Linecharts
Last updated: 2022-11-30
Checks: 7 0
Knit directory:
ampel-leipzig-meld/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 65d58c4 | Sebastian Gibb | 2022-07-18 | chore: rebuild site |
| 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 |
| Rmd | 0cdb21d | Sebastian Gibb | 2021-07-02 | feat: add plot MeldCategory vs mean std values |
| html | 81fcc75 | Sebastian Gibb | 2021-06-11 | chore: rebuild site |
| Rmd | 4ac1449 | Sebastian Gibb | 2021-06-11 | feat: add linecharts report |
library("targets")
tar_load(zlog_data)1 Compare Mean Zlog Values vs Status
labv <- sort(grep("_[SECQ]$", colnames(zlog_data), value = TRUE))
## divide data.frame by dead/alive
s <- split(zlog_data[labv], zlog_data$Deceased)
names(s) <- c("survived", "dead")
## calculate mean standardized lab values
s <- lapply(s, colMeans, na.rm = TRUE)
o <- order(s$dead)
## comparison plot
col <- palette.colors(2L)
## keep old graphic parameters and restore them afterwards
old.par <- par(no.readonly = TRUE)
par(mar = c(7.1, 4.1, 4.1, 2.1), cex = 0.5)
plot(
s$dead[o], type = "b", pch = 20, lwd = 2, col = col[1],
axes = FALSE, ann = FALSE
)
lines(s$survived[o], type = "b", pch = 20, lwd = 2, col = col[2])
legend(
"bottomright",
legend = c("dead", "survived"),
col = col, lwd = 2, pch = 20, bty = "n"
)
title(
main = "Mortality Status vs Mean Standardized Laboratory Values", adj = 0
)
title(xlab = "Laboratory Measurements", adj = 1L, line = 5)
title(ylab = "Mean Standardized Values", adj = 1L)
r <- range(unlist(s))
axis(
2, at = seq(from = floor(r[1]), to = ceiling(r[2])),
lwd.ticks = 0, col = "#808080"
)
axis(
1, at = seq_along(o), labels = names(s$dead[o]), las = 2,
lwd.ticks = 0L, col = "#808080"
)
par(old.par)2 Compare Mean Zlog Values vs MeldCategory
## divide data.frame by MELD
s <- split(zlog_data[labv], zlog_data$MeldCategory)
## calculate mean standardized lab values
s <- lapply(s, colMeans, na.rm = TRUE)
n <- length(s)
o <- order(s[[n]])
## comparison plot
col <- rev(palette.colors(n))
## keep old graphic parameters and restore them afterwards
old.par <- par(no.readonly = TRUE)
par(mar = c(7.1, 4.1, 4.1, 2.1), cex = 0.5)
plot(
s[[n]][o], type = "b", pch = 20, lwd = 2, col = col[n],
axes = FALSE, ann = FALSE
)
for (i in seq_len(n - 1)) {
lines(s[[i]][o], type = "b", pch = 20, lwd = 2, col = col[i])
}
legend(
"bottomright",
legend = names(s),
col = col, lwd = 2, pch = 20, bty = "n"
)
title(
main = "MELD Category vs Mean Standardized Laboratory Values", adj = 0
)
title(xlab = "Laboratory Measurements", adj = 1L, line = 5)
title(ylab = "Mean Standardized Values", adj = 1L)
r <- range(unlist(s))
axis(
2, at = seq(from = floor(r[1]), to = ceiling(r[2])),
lwd.ticks = 0, col = "#808080"
)
axis(
1, at = seq_along(o), labels = names(s[[n]][o]), las = 2,
lwd.ticks = 0L, col = "#808080"
)
abline(h = 0, col = "#808080", lty = 2)
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] 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