Last updated: 2022-06-15

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Knit directory: ampel-leipzig-meld/

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File Version Author Date Message
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
Rmd d38da01 Sebastian Gibb 2022-03-17 feat: list correlations in table
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 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
html aac7ea8 Sebastian Gibb 2021-06-11 chore: rebuild site
Rmd ba5de74 Sebastian Gibb 2021-06-11 fix: suppress package startup messages
html 6541fae Sebastian Gibb 2021-06-11 fix: add targets for missing/corrplot
Rmd 5d77d52 Sebastian Gibb 2021-06-11 fix: use imputed data for correlation
Rmd 3e38f5a Sebastian Gibb 2021-06-11 feat: add correlation plot 
library("corrplot")
library("targets")
tar_load(imp_data)

1 Correlation

1.1 Plot

labv <- grep("_[SECQ]$", colnames(imp_data), value = TRUE)
cr <- cor(imp_data[labv], use = "pairwise.complete.obs")
corrplot.mixed(
    cr,
    tl.pos = "lt", tl.col = "black", tl.cex = 0.75,
    number.cex = 0.25, number.font = 1L,
    order = "AOE"
)

Version Author Date
3810a79 Sebastian Gibb 2021-07-15
6541fae Sebastian Gibb 2021-06-11

1.2 Table

ut <- upper.tri(cr)
nms <- paste(
    colnames(cr)[col(cr)[ut]],
    rownames(cr)[row(cr)[ut]],
    sep = ":"
)
tbl <- data.frame(Values = nms, Correlation = cr[ut])
tbl <- tbl[order(-abs(tbl$Correlation)),]
knitr::kable(tbl, header = TRUE, row.names = FALSE, digits = 3L)
Values Correlation
CYSC_S:CRE_S 0.813
NA_S:CL_S 0.772
CA_S:ALB_S 0.734
CHE_S:ALB_S 0.730
PALB_S:CHE_S 0.670
CHE_S:CA_S 0.650
INR_C:BILI_S 0.613
PALB_S:ALB_S 0.592
PROT_S:ALB_S 0.565
PROT_S:CA_S 0.540
GGT_S:AP_S 0.534
PALB_S:CA_S 0.514
PROT_S:BILI_S -0.504
PTH_S:CRE_S 0.479
PROT_S:INR_C -0.475
PALB_S:CHOLG_S 0.470
CHOLG_S:CHE_S 0.467
PTH_S:CYSC_S 0.458
INR_C:ALB_S -0.445
PROT_S:CHE_S 0.442
INR_C:CHE_S -0.439
CRP_S:ALB_S -0.434
NA_S:CHE_S 0.427
INR_C:CHOLG_S -0.422
PALB_S:B_PLT_E 0.411
CHOLG_S:CA_S 0.408
CYSC_S:CHE_S -0.404
BILI_S:ASAT_S 0.394
PROT_S:CHOLG_S 0.393
P_S:CRE_S 0.389
CYSC_S:ALB_S -0.384
NA_S:ALB_S 0.383
BILI_S:ALB_S -0.375
PROT_S:CRP_S -0.374
CRP_S:CA_S -0.373
CRP_S:CHE_S -0.364
CYSC_S:CRP_S 0.362
BILI_S:B_WBC_E 0.359
CHE_S:BILI_S -0.356
PROT_S:CYSC_S -0.349
CHOLG_S:ALB_S 0.347
INR_C:CA_S -0.337
NA_S:CA_S 0.332
