Last updated: 2022-07-18

Checks: 7 0

Knit directory: ampel-leipzig-meld/

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    Ignored:    TODO
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/boxplots.Rmd) and HTML (docs/boxplots.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html fb43d01 Sebastian Gibb 2022-06-19 chore: rebuild site
html ebe29cf Sebastian Gibb 2022-06-16 chore: rebuild site
html 8035219 Sebastian Gibb 2022-06-15 chore: rebuild site
html d3e9462 Sebastian Gibb 2022-06-06 chore: rebuild site
html b20484a Sebastian Gibb 2022-06-06 chore: rebuild site
html 983ec69 Sebastian Gibb 2022-03-17 chore: rebuild site
html 373e7d8 Sebastian Gibb 2021-10-20 chore: rebuild site
html df8964f Sebastian Gibb 2021-10-15 chore: rebuild site
html c66640c Sebastian Gibb 2021-09-14 feat: first nnet tests
html afa48d9 Sebastian Gibb 2021-08-07 chore: rebuild site
Rmd 4478f6a Sebastian Gibb 2021-08-02 Revert "fix: working directory for targets"
Rmd cac14f6 Sebastian Gibb 2021-08-02 fix: working directory for targets
Rmd 3957af7 Sebastian Gibb 2021-08-02 refactor: move common yaml headers into _site.yml
html 3aab3e1 Sebastian Gibb 2021-08-01 chore: rebuild site
html 3810a79 Sebastian Gibb 2021-07-15 chore: rebuild site
html 13b68ca Sebastian Gibb 2021-07-04 chore: rebuild site
html 2869556 Sebastian Gibb 2021-07-02 chore: rebuild site
html d9c37ec Sebastian Gibb 2021-07-02 chore: rebuild site
html 81fcc75 Sebastian Gibb 2021-06-11 chore: rebuild site
html 783c49f Sebastian Gibb 2021-06-11 chore: rebuild site
Rmd 5ba50b5 Sebastian Gibb 2021-06-11 refactor: move boxplots in separate report

library("targets")
library("beeswarm")
library("viridisLite")
tar_load(imp_data)
tar_load(zlog_data)

.bp <- function(x, formula, col = cividis(ncol(x)), main = NULL,
                outline = FALSE) {
    boxplot(
        formula, data = x, col = gsub("..$", "40", col),
        pch = NA, outline = outline,
        main = main
    )
    beeswarm(formula, data = x, col = col, add = TRUE, pch = 19L)
}

1 Raw vs Zlog Data

1.1 Compare Sexes

old.par <- par(no.readonly = TRUE)
par(mfrow = c(1L, 2L))
log_data <- imp_data
labv <- sort(grep("_[SECQ]$", colnames(imp_data), value = TRUE))
log_data[labv] <- lapply(log_data[labv], log)
col <- cividis(2L)
for (v in labv) {
    cat('\n\n### ', v, '\n\n')
    fm <- as.formula(paste0(v, " ~ Sex"))
    .bp(log_data, fm, col = col, main = "log()")
    .bp(zlog_data, fm, col = col, main = "zlog()")
}

1.1.1 ALAT_S

Version Author Date
783c49f Sebastian Gibb 2021-06-11

1.1.2 ALB_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.3 AP_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.4 ASAT_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.5 B_MPV_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.6 B_PLT_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.7 B_WBC_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.8 BILI_S

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.9 BILID_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.10 CA_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.11 CHE_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.12 CHOLG_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.13 CL_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.14 CRE_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.15 CRP_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.16 CYSC_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.17 GGT_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.18 IL6_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.19 INR_C

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.20 NA_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
783c49f Sebastian Gibb 2021-06-11

1.1.21 P_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.22 PALB_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.23 PROT_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.24 PTH_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.1.25 VDT_OH_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11
par(old.par)

1.2 Compare Status

old.par <- par(no.readonly = TRUE)
par(mfrow = c(1L, 2L))
for (v in labv) {
    cat('\n\n### ', v, '\n\n')
    fm <- as.formula(paste0(v, " ~ Deceased"))
    .bp(log_data, fm, col = col, main = "log()")
    .bp(zlog_data, fm, col = col, main = "zlog()")
}

1.2.1 ALAT_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.2 ALB_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.3 AP_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.4 ASAT_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.5 B_MPV_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.6 B_PLT_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.7 B_WBC_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.8 BILI_S

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.9 BILID_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.10 CA_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.11 CHE_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.12 CHOLG_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.13 CL_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.14 CRE_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.15 CRP_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.16 CYSC_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.17 GGT_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.18 IL6_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.19 INR_C

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.20 NA_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.21 P_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.22 PALB_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.23 PROT_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.24 PTH_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.2.25 VDT_OH_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11
par(old.par)

1.3 Compare Sexes : Status

old.par <- par(no.readonly = TRUE)
par(mfrow = c(1L, 2L))
col <- cividis(4L)
for (v in labv) {
    cat('\n\n### ', v, '\n\n')
    fm <- as.formula(paste0(v, " ~ Sex + Deceased"))
    .bp(log_data, fm, col = col, main = "log()")
    .bp(zlog_data, fm, col = col, main = "zlog()")
}

1.3.1 ALAT_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.2 ALB_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.3 AP_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.4 ASAT_S

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.5 B_MPV_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.6 B_PLT_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.7 B_WBC_E

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.8 BILI_S

Version Author Date
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.9 BILID_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.10 CA_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.11 CHE_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.12 CHOLG_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.13 CL_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.14 CRE_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.15 CRP_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.16 CYSC_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.17 GGT_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.18 IL6_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.19 INR_C

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.20 NA_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.21 P_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.22 PALB_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.23 PROT_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.24 PTH_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11

1.3.25 VDT_OH_S

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
3810a79 Sebastian Gibb 2021-07-15
783c49f Sebastian Gibb 2021-06-11
par(old.par)

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

Matrix products: default
BLAS/LAPACK: /gnu/store/ras6dprsw3wm3swk23jjp8ww5dwxj333-openblas-0.3.18/lib/libopenblasp-r0.3.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] viridisLite_0.4.0 beeswarm_0.4.0    targets_0.12.1   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3      highr_0.9         pillar_1.7.0      compiler_4.2.0   
 [5] bslib_0.3.1       later_1.3.0       jquerylib_0.1.4   git2r_0.30.1     
 [9] workflowr_1.7.0   tools_4.2.0       digest_0.6.29     jsonlite_1.8.0   
[13] evaluate_0.15     lifecycle_1.0.1   tibble_3.1.7      pkgconfig_2.0.3  
[17] rlang_1.0.2       igraph_1.3.1      cli_3.3.0         yaml_2.3.5       
[21] xfun_0.31         fastmap_1.1.0     withr_2.5.0       stringr_1.4.0    
[25] knitr_1.39        fs_1.5.2          vctrs_0.4.1       sass_0.4.1       
[29] tidyselect_1.1.2  rprojroot_2.0.3   data.table_1.14.2 glue_1.6.2       
[33] R6_2.5.1          processx_3.5.3    fansi_1.0.3       base64url_1.4    
[37] rmarkdown_2.14    bookdown_0.26     purrr_0.3.4       callr_3.7.0      
[41] magrittr_2.0.3    whisker_0.4       codetools_0.2-18  ps_1.7.0         
[45] backports_1.4.1   promises_1.2.0.1  ellipsis_0.3.2    htmltools_0.5.2  
[49] httpuv_1.6.5      utf8_1.2.2        stringi_1.7.6     crayon_1.5.1