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
Rmd baac1e4 Sebastian Gibb 2022-06-06 fix: bootstraping elastic net
html 983ec69 Sebastian Gibb 2022-03-17 chore: rebuild site
Rmd 057f935 Sebastian Gibb 2022-03-17 feat: add elastic net bootstrap and timeROC evaluations
Rmd d586eff Sebastian Gibb 2022-02-10 feat: add benchmark table and plots
html 373e7d8 Sebastian Gibb 2021-10-20 chore: rebuild site
html df8964f Sebastian Gibb 2021-10-15 chore: rebuild site
Rmd 0ac3045 Sebastian Gibb 2021-10-15 refactor: reset figure width
Rmd 173a1ca Sebastian Gibb 2021-10-14 refactor: increase figure width
Rmd 1e08cb2 Sebastian Gibb 2021-09-21 fix: load bmrk_aggr and set p.value
Rmd 939fcae Sebastian Gibb 2021-09-20 feat: add benchmark comparison across datasets
Rmd c66640c Sebastian Gibb 2021-09-14 feat: first nnet tests
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
Rmd 1dc8b12 Sebastian Gibb 2021-07-14 feat: add mlr benchmarks

library("targets")
library("data.table")
library("mlr3")
library("mlr3misc")
library("mlr3proba")
library("mlr3viz")
library("viridis")
library("ggplot2")
tar_load(bmrk_results)
tar_load(bmrk_aggr)

agg <- bmrk_results$aggregate(msr("surv.cindex", id = "harrell"))
agg[, `:=`
    (nr = NULL, resample_result = NULL, resampling_id = NULL, iters = NULL)
]
setorder(agg, task_id, -harrell)
p.value <- 0.05

1 Overview

1.1 Table

lapply(split(agg, agg$task_id), knitr::kable, digits = 4)

$ln_eldd

task_id learner_id harrell
ln_eldd scale.svmregression.tuned 0.9210
ln_eldd scale.ridge.tuned 0.9208
ln_eldd scale.elasticnet.tuned 0.9188
ln_eldd scale.penridge.tuned 0.9178
ln_eldd scale.penlasso.tuned 0.9159
ln_eldd penridge.tuned 0.9152
ln_eldd ridge.tuned 0.9145
ln_eldd scale.ranger.tuned 0.9110
ln_eldd ranger.tuned 0.9104
ln_eldd scale.surv.rfsrc.tuned 0.9077
ln_eldd elasticnet.tuned 0.9052
ln_eldd surv.rfsrc.tuned 0.9046
ln_eldd penlasso.tuned 0.8991
ln_eldd scale.lasso.tuned 0.8677
ln_eldd lasso.tuned 0.8616
ln_eldd scale.cox 0.8580
ln_eldd cox 0.8578
ln_eldd scale.surv.xgboost.tuned 0.8413
ln_eldd scale.deepsurv.tuned 0.8399
ln_eldd surv.xgboost.tuned 0.8357
ln_eldd scale.coxtime.tuned 0.8346
ln_eldd scale.svmvanbelle1.tuned 0.8231
ln_eldd svmvanbelle1.tuned 0.7927
ln_eldd coxtime.tuned 0.7720
ln_eldd deepsurv.tuned 0.7438
ln_eldd svmregression.tuned 0.5695

$zlog_eldd

task_id learner_id harrell
zlog_eldd scale.ridge.tuned 0.9213
zlog_eldd scale.svmregression.tuned 0.9191
zlog_eldd scale.penridge.tuned 0.9172
zlog_eldd scale.elasticnet.tuned 0.9168
zlog_eldd ridge.tuned 0.9148
zlog_eldd scale.ranger.tuned 0.9141
zlog_eldd scale.penlasso.tuned 0.9134
zlog_eldd elasticnet.tuned 0.9134
zlog_eldd ranger.tuned 0.9126
zlog_eldd penlasso.tuned 0.9112
zlog_eldd penridge.tuned 0.9091
zlog_eldd lasso.tuned 0.9087
zlog_eldd scale.surv.rfsrc.tuned 0.9079
zlog_eldd surv.rfsrc.tuned 0.9060
zlog_eldd scale.cox 0.8754
zlog_eldd cox 0.8715
zlog_eldd scale.lasso.tuned 0.8412
zlog_eldd deepsurv.tuned 0.8333
zlog_eldd scale.surv.xgboost.tuned 0.8317
zlog_eldd scale.coxtime.tuned 0.8308
zlog_eldd surv.xgboost.tuned 0.8279
zlog_eldd scale.svmvanbelle1.tuned 0.8254
zlog_eldd svmvanbelle1.tuned 0.8233
zlog_eldd coxtime.tuned 0.8185
zlog_eldd scale.deepsurv.tuned 0.8169
zlog_eldd svmregression.tuned 0.8091

1.2 Boxplots

m <- agg[, max(harrell), by = task_id]
autoplot(bmrk_results) +
    geom_boxplot(aes(fill = learner_id)) +
    geom_jitter(position = position_jitter(0.2)) +
    scale_fill_viridis(discrete = TRUE) +
    geom_hline(
        aes(yintercept = V1), linetype = "dashed", color = "red", data = m
    )

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
983ec69 Sebastian Gibb 2022-03-17
373e7d8 Sebastian Gibb 2021-10-20
df8964f Sebastian Gibb 2021-10-15
c66640c Sebastian Gibb 2021-09-14
afa48d9 Sebastian Gibb 2021-08-07
3810a79 Sebastian Gibb 2021-07-15
autoplot(
    bmrk_results,
    measure = msr("surv.cindex", id = "uno", weight_meth = "G2")) +
    geom_boxplot(aes(fill = learner_id)) +
    geom_jitter(position = position_jitter(0.2)) +
    scale_fill_viridis(discrete = TRUE)
Warning: Removed 135 rows containing non-finite values (stat_boxplot).
Removed 135 rows containing non-finite values (stat_boxplot).
Warning: Removed 135 rows containing missing values (geom_point).