CRP_S:B_WBC_E 0.331
P_S:CYSC_S 0.330
CYSC_S:BILI_S 0.330
INR_C:ASAT_S 0.329
PALB_S:INR_C -0.329
CHOLG_S:BILI_S -0.327
CHOLG_S:B_PLT_E 0.323
CHE_S:B_PLT_E 0.312
CRP_S:BILI_S 0.308
CA_S:BILI_S -0.306
PALB_S:CRP_S -0.295
B_WBC_E:ASAT_S 0.293
PTH_S:PROT_S -0.292
PROT_S:B_WBC_E -0.286
CYSC_S:B_WBC_E 0.282
B_PLT_E:ALB_S 0.280
CA_S:B_PLT_E 0.278
INR_C:CYSC_S 0.278
VDT_OH_S:CA_S 0.276
VDT_OH_S:CHE_S 0.272
B_PLT_E:B_MPV_E -0.271
CRP_S:CHOLG_S -0.270
P_S:B_WBC_E 0.269
GGT_S:CHOLG_S 0.262
INR_C:B_WBC_E 0.262
PROT_S:PALB_S 0.261
NA_S:B_WBC_E -0.261
CL_S:B_WBC_E -0.259
CYSC_S:CHOLG_S -0.259
VDT_OH_S:ALB_S 0.255
INR_C:CRP_S 0.252
B_WBC_E:B_PLT_E 0.251
VDT_OH_S:PALB_S 0.250
CRE_S:B_WBC_E 0.246
CRP_S:CRE_S 0.246
PROT_S:CRE_S -0.245
PROT_S:ASAT_S -0.245
ASAT_S:ALB_S -0.245
CYSC_S:CA_S -0.243
INR_C:B_PLT_E -0.242
CRE_S:ALB_S -0.241
CRE_S:CHE_S -0.239
P_S:B_PLT_E 0.238
PALB_S:BILI_S -0.237
ASAT_S:ALAT_S 0.233
PALB_S:NA_S 0.231
PTH_S:CA_S -0.218
AP_S:ALB_S -0.215
NA_S:INR_C -0.214
GGT_S:B_PLT_E 0.213
VDT_OH_S:INR_C -0.210
B_WBC_E:ALB_S -0.210
PROT_S:B_PLT_E 0.208
VDT_OH_S:CRP_S -0.208
VDT_OH_S:PROT_S 0.207
VDT_OH_S:CYSC_S -0.206
CL_S:CHE_S 0.205
NA_S:BILI_S -0.205
NA_S:CHOLG_S 0.205
CL_S:B_MPV_E 0.202
CRP_S:AP_S 0.199
VDT_OH_S:CHOLG_S 0.199
CRE_S:CA_S -0.195
NA_S:CYSC_S -0.189
VDT_OH_S:BILI_S -0.189
CRE_S:CHOLG_S -0.186
NA_S:CRE_S -0.182
IL6_S:CRP_S 0.179
PTH_S:BILI_S 0.179
BILI_S:B_PLT_E -0.176
VDT_OH_S:PTH_S -0.176
NA_S:CRP_S -0.175
CRP_S:ALAT_S 0.175
P_S:CL_S -0.173
NA_S:B_MPV_E 0.171
INR_C:IL6_S 0.169
P_S:NA_S -0.167
CHE_S:AP_S -0.165
PTH_S:CHOLG_S -0.164
VDT_OH_S:NA_S 0.164
PTH_S:B_WBC_E 0.161
PALB_S:CYSC_S -0.159
CYSC_S:AP_S 0.158
CRP_S:ASAT_S 0.157
PROT_S:IL6_S -0.156
VDT_OH_S:B_WBC_E -0.154
IL6_S:BILI_S 0.149
PTH_S:ALB_S -0.145
CYSC_S:ASAT_S 0.142
CL_S:ALB_S 0.140
BILI_S:AP_S 0.132
CA_S:B_WBC_E -0.132
CHE_S:ASAT_S -0.130
PROT_S:NA_S 0.129
CHOLG_S:ASAT_S -0.128
IL6_S:ALB_S -0.128
B_PLT_E:AP_S 0.128
IL6_S:CHOLG_S -0.127
PTH_S:CHE_S -0.126
PROT_S:ALAT_S -0.126
CL_S:BILI_S -0.125
IL6_S:CYSC_S 0.125
PALB_S:ASAT_S -0.122
PALB_S:GGT_S 0.121
GGT_S:CRP_S 0.121
CA_S:AP_S -0.120
CA_S:ASAT_S -0.117
PTH_S:P_S 0.116
CRE_S:BILI_S 0.115
CL_S:B_PLT_E -0.112
ASAT_S:AP_S 0.111
CRP_S:CL_S -0.110
NA_S:AP_S -0.109
PALB_S:P_S 0.109
PTH_S:INR_C 0.108
PTH_S:CRP_S 0.105
CHOLG_S:AP_S 0.105
CL_S:CA_S 0.101
CHE_S:B_WBC_E -0.101
