Missing Data
Last updated: 2021-06-11
Checks: 7 0
Knit directory: ampel-leipzig-meld/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 6541fae | Sebastian Gibb | 2021-06-11 | fix: add targets for missing/corrplot |
| Rmd | 76196cb | Sebastian Gibb | 2021-06-11 | fix: wrong plot call |
| Rmd | ecd9fde | Sebastian Gibb | 2021-06-11 | feat: plot missing values |
| Rmd | 851d2e1 | Sebastian Gibb | 2021-06-11 | feat: add missing data overview |
library("targets")
tar_load(raw_data)
.dotplot <- function(x, xlim = c(0, length(x)),
col = palette.colors(2L)[2L], pch = 19L) {
old.par <- par(no.readonly = TRUE)
on.exit(par(old.par))
n <- length(x)
mai <- par("mai")
w <- max(strwidth(names(x), "inch"), na.rm = TRUE) + 1/16
if (mai[2L] < w)
mai[2L] <- mai[4L] + w # taken from dotchart
par(mai = mai)
plot(NA, xlim = xlim, ylim = c(0L, n + 1L), axes = FALSE)
title(main = "Missing Data", adj = 0L)
title(xlab = "Frequency", adj = 1L)
y <- seq_len(n)
mtext(
names(x), at = y, adj = 0L, side = 2L, las = 2L,
line = (w + 0.1) / par("csi"), cex = 0.8
)
abline(h = y, col = "#808080", lty = "dotted", lwd = 1L)
points(x, y, col = col, pch = pch)
axis(1L, lwd.ticks = 0L, col = "#808080")
}
.image <- function(x, col = c("white", palette.colors(2L)[2L])) {
old.par <- par(no.readonly = TRUE)
on.exit(par(old.par))
nr <- nrow(x)
nc <- ncol(x)
nms <- colnames(x)
mai <- par("mai")
w <- max(strwidth(nms, "inch"), na.rm = TRUE) + 1/16
if (mai[2L] < w)
mai[2L] <- mai[4L] + w # taken from dotchart
par(mai = mai)
y <- seq_len(nc)
image(
1L:nr, y, x[, rev(y)], col = col,
xlim = 0.5 + c(0L, nr), ylim = 0.5 + c(0L, nc),
axes = FALSE, xlab = "", ylab = ""
)
title(main = "Missing Data", adj = 0L)
title(xlab = "Rows", adj = 1L)
mtext(
rev(nms), at = y, adj = 0L, side = 2L, las = 2L,
line = (w + 0.1) / par("csi"), cex = 0.75
)
abline(h = y, col = "#808080", lty = "dotted", lwd = 1L)
}Missing Data
m <- raw_data
m$Sex <- as.numeric(m$Sex)
m <- as.matrix(m)
mna <- is.na(m)
mode(mna) <- "numeric"
tbl <- colSums(mna)
na <- sort(tbl[tbl > 0L], decreasing = TRUE)
knitr::kable(
cbind(na, round(colMeans(mna[, names(na)]) * 100, 2)),
col.names = c("# Missing Data", "% of Missing Data")
)| # Missing Data | % of Missing Data | |
|---|---|---|
| BILID_S | 82 | 12.54 |
| B_MPV_E | 64 | 9.79 |
| IL6_S | 56 | 8.56 |
| VDT_OH_S | 47 | 7.19 |
| B_PLT_E | 26 | 3.98 |
| B_WBC_E | 23 | 3.52 |
| CRP_S | 14 | 2.14 |
| ALAT_S | 10 | 1.53 |
| NA_S | 9 | 1.38 |
| ASAT_S | 8 | 1.22 |
| PTH_S | 8 | 1.22 |
| AP_S | 7 | 1.07 |
| CYSC_S | 7 | 1.07 |
| ALB_S | 6 | 0.92 |
| CHE_S | 6 | 0.92 |
| GGT_S | 6 | 0.92 |
| PROT_S | 6 | 0.92 |
| PALB_S | 5 | 0.76 |
| Dialysis | 2 | 0.31 |
| INR_C | 2 | 0.31 |
| Cirrhosis | 1 | 0.15 |
| SBP | 1 | 0.15 |
| CA_S | 1 | 0.15 |
| CL_S | 1 | 0.15 |
| P_S | 1 | 0.15 |
| Version | Author | Date |
|---|---|---|
| 6541fae | Sebastian Gibb | 2021-06-11 |
| Version | Author | Date |
|---|---|---|
| 6541fae | Sebastian Gibb | 2021-06-11 |
R version 4.1.0 (2021-05-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Matrix products: default
BLAS/LAPACK: /gnu/store/bs9pl1f805ins80xaf4s3n35a0x2lyq3-openblas-0.3.9/lib/libopenblasp-r0.3.9.so
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] targets_0.4.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 highr_0.9 pillar_1.6.1 compiler_4.1.0
[5] later_1.2.0 git2r_0.28.0 workflowr_1.6.2 tools_4.1.0
[9] digest_0.6.27 evaluate_0.14 lifecycle_1.0.0 tibble_3.1.2
[13] pkgconfig_2.0.3 rlang_0.4.11 igraph_1.2.6 cli_2.5.0
[17] yaml_2.2.1 xfun_0.23 withr_2.4.2 stringr_1.4.0
[21] knitr_1.33 fs_1.5.0 vctrs_0.3.8 tidyselect_1.1.1
[25] rprojroot_2.0.2 glue_1.4.2 data.table_1.14.0 R6_2.5.0
[29] processx_3.5.2 fansi_0.5.0 rmarkdown_2.8 purrr_0.3.4
[33] callr_3.7.0 magrittr_2.0.1 whisker_0.4 promises_1.2.0.1
[37] ps_1.6.0 codetools_0.2-18 ellipsis_0.3.2 htmltools_0.5.1.1
[41] httpuv_1.6.1 utf8_1.2.1 stringi_1.6.2 crayon_1.4.1