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
983ec69 Sebastian Gibb 2022-03-17

2 Aggregated performance

Aggregated performance across all 2 datasets.

autoplot(bmrk_aggr, type = "box", meas = "harrell") +
    geom_boxplot(aes(fill = learner_id)) +
    geom_jitter(position = position_jitter(0.2)) +
    scale_fill_viridis(discrete = TRUE)

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
983ec69 Sebastian Gibb 2022-03-17
373e7d8 Sebastian Gibb 2021-10-20
df8964f Sebastian Gibb 2021-10-15
autoplot(bmrk_aggr, type = "box", meas = "uno") +
    geom_boxplot(aes(fill = learner_id)) +
    geom_jitter(position = position_jitter(0.2)) +
    scale_fill_viridis(discrete = TRUE)
Warning: Removed 49 rows containing non-finite values (stat_boxplot).
Removed 49 rows containing non-finite values (stat_boxplot).
Warning: Removed 49 rows containing missing values (geom_point).

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
983ec69 Sebastian Gibb 2022-03-17

3 Pairwise comparison

p-value is set to 0.05 (otherwise an error is thrown because of insignificant results).

autoplot(
    bmrk_aggr, type = "fn", meas = "harrell", p.value = p.value,
    col = palette.colors(2L)[2L]
)

Version Author Date
983ec69 Sebastian Gibb 2022-03-17
df8964f Sebastian Gibb 2021-10-15

4 Critical difference

p-value is set to 0.05 (otherwise an error is thrown because of insignificant results).

autoplot(
    bmrk_aggr, type = "cd", meas = "harrell", style = 2, p.value = p.value,
    minimize = FALSE
) + scale_color_viridis(discrete = TRUE)

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
983ec69 Sebastian Gibb 2022-03-17
373e7d8 Sebastian Gibb 2021-10-20
df8964f Sebastian Gibb 2021-10-15

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] ggplot2_3.3.6     viridis_0.6.2     viridisLite_0.4.0 mlr3viz_0.5.9    
[5] mlr3proba_0.4.11  mlr3misc_0.10.0   mlr3_0.13.3       data.table_1.14.2
[9] targets_0.12.1   

loaded via a namespace (and not attached):
 [1] fs_1.5.2                 bbotk_0.5.3              rprojroot_2.0.3         
 [4] mlr3pipelines_0.4.1      tools_4.2.0              backports_1.4.1         
 [7] bslib_0.3.1              utf8_1.2.2               R6_2.5.1                
[10] colorspace_2.0-3         withr_2.5.0              tidyselect_1.1.2        
[13] gridExtra_2.3            processx_3.5.3           compiler_4.2.0          
[16] git2r_0.30.1             cli_3.3.0                ooplah_0.2.0            
[19] lgr_0.4.3                labeling_0.4.2           bookdown_0.26           
[22] sass_0.4.1               BWStest_0.2.2            scales_1.2.0            
[25] checkmate_2.1.0          mvtnorm_1.1-3            callr_3.7.0             
[28] multcompView_0.1-8       palmerpenguins_0.1.0     mlr3tuning_0.13.1       
[31] stringr_1.4.0            digest_0.6.29            mlr3extralearners_0.5.37
[34] rmarkdown_2.14           param6_0.2.4             paradox_0.9.0           
[37] set6_0.2.4               pkgconfig_2.0.3          htmltools_0.5.2         
[40] parallelly_1.31.1        mlr3benchmark_0.1.3      fastmap_1.1.0           
[43] highr_0.9                rlang_1.0.2              SuppDists_1.1-9.7       
[46] jquerylib_0.1.4          generics_0.1.2           farver_2.1.0            
[49] jsonlite_1.8.0           dplyr_1.0.9              magrittr_2.0.3          
[52] Matrix_1.4-1             Rcpp_1.0.8.3             munsell_0.5.0           
[55] fansi_1.0.3              lifecycle_1.0.1          stringi_1.7.6           
[58] whisker_0.4              yaml_2.3.5               MASS_7.3-57             
[61] grid_4.2.0               parallel_4.2.0           dictionar6_0.1.3        
[64] listenv_0.8.0            promises_1.2.0.1         crayon_1.5.1            
[67] lattice_0.20-45          PMCMRplus_1.9.4          splines_4.2.0           
[70] knitr_1.39               ps_1.7.0                 pillar_1.7.0            
[73] igraph_1.3.1             uuid_1.1-0               base64url_1.4           
[76] kSamples_1.2-9           codetools_0.2-18         glue_1.6.2              
[79] evaluate_0.15            vctrs_0.4.1              httpuv_1.6.5            
[82] distr6_1.6.9             gtable_0.3.0             purrr_0.3.4             
[85] future_1.26.1            cachem_1.0.6             xfun_0.31               
[88] Rmpfr_0.8-7              later_1.3.0              survival_3.3-1          
[91] tibble_3.1.7             memoise_2.0.1            workflowr_1.7.0         
[94] gmp_0.6-5                globals_0.15.0           ellipsis_0.3.2