Last updated: 2021-06-11

Checks: 7 0

Knit directory: ampel-leipzig-meld/

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html 783c49f Sebastian Gibb 2021-06-11 chore: rebuild site
Rmd 866c61e Sebastian Gibb 2021-06-11 feat: add skimr tables

library("targets")
library("skimr")
tar_load(raw_data)
tar_load(imp_data)
tar_load(zlog_data)

Raw Data

skim(raw_data)
Data summary
Name raw_data
Number of rows 654
Number of columns 44
_______________________
Column type frequency:
factor 1
numeric 43
________________________
Group variables None

Variable type: factor

skim_variable n_missing complete_rate ordered n_unique top_counts
Sex 0 1 FALSE 2 mal: 414, fem: 240

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
Age 0 1.00 56.79 10.09 18.00 52.00 58.00 64.00 81.00 ▁▁▅▇▂
DaysAtRisk 0 1.00 265.08 258.76 1.00 38.00 191.00 383.75 1080.00 ▇▃▂▂▁
Deceased 0 1.00 0.16 0.37 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
LTx 0 1.00 0.09 0.29 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Cirrhosis 1 1.00 0.91 0.29 0.00 1.00 1.00 1.00 1.00 ▁▁▁▁▇
ALF 0 1.00 0.01 0.11 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Ethyltoxic 0 1.00 0.63 0.48 0.00 0.00 1.00 1.00 1.00 ▅▁▁▁▇
HBV 0 1.00 0.03 0.17 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
HCV 0 1.00 0.07 0.25 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
AIH 0 1.00 0.05 0.21 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
PBC 0 1.00 0.03 0.16 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
PSC 0 1.00 0.02 0.15 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
NASH 0 1.00 0.07 0.26 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Cryptogenic 0 1.00 0.10 0.31 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Dialysis 2 1.00 0.05 0.22 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
GIB 0 1.00 0.25 0.43 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
HCC 0 1.00 0.19 0.39 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
SBP 1 1.00 0.14 0.35 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
ALAT_S 10 0.98 0.66 3.17 0.08 0.22 0.33 0.48 56.03 ▇▁▁▁▁
ALB_S 6 0.99 38.54 7.56 16.10 33.50 39.25 44.62 52.40 ▁▃▆▇▅
AP_S 7 0.99 2.48 2.63 0.35 1.46 1.95 2.83 52.97 ▇▁▁▁▁
ASAT_S 8 0.99 1.23 2.54 0.27 0.55 0.77 1.16 32.69 ▇▁▁▁▁
B_MPV_E 64 0.90 11.06 1.11 8.40 10.30 11.00 11.80 14.50 ▂▇▇▃▁
B_PLT_E 26 0.96 136.51 84.99 10.00 72.75 118.00 183.00 742.00 ▇▃▁▁▁
B_WBC_E 23 0.96 7.12 3.89 1.50 4.65 6.30 8.30 30.20 ▇▅▁▁▁
BILI_S 0 1.00 59.30 107.03 2.20 12.80 24.45 50.38 1096.80 ▇▁▁▁▁
BILID_S 82 0.87 40.59 78.43 3.00 6.20 12.55 30.83 497.90 ▇▁▁▁▁
CA_S 1 1.00 2.28 0.17 1.73 2.16 2.30 2.40 2.96 ▁▅▇▂▁
CHE_S 6 0.99 72.74 40.43 4.50 39.70 67.65 102.55 191.90 ▆▇▆▃▁
CHOLG_S 0 1.00 4.41 1.82 0.88 3.34 4.40 5.31 20.53 ▇▅▁▁▁
CL_S 1 1.00 99.20 5.89 61.70 96.50 99.90 102.90 118.50 ▁▁▂▇▁
CRE_S 0 1.00 99.07 66.86 26.00 65.00 80.00 104.00 604.00 ▇▁▁▁▁
CRP_S 14 0.98 15.93 26.89 0.30 2.19 5.80 16.73 210.07 ▇▁▁▁▁
CYSC_S 7 0.99 1.58 0.87 0.61 1.07 1.32 1.79 6.72 ▇▂▁▁▁
GGT_S 6 0.99 2.87 4.21 0.15 0.85 1.64 3.15 51.07 ▇▁▁▁▁
IL6_S 56 0.91 228.80 2264.02 1.50 5.66 12.53 41.83 39474.00 ▇▁▁▁▁
INR_C 2 1.00 1.40 0.61 0.84 1.09 1.21 1.45 6.66 ▇▁▁▁▁
NA_S 9 0.99 137.28 5.29 100.80 135.20 138.10 140.40 157.90 ▁▁▂▇▁
P_S 1 1.00 1.05 0.28 0.17 0.88 1.03 1.17 2.94 ▁▇▂▁▁
PALB_S 5 0.99 0.14 0.09 0.03 0.08 0.12 0.19 0.68 ▇▃▁▁▁
PROT_S 6 0.99 69.45 9.77 29.10 64.80 70.95 76.10 91.50 ▁▁▃▇▂
PTH_S 8 0.99 5.49 8.78 0.48 2.84 3.88 5.45 180.50 ▇▁▁▁▁
VDT_OH_S 47 0.93 22.69 15.43 3.20 11.15 19.30 30.40 111.80 ▇▃▁▁▁

