nearest_neighbor error

[royfrancis]

library(tidymodels)
#> ── Attaching packages ────────────────────────────────────── tidymodels 0.1.2 ──
#> ✓ broom     0.7.3      ✓ recipes   0.1.15
#> ✓ dials     0.0.9      ✓ rsample   0.0.8 
#> ✓ dplyr     1.0.2      ✓ tibble    3.0.4 
#> ✓ ggplot2   3.3.2      ✓ tidyr     1.1.2 
#> ✓ infer     0.5.3      ✓ tune      0.1.2 
#> ✓ modeldata 0.1.0      ✓ workflows 0.2.1 
#> ✓ parsnip   0.1.4      ✓ yardstick 0.0.7 
#> ✓ purrr     0.3.4
#> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
#> x purrr::discard() masks scales::discard()
#> x dplyr::filter()  masks stats::filter()
#> x dplyr::lag()     masks stats::lag()
#> x recipes::step()  masks stats::step()

set.seed(777)
df_split <- initial_split(iris,prob=0.80,strata=Species)
df_train <- training(df_split)

recipe_nn <- df_train %>%
  recipe(Species ~ .) %>%
  step_zv(all_predictors()) %>%
  step_corr(all_predictors()) %>%
  step_normalize(all_predictors(), -all_nominal())

spec_nn <- nearest_neighbor(neighbors = 27.7, weight_func = "rectangular", dist_power = 0.816) %>% 
  set_mode("classification") %>% 
  set_engine("kknn") 

wf_nn <- workflow() %>%
  add_recipe(recipe_nn) %>%
  add_model(spec_nn)

fit_nn_training <- wf_nn %>%
  fit(df_train,control=control_grid(save_pred=TRUE,verbose=TRUE))
#> Error: `neighbors` must be a length 1 positive integer.

^{Created on 2021-01-05 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.0 (2020-04-24)
#>  os       Ubuntu 20.04.1 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_GB:en                    
#>  collate  en_GB.UTF-8                 
#>  ctype    en_GB.UTF-8                 
#>  tz       Europe/Stockholm            
#>  date     2021-01-05                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
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#>  ggplot2     * 3.3.2      2020-06-19 [1] CRAN (R 4.0.0)
#>  globals       0.14.0     2020-11-22 [1] CRAN (R 4.0.0)
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#>  gower         0.2.2      2020-06-23 [1] CRAN (R 4.0.0)
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#>  gtable        0.3.0      2019-03-25 [1] CRAN (R 4.0.0)
#>  hardhat       0.1.5      2020-11-09 [1] CRAN (R 4.0.0)
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#>  htmltools     0.5.0      2020-06-16 [1] CRAN (R 4.0.0)
#>  igraph        1.2.6      2020-10-06 [1] CRAN (R 4.0.0)
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#>  iterators     1.0.13     2020-10-15 [1] CRAN (R 4.0.0)
#>  kknn          1.3.1      2016-03-26 [1] CRAN (R 4.0.0)
#>  knitr         1.30       2020-09-22 [1] CRAN (R 4.0.0)
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#>  lubridate     1.7.9.2    2020-11-13 [1] CRAN (R 4.0.0)
#>  magrittr      2.0.1      2020-11-17 [1] CRAN (R 4.0.0)
#>  MASS          7.3-53     2020-09-09 [1] CRAN (R 4.0.0)
#>  Matrix        1.2-18     2019-11-27 [2] CRAN (R 4.0.0)
#>  memoise       1.1.0      2017-04-21 [1] CRAN (R 4.0.0)
#>  modeldata   * 0.1.0      2020-10-22 [1] CRAN (R 4.0.0)
#>  munsell       0.5.0      2018-06-12 [1] CRAN (R 4.0.0)
#>  nnet          7.3-13     2020-02-25 [2] CRAN (R 4.0.0)
#>  parallelly    1.22.0     2020-12-13 [1] CRAN (R 4.0.0)
#>  parsnip     * 0.1.4      2020-10-27 [1] CRAN (R 4.0.0)
#>  pillar        1.4.7      2020-11-20 [1] CRAN (R 4.0.0)
#>  pkgbuild      1.2.0      2020-12-15 [1] CRAN (R 4.0.0)
#>  pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.0.0)
#>  pkgload       1.1.0      2020-05-29 [1] CRAN (R 4.0.0)
#>  plyr          1.8.6      2020-03-03 [1] CRAN (R 4.0.0)
#>  prettyunits   1.1.1      2020-01-24 [1] CRAN (R 4.0.0)
#>  pROC          1.16.2     2020-03-19 [1] CRAN (R 4.0.0)
#>  processx      3.4.5      2020-11-30 [1] CRAN (R 4.0.0)
#>  prodlim       2019.11.13 2019-11-17 [1] CRAN (R 4.0.0)
#>  ps            1.5.0      2020-12-05 [1] CRAN (R 4.0.0)
#>  purrr       * 0.3.4      2020-04-17 [1] CRAN (R 4.0.0)
#>  R6            2.5.0      2020-10-28 [1] CRAN (R 4.0.0)
#>  Rcpp          1.0.5      2020-07-06 [1] CRAN (R 4.0.0)
#>  recipes     * 0.1.15     2020-11-11 [1] CRAN (R 4.0.0)
#>  remotes       2.2.0      2020-07-21 [1] CRAN (R 4.0.0)
#>  rlang         0.4.9      2020-11-26 [1] CRAN (R 4.0.0)
#>  rmarkdown     2.6        2020-12-14 [1] CRAN (R 4.0.0)
#>  rpart         4.1-15     2019-04-12 [2] CRAN (R 4.0.0)
#>  rprojroot     2.0.2      2020-11-15 [1] CRAN (R 4.0.0)
#>  rsample     * 0.0.8      2020-09-23 [1] CRAN (R 4.0.0)
#>  rstudioapi    0.13       2020-11-12 [1] CRAN (R 4.0.0)
#>  scales      * 1.1.1      2020-05-11 [1] CRAN (R 4.0.0)
#>  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 4.0.0)
#>  stringi       1.5.3      2020-09-09 [1] CRAN (R 4.0.0)
#>  stringr       1.4.0      2019-02-10 [1] CRAN (R 4.0.0)
#>  survival      3.1-12     2020-04-10 [2] CRAN (R 4.0.0)
#>  testthat      3.0.1      2020-12-17 [1] CRAN (R 4.0.0)
#>  tibble      * 3.0.4      2020-10-12 [1] CRAN (R 4.0.0)
#>  tidymodels  * 0.1.2      2020-11-22 [1] CRAN (R 4.0.0)
#>  tidyr       * 1.1.2      2020-08-27 [1] CRAN (R 4.0.0)
#>  tidyselect    1.1.0      2020-05-11 [1] CRAN (R 4.0.0)
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#>  tune        * 0.1.2      2020-11-17 [1] CRAN (R 4.0.0)
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#>  vctrs         0.3.6      2020-12-17 [1] CRAN (R 4.0.0)
#>  withr         2.3.0      2020-09-22 [1] CRAN (R 4.0.0)
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#> 
#> [1] /home/roy/R/x86_64-pc-linux-gnu-library/4.0.0
#> [2] /usr/local/R/4.0.0/lib/R/library