INR_C:CRE_S 0.099
IL6_S:CRE_S 0.099
BILI_S:ALAT_S 0.095
VDT_OH_S:CRE_S -0.094
VDT_OH_S:AP_S -0.094
INR_C:GGT_S -0.093
CRE_S:CL_S -0.092
IL6_S:CHE_S -0.091
CHOLG_S:B_WBC_E -0.090
PROT_S:AP_S -0.088
PALB_S:B_MPV_E -0.084
CYSC_S:CL_S -0.083
PALB_S:IL6_S -0.082
IL6_S:B_PLT_E -0.081
VDT_OH_S:CL_S 0.080
P_S:ASAT_S 0.079
INR_C:CL_S -0.078
PTH_S:ASAT_S 0.078
VDT_OH_S:ASAT_S -0.075
CRE_S:ASAT_S 0.075
ALB_S:ALAT_S -0.074
VDT_OH_S:B_MPV_E 0.072
PALB_S:CL_S 0.072
P_S:AP_S 0.072
CYSC_S:B_PLT_E -0.071
P_S:INR_C -0.070
PROT_S:GGT_S 0.068
IL6_S:B_MPV_E 0.067
B_PLT_E:ASAT_S -0.067
PALB_S:AP_S -0.067
IL6_S:ASAT_S 0.065
P_S:CRP_S 0.063
GGT_S:B_WBC_E 0.061
CL_S:AP_S -0.060
PROT_S:CL_S -0.060
IL6_S:CL_S 0.059
IL6_S:CA_S -0.058
B_MPV_E:ASAT_S 0.057
VDT_OH_S:IL6_S -0.047
PROT_S:B_MPV_E -0.047
CHOLG_S:B_MPV_E -0.046
VDT_OH_S:GGT_S -0.046
INR_C:ALAT_S 0.044
NA_S:ASAT_S -0.044
CL_S:ASAT_S -0.044
B_WBC_E:ALAT_S 0.043
PTH_S:B_MPV_E -0.043
B_WBC_E:AP_S 0.043
B_PLT_E:ALAT_S 0.042
INR_C:AP_S 0.039
GGT_S:ASAT_S 0.039
CRP_S:B_PLT_E -0.038
CA_S:ALAT_S -0.038
CA_S:B_MPV_E 0.038
IL6_S:GGT_S -0.038
BILI_S:B_MPV_E 0.038
CRE_S:B_PLT_E -0.036
CRE_S:ALAT_S 0.035
CYSC_S:B_MPV_E 0.034
GGT_S:CRE_S -0.034
GGT_S:ALAT_S 0.033
NA_S:IL6_S 0.032
P_S:CHOLG_S 0.031
GGT_S:CHE_S 0.030
VDT_OH_S:P_S -0.030
P_S:ALAT_S 0.029
IL6_S:ALAT_S 0.028
PALB_S:ALAT_S 0.028
B_MPV_E:ALAT_S 0.028
PALB_S:B_WBC_E 0.027
PTH_S:NA_S -0.027
CHE_S:B_MPV_E 0.026
PTH_S:PALB_S 0.026
B_WBC_E:B_MPV_E -0.026
P_S:CA_S 0.026
CL_S:CHOLG_S 0.025
IL6_S:AP_S -0.025
GGT_S:CL_S -0.024
P_S:B_MPV_E -0.024
PTH_S:B_PLT_E -0.023
B_MPV_E:ALB_S -0.022
PTH_S:CL_S -0.021
PALB_S:CRE_S -0.021
AP_S:ALAT_S 0.019
NA_S:B_PLT_E 0.019
CHOLG_S:ALAT_S -0.019
P_S:CHE_S -0.018
VDT_OH_S:B_PLT_E -0.018
VDT_OH_S:ALAT_S -0.017
CRE_S:B_MPV_E 0.016
NA_S:GGT_S -0.016
P_S:GGT_S 0.015
PTH_S:ALAT_S 0.013
GGT_S:BILI_S -0.012
CL_S:ALAT_S 0.012
NA_S:ALAT_S 0.012
CRP_S:B_MPV_E 0.012
P_S:IL6_S -0.011
IL6_S:B_WBC_E 0.010
CRE_S:AP_S -0.010
PROT_S:P_S 0.008
PTH_S:GGT_S 0.007
GGT_S:ALB_S -0.007
PTH_S:AP_S 0.006
P_S:ALB_S -0.006
B_MPV_E:AP_S 0.005
GGT_S:CA_S 0.005
GGT_S:CYSC_S 0.004
PTH_S:IL6_S -0.004
CYSC_S:ALAT_S -0.004
GGT_S:B_MPV_E -0.003
INR_C:B_MPV_E 0.003
CHE_S:ALAT_S 0.002
P_S:BILI_S 0.001 

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 corrplot_0.92 

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