Raw Data (imputed)

skim(imp_data)
Data summary
Name imp_data
Number of rows 654
Number of columns 44
_______________________
Column type frequency:
factor 1
numeric 43
________________________
Group variables None

Variable type: factor

skim_variable n_missing complete_rate ordered n_unique top_counts
Sex 0 1 FALSE 2 mal: 414, fem: 240

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
Age 0 1 56.79 10.09 18.00 52.00 58.00 64.00 81.00 ▁▁▅▇▂
DaysAtRisk 0 1 265.08 258.76 1.00 38.00 191.00 383.75 1080.00 ▇▃▂▂▁
Deceased 0 1 0.16 0.37 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
LTx 0 1 0.09 0.29 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Cirrhosis 1 1 0.91 0.29 0.00 1.00 1.00 1.00 1.00 ▁▁▁▁▇
ALF 0 1 0.01 0.11 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Ethyltoxic 0 1 0.63 0.48 0.00 0.00 1.00 1.00 1.00 ▅▁▁▁▇
HBV 0 1 0.03 0.17 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
HCV 0 1 0.07 0.25 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
AIH 0 1 0.05 0.21 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
PBC 0 1 0.03 0.16 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
PSC 0 1 0.02 0.15 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
NASH 0 1 0.07 0.26 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Cryptogenic 0 1 0.10 0.31 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Dialysis 2 1 0.05 0.22 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
GIB 0 1 0.25 0.43 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
HCC 0 1 0.19 0.39 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
SBP 1 1 0.14 0.35 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
ALAT_S 0 1 0.66 3.15 0.08 0.22 0.33 0.48 56.03 ▇▁▁▁▁
ALB_S 0 1 38.58 7.54 16.10 33.50 39.40 44.58 52.40 ▁▃▆▇▅
AP_S 0 1 2.47 2.62 0.35 1.45 1.94 2.81 52.97 ▇▁▁▁▁
ASAT_S 0 1 1.22 2.53 0.27 0.54 0.76 1.15 32.69 ▇▁▁▁▁
B_MPV_E 0 1 11.06 1.06 8.40 10.40 11.01 11.70 14.50 ▂▆▇▂▁
B_PLT_E 0 1 140.00 85.04 10.00 74.00 121.50 189.00 742.00 ▇▅▁▁▁
B_WBC_E 0 1 7.07 3.83 1.50 4.70 6.30 8.17 30.20 ▇▃▁▁▁
BILI_S 0 1 59.30 107.03 2.20 12.80 24.45 50.38 1096.80 ▇▁▁▁▁
BILID_S 0 1 35.75 74.45 1.98 4.80 10.20 26.67 497.90 ▇▁▁▁▁
CA_S 0 1 2.28 0.17 1.73 2.16 2.30 2.40 2.96 ▁▅▇▂▁
CHE_S 0 1 73.30 40.68 4.50 39.90 68.05 103.35 191.90 ▆▇▆▃▁
CHOLG_S 0 1 4.41 1.82 0.88 3.34 4.40 5.31 20.53 ▇▅▁▁▁
CL_S 0 1 99.20 5.88 61.70 96.50 99.95 102.90 118.50 ▁▁▂▇▁
CRE_S 0 1 99.07 66.86 26.00 65.00 80.00 104.00 604.00 ▇▁▁▁▁
CRP_S 0 1 15.63 26.68 0.30 2.10 5.59 16.27 210.07 ▇▁▁▁▁
CYSC_S 0 1 1.57 0.87 0.61 1.06 1.30 1.77 6.72 ▇▂▁▁▁
GGT_S 0 1 2.85 4.20 0.15 0.83 1.62 3.08 51.07 ▇▁▁▁▁
IL6_S 0 1 209.44 2165.69 1.50 4.42 10.57 37.42 39474.00 ▇▁▁▁▁
INR_C 0 1 1.40 0.61 0.84 1.09 1.21 1.45 6.66 ▇▁▁▁▁
NA_S 0 1 137.32 5.26 100.80 135.20 138.20 140.40 157.90 ▁▁▂▇▁
P_S 0 1 1.05 0.28 0.17 0.88 1.03 1.17 2.94 ▁▇▂▁▁
PALB_S 0 1 0.14 0.09 0.03 0.08 0.12 0.19 0.68 ▇▃▁▁▁
PROT_S 0 1 69.48 9.73 29.10 64.90 71.00 75.97 91.50 ▁▁▃▇▂
PTH_S 0 1 5.46 8.73 0.48 2.85 3.87 5.38 180.50 ▇▁▁▁▁
VDT_OH_S 0 1 22.20 14.98 3.20 11.65 18.05 29.37 111.80 ▇▃▁▁▁