[royfrancis]

Changed neighbors from 27.7 to an integer 27.

library(tidymodels)

set.seed(777)
df_split <- initial_split(iris,prob=0.80,strata=Species)
df_train <- training(df_split)

recipe_nn <- df_train %>%
  recipe(Species ~ .) %>%
  step_zv(all_predictors()) %>%
  step_corr(all_predictors()) %>%
  step_normalize(all_predictors(), -all_nominal())

spec_nn <- nearest_neighbor(neighbors = 27, weight_func = "rectangular", dist_power = 0.816) %>% 
  set_mode("classification") %>% 
  set_engine("kknn") 

wf_nn <- workflow() %>%
  add_recipe(recipe_nn) %>%
  add_model(spec_nn)

fit_nn_training <- wf_nn %>%
  fit(df_train,control=control_grid(save_pred=TRUE,verbose=TRUE))
#> Error in if (capture) {: argument is of length zero
#> Timing stopped at: 0.001 0 0

^{Created on 2021-01-05 by the reprex package (v0.3.0)}

[juliasilge]

This looks like a new bug 🐛 in workflows. I think maybe we lost control_parsnip when we made some of the recent changes in workflows?

This is from within workflows:::fit.action_model():

Browse[2]> names(control)
[1] "verbose"       "allow_par"     "extract"       "save_pred"     "pkgs"         
[6] "save_workflow" "event_level"   "parallel_over"

So then here:

workflows/R/fit-action-model.R

Line 93 in 0e40b9e

control_parsnip <- control$control_parsnip

that gets set to NULL and things go bad from that stage forward.

I'm moving this to workflows.

