 12.09
2 12.09
3 11.97
4 14.54
5 13.47
6 13.17
skin_reflectance_right_upper_inner_armb_1
1 7.97
2 9.29
3 12.24
4 14.37
5 9.77
6 9.62
skin_reflectance_right_upper_inner_armb_2
1 9.18
2 8.25
3 12.04
4 15.54
5 9.15
6 10.73
skin_reflectance_right_upper_inner_armb_3
1 8.25
2 8.25
3 10.95
4 14.65
5 11.03
6 9.68
skin_reflectance_left_upper_inner_arm_e1
1 18.45
2 19.83
3 17.43
4 16.39
5 21.18
6 20.32
skin_reflectance_left_upper_inner_arm_e2
1 18.08
2 20.32
3 17.19
4 14.77
5 21.63
6 20.12
skin_reflectance_left_upper_inner_arm_e3
1 20.77
2 18.59
3 16.80
4 14.96
5 20.96
6 19.72
skin_reflectance_left_upper_inner_arm_m1
1 73.11
2 70.30
3 62.95
4 49.64
5 69.23
6 65.55
skin_reflectance_left_upper_inner_arm_m2
1 67.04
2 71.82
3 63.65
4 46.54
5 67.67
6 67.04
skin_reflectance_left_upper_inner_arm_m3
1 69.36
2 70.99
3 65.19
4 46.78
5 65.67
6 66.66
skin_reflectance_left_upper_inner_arm_r1
1 50
2 51
3 59
4 81
5 51
6 57
skin_reflectance_left_upper_inner_arm_r2
1 53
2 49
3 59
4 86
5 52
6 55
skin_reflectance_left_upper_inner_arm_r3
1 51
2 50
3 57
4 85
5 55
6 55
skin_reflectance_left_upper_inner_arm_g1
1 33
2 32
3 40
4 56
5 31
6 35
skin_reflectance_left_upper_inner_arm_g2
1 35
2 31
3 40
4 60
5 32
6 34
skin_reflectance_left_upper_inner_arm_g3
1 31
2 33
3 39
4 59
5 34
6 35
skin_reflectance_left_upper_inner_arm_b1
1 30
2 29
3 35
4 50
5 29
6 32
skin_reflectance_left_upper_inner_arm_b2
1 33
2 28
3 36
4 54
5 30
6 31
skin_reflectance_left_upper_inner_arm_b3
1 28
2 29
3 34
4 54
5 31
6 31
skin_reflectance_left_upper_inner_arm_l_1
1 13.10
2 12.82
3 16.55
4 24.07
5 12.31
6 14.38
skin_reflectance_left_upper_inner_arm_l_2
1 14.05
2 12.27
3 16.50
4 25.79
5 12.86
6 13.88
skin_reflectance_left_upper_inner_arm_l_3
1 12.36
2 12.73
3 16.55
4 24.95
5 13.56
6 13.92
skin_reflectance_left_upper_inner_arma_1
1 11.16
2 12.65
3 11.89
4 14.94
5 12.87
6 13.87
skin_reflectance_left_upper_inner_arma_2
1 11.91
2 12.00
3 12.03
4 15.52
5 13.51
6 13.08
skin_reflectance_left_upper_inner_arma_3
1 12.71
2 11.94
3 11.89
4 15.62
5 14.72
6 13.94
skin_reflectance_left_upper_inner_armb_1
1 9.28
2 9.39
3 11.96
4 14.26
5 8.28
6 9.77
skin_reflectance_left_upper_inner_armb_2
1 8.43
2 9.18
3 10.90
4 13.55
5 8.46
6 10.68
skin_reflectance_left_upper_inner_armb_3 pathcare_sticker_barcode req_num
1 9.28 785293139 785293139
2 9.29 785293140 785293140
3 11.96 785293141 785293141
4 13.45 785293142 NA
5 9.76 785293143 785293143
6 9.72 785293144 785293144
serv_date vit_d_result res_date_time collection_period
1 2013-02-11 10:40:00 29.50 2013-02-13 12:13:00 Summer
2 2013-02-11 11:00:00 17.80 2013-02-13 12:13:00 Summer
3 2013-02-11 00:00:11 25.00 2013-02-13 12:13:00 Summer
4 2013-02-12 20.83 <NA> Summer
5 2013-02-12 00:00:11 29.20 2013-02-13 14:39:00 Summer
6 2013-02-12 00:00:11 20.50 2013-02-13 12:13:00 Summer
continued_in_study if_not_continued_in_study_reason
1 <NA> <NA>
2 <NA> <NA>
3 <NA> <NA>
4 <NA> <NA>
5 <NA> <NA>
6 <NA> <NA>data_long <- pivot_longer(data,
cols = starts_with("skin_reflectance"),
names_to = "measurement",
values_to = "reflectance")data_long <- separate(data_long,
col = "measurement",
into = c("Prefix", "body_site", "reflectance_type"),
sep = "_",
extra = "drop")
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] tidyr_1.3.1
loaded via a namespace (and not attached):
[1] jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.1 promises_1.3.0
[5] tidyselect_1.2.1 Rcpp_1.0.13 stringr_1.5.1 git2r_0.33.0
[9] later_1.3.2 jquerylib_0.1.4 yaml_2.3.10 fastmap_1.2.0
[13] R6_2.5.1 generics_0.1.3 workflowr_1.7.1 knitr_1.48
[17] tibble_3.2.1 rprojroot_2.0.4 bslib_0.8.0 pillar_1.9.0
[21] rlang_1.1.4 utf8_1.2.4 cachem_1.1.0 stringi_1.8.4
[25] httpuv_1.6.15 xfun_0.47 fs_1.6.4 sass_0.4.9
[29] cli_3.6.3 withr_3.0.1 magrittr_2.0.3 digest_0.6.37
[33] rstudioapi_0.16.0 lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.0
[37] glue_1.7.0 fansi_1.0.6 rmarkdown_2.28 purrr_1.0.2
[41] tools_4.4.1 pkgconfig_2.0.3 htmltools_0.5.8.1