Zlog Data

skim(zlog_data)
Data summary
Name zlog_data
Number of rows 654
Number of columns 44
_______________________
Column type frequency:
factor 1
numeric 43
________________________
Group variables None

Variable type: factor

skim_variable n_missing complete_rate ordered n_unique top_counts
Sex 0 1 FALSE 2 mal: 414, fem: 240

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
Age 0 1 56.79 10.09 18.00 52.00 58.00 64.00 81.00 ▁▁▅▇▂
DaysAtRisk 0 1 265.08 258.76 1.00 38.00 191.00 383.75 1080.00 ▇▃▂▂▁
Deceased 0 1 0.16 0.37 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
LTx 0 1 0.09 0.29 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Cirrhosis 1 1 0.91 0.29 0.00 1.00 1.00 1.00 1.00 ▁▁▁▁▇
ALF 0 1 0.01 0.11 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Ethyltoxic 0 1 0.63 0.48 0.00 0.00 1.00 1.00 1.00 ▅▁▁▁▇
HBV 0 1 0.03 0.17 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
HCV 0 1 0.07 0.25 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
AIH 0 1 0.05 0.21 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
PBC 0 1 0.03 0.16 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
PSC 0 1 0.02 0.15 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
NASH 0 1 0.07 0.26 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Cryptogenic 0 1 0.10 0.31 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
Dialysis 2 1 0.05 0.22 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
GIB 0 1 0.25 0.43 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
HCC 0 1 0.19 0.39 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▂
SBP 1 1 0.14 0.35 0.00 0.00 0.00 0.00 1.00 ▇▁▁▁▁
ALAT_S 0 1 0.04 2.02 -4.37 -1.22 -0.15 0.93 16.55 ▇▇▁▁▁
ALB_S 0 1 -1.21 2.13 -9.65 -2.39 -0.79 0.43 2.04 ▁▁▃▇▇
AP_S 0 1 2.07 1.89 -3.76 0.84 1.85 3.09 14.15 ▁▇▂▁▁
ASAT_S 0 1 2.33 1.79 -0.83 1.15 1.96 3.08 14.39 ▇▅▁▁▁
B_MPV_E 0 1 -0.01 1.18 -3.35 -0.71 0.00 0.75 3.41 ▁▃▇▃▁
B_PLT_E 0 1 -2.74 2.68 -12.91 -4.61 -2.55 -0.71 4.96 ▁▂▇▇▁