[juliasilge]

Actually, scratch all that. 🐒

I had a mix of CRAN and GitHub versions installed because of doing some demos and I could reproduce the problem. When I updated to GitHub versions of parsnip and workflows, it looks like we have already solved this problem:

library(tidymodels)
#> ── Attaching packages ────────────────────────────────────── tidymodels 0.1.2 ──
#> ✓ broom     0.7.3          ✓ recipes   0.1.15    
#> ✓ dials     0.0.9          ✓ rsample   0.0.8     
#> ✓ dplyr     1.0.2          ✓ tibble    3.0.4     
#> ✓ ggplot2   3.3.3          ✓ tidyr     1.1.2     
#> ✓ infer     0.5.3          ✓ tune      0.1.2     
#> ✓ modeldata 0.1.0          ✓ workflows 0.2.1.9000
#> ✓ parsnip   0.1.4.9000     ✓ yardstick 0.0.7     
#> ✓ purrr     0.3.4
#> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
#> x purrr::discard() masks scales::discard()
#> x dplyr::filter()  masks stats::filter()
#> x dplyr::lag()     masks stats::lag()
#> x recipes::step()  masks stats::step()

set.seed(777)
df_split <- initial_split(iris, prob=0.80, strata=Species)
df_train <- training(df_split)

recipe_nn <- recipe(Species ~ ., data = df_train) %>%
  step_zv(all_predictors()) %>%
  step_corr(all_predictors()) %>%
  step_normalize(all_predictors(), -all_nominal())

spec_nn <- nearest_neighbor(neighbors = 27, weight_func = "rectangular", dist_power = 0.816) %>% 
  set_mode("classification") %>% 
  set_engine("kknn") 

wf_nn <- workflow() %>%
  add_recipe(recipe_nn) %>%
  add_model(spec_nn)

fit(wf_nn, df_train)
#> ══ Workflow [trained] ══════════════════════════════════════════════════════════
#> Preprocessor: Recipe
#> Model: nearest_neighbor()
#> 
#> ── Preprocessor ────────────────────────────────────────────────────────────────
#> 3 Recipe Steps
#> 
#> ● step_zv()
#> ● step_corr()
#> ● step_normalize()
#> 
#> ── Model ───────────────────────────────────────────────────────────────────────
#> 
#> Call:
#> kknn::train.kknn(formula = ..y ~ ., data = data, ks = min_rows(27,     data, 5), distance = ~0.816, kernel = ~"rectangular")
#> 
#> Type of response variable: nominal
#> Minimal misclassification: 0.07894737
#> Best kernel: rectangular
#> Best k: 27

^{Created on 2021-01-05 by the reprex package (v0.3.0)}

@royfrancis can you update both parsnip and workflows (I believe we have already solved this problem) and try again?

remotes::install_github("tidymodels/parsnip")
remotes::install_github("tidymodels/workflows")

[royfrancis]

Hi, I have updated both both these packages, but I continue to see the same error message. The new session info compared to my initial session shows that the packages have been updated. So, perhaps the issue is something else?

library(tidymodels)

set.seed(777)
df_split <- initial_split(iris,prob=0.80,strata=Species)
df_train <- training(df_split)

recipe_nn <- df_train %>%
  recipe(Species ~ .) %>%
  step_zv(all_predictors()) %>%
  step_corr(all_predictors()) %>%
  step_normalize(all_predictors(), -all_nominal())

spec_nn <- nearest_neighbor(neighbors = 27, weight_func = "rectangular", dist_power = 0.816) %>% 
  set_mode("classification") %>% 
  set_engine("kknn") 

wf_nn <- workflow() %>%
  add_recipe(recipe_nn) %>%
  add_model(spec_nn)

fit_nn_training <- wf_nn %>%
  fit(df_train,control=control_grid(save_pred=TRUE,verbose=TRUE))
#> Error in if (capture) {: argument is of length zero
#> Timing stopped at: 0 0 0.001

