Boxplots
Last updated: 2022-07-18
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Knit directory:
ampel-leipzig-meld/
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| 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()")
}
1.1.4 ASAT_S
1.1.5 B_MPV_E
1.1.6 B_PLT_E
1.1.7 B_WBC_E
1.1.8 BILI_S
1.1.9 BILID_S
1.1.10 CA_S
1.1.11 CHE_S
1.1.12 CHOLG_S
1.1.13 CL_S
1.1.14 CRE_S
1.1.15 CRP_S
1.1.16 CYSC_S
1.1.17 GGT_S
1.1.18 IL6_S
1.1.19 INR_C
1.1.20 NA_S
1.1.21 P_S
1.1.22 PALB_S
1.1.23 PROT_S
1.1.24 PTH_S
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
1.2.4 ASAT_S
1.2.5 B_MPV_E
1.2.6 B_PLT_E
1.2.7 B_WBC_E
1.2.8 BILI_S
1.2.9 BILID_S
1.2.10 CA_S
1.2.11 CHE_S
1.2.12 CHOLG_S
1.2.13 CL_S
1.2.14 CRE_S
1.2.15 CRP_S
1.2.16 CYSC_S
1.2.17 GGT_S
1.2.18 IL6_S
1.2.19 INR_C
1.2.20 NA_S
1.2.21 P_S
1.2.22 PALB_S
1.2.23 PROT_S
1.2.24 PTH_S
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
1.3.4 ASAT_S
1.3.5 B_MPV_E
1.3.6 B_PLT_E
1.3.7 B_WBC_E
1.3.8 BILI_S
1.3.9 BILID_S
1.3.10 CA_S
1.3.11 CHE_S
1.3.12 CHOLG_S
1.3.13 CL_S
1.3.14 CRE_S
1.3.15 CRP_S
1.3.16 CYSC_S
1.3.17 GGT_S
1.3.18 IL6_S
1.3.19 INR_C
1.3.20 NA_S
1.3.21 P_S
1.3.22 PALB_S
1.3.23 PROT_S
1.3.24 PTH_S
1.3.25 VDT_OH_S
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