data-raw/05b0_glmnet_grid.md

In bennysalo/predict-recidivism: Analyses for prediction of recidivism in Finnish data using supervised learning

title: "Create glmnet_grid" author: "Benny Salo" date: "2019-02-14" output: github_document

Clear environment. Load previous results from the package.

rm(list = ls())
devtools::load_all(".")

library(dplyr)

Get the part of model_grid that are elastic net models.

glmnet_grid <- model_grid %>% filter(
  model_type == "Elastic net")

We use the formula method of caret::train for glmnet (to make the script work, unknown bug for other methods).

We introduce a new column where we write the formula.

glmnet_grid$formula <- 
  purrr::map2(.x = glmnet_grid$lhs, 
              .y = glmnet_grid$rhs,
              .f = ~write_formula(.x, .y))

Checks:

# All entries in glmnet_grid$formula should be formulas
stopifnot(all(purrr::map(glmnet_grid$formula, class) == "formula"))

# All formulas should include the corresponding outcome
outcome_in_formula <-
  purrr::map2_lgl(
    .x = as.character(glmnet_grid$formula),
    .y = glmnet_grid$lhs,
    .f = ~ stringr::str_detect(string = .x, pattern = .y)
    )
stopifnot(all(outcome_in_formula))

# The number of plusses in the formula should equal 
# the number of predictors - 1

n_plusses <- purrr::map2_int(
  .x = as.character(glmnet_grid$formula),
  .y = glmnet_grid$lhs,
  .f = ~ stringr::str_count(string = .x, pattern = "\\+")
  ) 

n_preds <- purrr::map_dbl(.x = glmnet_grid$rhs,
                      .f = ~ length(.x))


stopifnot(all(n_plusses == n_preds - 1))

We are also going to want to adjust the tested values for parameter alpha. We create a new column for this. The tested values in the first run will be values between 0 and 1 with an interval of 0.1.

glmnet_grid$alpha <- vector("list", nrow(glmnet_grid))
glmnet_grid$alpha <- purrr::map(.x = glmnet_grid$alpha, 
                                .f = ~seq(0, 1, by = 0.1))

Checks

stopifnot(length(glmnet_grid$alpha) == 8,
          all(purrr::map(glmnet_grid$alpha, length) == 11),
          all(purrr::map(glmnet_grid$alpha, class) == "numeric"))

Save and make available in /data

usethis::use_data(glmnet_grid, overwrite = TRUE)

## <U+2714> Saving 'glmnet_grid' to 'data/glmnet_grid.rda'

Print sessionInfo

sessionInfo()

## R version 3.5.2 (2018-12-20)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows >= 8 x64 (build 9200)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=Swedish_Finland.1252  LC_CTYPE=Swedish_Finland.1252   
## [3] LC_MONETARY=Swedish_Finland.1252 LC_NUMERIC=C                    
## [5] LC_TIME=Swedish_Finland.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] recidivismsl_0.0.0.9000 assertthat_0.2.0       
##  [3] caret_6.0-81            lattice_0.20-38        
##  [5] bindrcpp_0.2.2          ggplot2_3.1.0          
##  [7] dplyr_0.7.8             testthat_2.0.1         
##  [9] purrr_0.2.5             magrittr_1.5           
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-137            fs_1.2.6               
##  [3] xopen_1.0.0             usethis_1.4.0          
##  [5] lubridate_1.7.4         devtools_2.0.1         
##  [7] rprojroot_1.3-2         tools_3.5.2            
##  [9] backports_1.1.3         utf8_1.1.4             
## [11] R6_2.3.0                rpart_4.1-13           
## [13] lazyeval_0.2.1          colorspace_1.4-0       
## [15] nnet_7.3-12             withr_2.1.2            
## [17] ResourceSelection_0.3-4 tidyselect_0.2.5       
## [19] prettyunits_1.0.2       processx_3.2.1         
## [21] compiler_3.5.2          glmnet_2.0-16          
## [23] cli_1.0.1               xml2_1.2.0             
## [25] desc_1.2.0              scales_1.0.0           
## [27] randomForest_4.6-14     readr_1.3.1            
## [29] callr_3.1.1             commonmark_1.7         
## [31] stringr_1.3.1           digest_0.6.18          
## [33] pkgconfig_2.0.2         sessioninfo_1.1.1      
## [35] highr_0.7               rlang_0.3.1            
## [37] ggthemes_4.0.1          rstudioapi_0.9.0       
## [39] bindr_0.1.1             generics_0.0.2         
## [41] ModelMetrics_1.2.2      Matrix_1.2-15          
## [43] Rcpp_1.0.0              munsell_0.5.0          
## [45] fansi_0.4.0             furniture_1.8.7        
## [47] stringi_1.2.4           pROC_1.13.0            
## [49] yaml_2.2.0              MASS_7.3-51.1          
## [51] pkgbuild_1.0.2          plyr_1.8.4             
## [53] recipes_0.1.4           grid_3.5.2             
## [55] forcats_0.3.0           crayon_1.3.4           
## [57] splines_3.5.2           hms_0.4.2              
## [59] knitr_1.21              ps_1.3.0               
## [61] pillar_1.3.1            reshape2_1.4.3         
## [63] codetools_0.2-15        clisymbols_1.2.0       
## [65] stats4_3.5.2            pkgload_1.0.2          
## [67] glue_1.3.0              evaluate_0.12          
## [69] data.table_1.12.0       remotes_2.0.2          
## [71] foreach_1.4.4           gtable_0.2.0           
## [73] rcmdcheck_1.3.2         tidyr_0.8.2            
## [75] xfun_0.4                gower_0.1.2            
## [77] prodlim_2018.04.18      roxygen2_6.1.1         
## [79] class_7.3-14            survival_2.43-3        
## [81] timeDate_3043.102       tibble_2.0.1           
## [83] iterators_1.0.10        memoise_1.1.0          
## [85] lava_1.6.4              ipred_0.9-8

bennysalo/predict-recidivism documentation built on May 29, 2019, 10:34 a.m.