^{Created on 2021-01-06 by the reprex package (v0.3.0.9001)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.0 (2020-04-24)
#>  os       Ubuntu 20.04.1 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_GB:en                    
#>  collate  en_GB.UTF-8                 
#>  ctype    en_GB.UTF-8                 
#>  tz       Europe/Stockholm            
#>  date     2021-01-06                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version    date       lib source                               
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#>  dials       * 0.0.9      2020-09-16 [1] CRAN (R 4.0.0)                       
#>  DiceDesign    1.8-1      2019-07-31 [1] CRAN (R 4.0.0)                       
#>  digest        0.6.27     2020-10-24 [1] CRAN (R 4.0.0)                       
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#>  ellipsis      0.3.1      2020-05-15 [1] CRAN (R 4.0.0)                       
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 4.0.0)                       
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#>  ggplot2     * 3.3.3      2020-12-30 [1] CRAN (R 4.0.0)                       
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#>  gower         0.2.2      2020-06-23 [1] CRAN (R 4.0.0)                       
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#>  iterators     1.0.13     2020-10-15 [1] CRAN (R 4.0.0)                       
#>  kknn          1.3.1      2016-03-26 [1] CRAN (R 4.0.0)                       
#>  knitr         1.30       2020-09-22 [1] CRAN (R 4.0.0)                       
#>  lattice       0.20-41    2020-04-02 [2] CRAN (R 4.0.0)                       
#>  lava          1.6.8.1    2020-11-04 [1] CRAN (R 4.0.0)                       
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#>  lubridate     1.7.9.2    2020-11-13 [1] CRAN (R 4.0.0)                       
#>  magrittr      2.0.1      2020-11-17 [1] CRAN (R 4.0.0)                       
#>  MASS          7.3-53     2020-09-09 [1] CRAN (R 4.0.0)                       
#>  Matrix        1.2-18     2019-11-27 [2] CRAN (R 4.0.0)                       
#>  modeldata   * 0.1.0      2020-10-22 [1] CRAN (R 4.0.0)                       
#>  munsell       0.5.0      2018-06-12 [1] CRAN (R 4.0.0)                       
#>  nnet          7.3-13     2020-02-25 [2] CRAN (R 4.0.0)                       
#>  parallelly    1.23.0     2021-01-04 [1] CRAN (R 4.0.0)                       
#>  parsnip     * 0.1.4.9000 2021-01-05 [1] Github (tidymodels/parsnip@a82ed40)  
#>  pillar        1.4.7      2020-11-20 [1] CRAN (R 4.0.0)                       
#>  pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.0.0)                       
#>  plyr          1.8.6      2020-03-03 [1] CRAN (R 4.0.0)                       
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#>  prodlim       2019.11.13 2019-11-17 [1] CRAN (R 4.0.0)                       
#>  purrr       * 0.3.4      2020-04-17 [1] CRAN (R 4.0.0)                       
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#>  Rcpp          1.0.5      2020-07-06 [1] CRAN (R 4.0.0)                       
#>  recipes     * 0.1.15     2020-11-11 [1] CRAN (R 4.0.0)                       
#>  reprex        0.3.0.9001 2021-01-05 [1] Github (tidyverse/reprex@5819879)    
#>  rlang         0.4.10     2020-12-30 [1] CRAN (R 4.0.0)                       
#>  rmarkdown     2.6        2020-12-14 [1] CRAN (R 4.0.0)                       
#>  rpart         4.1-15     2019-04-12 [2] CRAN (R 4.0.0)                       
#>  rsample     * 0.0.8      2020-09-23 [1] CRAN (R 4.0.0)                       
#>  rstudioapi    0.13       2020-11-12 [1] CRAN (R 4.0.0)                       
#>  scales      * 1.1.1      2020-05-11 [1] CRAN (R 4.0.0)                       
#>  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 4.0.0)                       
#>  stringi       1.5.3      2020-09-09 [1] CRAN (R 4.0.0)                       
#>  stringr       1.4.0      2019-02-10 [1] CRAN (R 4.0.0)                       
#>  styler        1.3.2      2020-02-23 [1] CRAN (R 4.0.0)                       
#>  survival      3.1-12     2020-04-10 [2] CRAN (R 4.0.0)                       
#>  tibble      * 3.0.4      2020-10-12 [1] CRAN (R 4.0.0)                       
#>  tidymodels  * 0.1.2      2020-11-22 [1] CRAN (R 4.0.0)                       
#>  tidyr       * 1.1.2      2020-08-27 [1] CRAN (R 4.0.0)                       
#>  tidyselect    1.1.0      2020-05-11 [1] CRAN (R 4.0.0)                       
#>  timeDate      3043.102   2018-02-21 [1] CRAN (R 4.0.0)                       
#>  tune        * 0.1.2      2020-11-17 [1] CRAN (R 4.0.0)                       
#>  vctrs         0.3.6      2020-12-17 [1] CRAN (R 4.0.0)                       
#>  withr         2.3.0      2020-09-22 [1] CRAN (R 4.0.0)                       
#>  workflows   * 0.2.1.9000 2021-01-05 [1] Github (tidymodels/workflows@0e40b9e)
#>  xfun          0.19       2020-10-30 [1] CRAN (R 4.0.0)                       
#>  yaml          2.2.1      2020-02-01 [1] CRAN (R 4.0.0)                       
#>  yardstick   * 0.0.7      2020-07-13 [1] CRAN (R 4.0.0)                       
#> 
#> [1] /home/roy/R/x86_64-pc-linux-gnu-library/4.0.0
#> [2] /usr/local/R/4.0.0/lib/R/library

[topepo]

Use control_workflow() instead of control_grid(). The latter has the wrong elements needed by fit().

I'll close this but make new issues that fit() should check for the correct control object class.

[github-actions]

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