B_WBC_E 0 1 0.29 1.75 -5.19 -0.84 0.28 1.27 6.24 ▁▅▇▂▁
BILI_S 0 1 2.98 2.29 -2.28 1.36 2.70 4.19 10.56 ▂▇▆▂▁
BILID_S 0 1 3.82 2.75 0.00 1.83 3.39 5.38 11.43 ▇▇▅▂▁
CA_S 0 1 -0.76 2.05 -8.19 -1.96 -0.44 0.68 6.35 ▁▃▇▅▁
CHE_S 0 1 -3.67 3.07 -15.22 -5.47 -3.10 -1.28 1.74 ▁▂▃▇▆
CHOLG_S 0 1 1.43 0.94 -1.71 1.05 1.62 2.00 4.80 ▁▂▇▂▁
CL_S 0 1 -1.33 2.64 -22.60 -2.28 -0.84 0.25 6.51 ▁▁▁▇▂
CRE_S 0 1 1.32 2.96 -7.11 -0.49 0.72 2.39 14.13 ▁▇▅▁▁
CRP_S 0 1 2.36 2.88 -3.85 0.17 2.19 4.40 9.68 ▂▇▇▅▂
CYSC_S 0 1 5.48 3.81 -1.96 2.93 4.74 7.45 19.27 ▃▇▃▁▁
GGT_S 0 1 3.03 1.96 -2.21 1.60 2.92 4.21 9.53 ▁▆▇▂▁
IL6_S 0 1 3.56 3.37 -1.22 1.01 2.81 5.42 19.81 ▇▅▂▁▁
INR_C 0 1 2.88 2.97 -1.49 1.03 2.04 3.79 18.53 ▇▅▁▁▁
NA_S 0 1 -1.07 2.19 -17.99 -1.88 -0.67 0.19 6.64 ▁▁▁▇▁
P_S 0 1 -0.65 2.02 -13.43 -1.63 -0.50 0.42 7.04 ▁▁▅▇▁
PALB_S 0 1 -4.79 3.41 -12.69 -7.14 -4.85 -2.25 4.96 ▂▇▇▅▁
PROT_S 0 1 -0.89 2.34 -13.84 -1.75 -0.39 0.63 3.43 ▁▁▂▇▇
PTH_S 0 1 0.58 1.68 -5.19 -0.41 0.41 1.29 10.71 ▁▇▃▁▁
VDT_OH_S 1 1 0.25 1.27 -3.15 -0.54 0.31 1.14 3.70 ▂▃▇▅▁

sessionInfo()
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] skimr_2.1.3   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   base64enc_0.1-3  
 [9] tools_4.1.0       digest_0.6.27     jsonlite_1.7.2    evaluate_0.14    
[13] lifecycle_1.0.0   tibble_3.1.2      pkgconfig_2.0.3   rlang_0.4.11     
[17] igraph_1.2.6      cli_2.5.0         yaml_2.2.1        xfun_0.23        
[21] repr_1.1.3        dplyr_1.0.6       withr_2.4.2       stringr_1.4.0    
[25] knitr_1.33        generics_0.1.0    fs_1.5.0          vctrs_0.3.8      
[29] tidyselect_1.1.1  rprojroot_2.0.2   glue_1.4.2        data.table_1.14.0
[33] R6_2.5.0          processx_3.5.2    fansi_0.5.0       rmarkdown_2.8    
[37] tidyr_1.1.3       purrr_0.3.4       callr_3.7.0       magrittr_2.0.1   
[41] whisker_0.4       promises_1.2.0.1  ps_1.6.0          codetools_0.2-18 
[45] ellipsis_0.3.2    htmltools_0.5.1.1 httpuv_1.6.1      utf8_1.2.1       
[49] stringi_1.6.2     crayon_1.4.1