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intercepts in cubist formula #58

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topepo opened this issue Jul 17, 2019 · 0 comments
Open

intercepts in cubist formula #58

topepo opened this issue Jul 17, 2019 · 0 comments
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bug an unexpected problem or unintended behavior

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@topepo
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topepo commented Jul 17, 2019

The intercept object is being added to the parsed model formula (I think instead of its value).

In the example below should list(list(col = "(Intercept)", val = 15.173, op = "none", is_intercept = 1)) be 15.173?

``` r
library(Cubist)
#> Loading required package: lattice
library(tidymodels)
#> Registered S3 method overwritten by 'xts':
#>   method     from
#>   as.zoo.xts zoo
#> ── Attaching packages ────────────────────────────────────────────────────────── tidymodels 0.0.2 ──
#> ✔ broom     0.5.1          ✔ purrr     0.3.2     
#> ✔ dials     0.0.2.9000     ✔ recipes   0.1.6     
#> ✔ dplyr     0.8.3          ✔ rsample   0.0.5.9000
#> ✔ ggplot2   3.2.0          ✔ tibble    2.1.3     
#> ✔ infer     0.4.0          ✔ yardstick 0.0.2     
#> ✔ parsnip   0.0.2.9000
#> ── Conflicts ───────────────────────────────────────────────────────────── tidymodels_conflicts() ──
#> ✖ purrr::discard()  masks scales::discard()
#> ✖ dplyr::filter()   masks stats::filter()
#> ✖ dplyr::lag()      masks stats::lag()
#> ✖ ggplot2::margin() masks dials::margin()
#> ✖ recipes::step()   masks stats::step()
library(tidypredict)
library(sessioninfo)
options(width = 100)

data(biomass)

biomass_tr <-
  biomass %>%
  dplyr::filter(dataset == "Training") %>%
  dplyr::select(-dataset, -sample)

biomass_te <-
  biomass %>%
  dplyr::filter(dataset == "Testing") %>%
  dplyr::select(-dataset, -sample)

set.seed(1)
mod <- cubist(x = biomass_tr %>% dplyr::select(-HHV), y = biomass_tr$HHV)
tidypredict_fit(mod)
#> (ifelse(oxygen >= 51.59, list(list(col = "(Intercept)", val = 15.173, 
#>     op = "none", is_intercept = 1)), 0) + ifelse(oxygen < 42.49 & 
#>     carbon < 60.97 & hydrogen < 6.85, 0.12089 + carbon * 0.362 + 
#>     hydrogen * 0.31 + oxygen * -0.009 + sulfur * 0.3, 0) + ifelse(oxygen >= 
#>     42.49 & oxygen < 51.59, 10.20375 + carbon * 0.299 + oxygen * 
#>     -0.123, 0) + ifelse(hydrogen >= 6.85 & carbon < 60.97, -13.1916 + 
#>     carbon * 0.693, 0) + ifelse(carbon >= 60.97 & nitrogen >= 
#>     1.36, 64.2476 + carbon * 0.028 + hydrogen * 0.09 + nitrogen * 
#>     -24.5, 0) + ifelse(carbon >= 60.97 & nitrogen < 1.36, -2.69375 + 
#>     carbon * 0.363 + hydrogen * 1.38 + nitrogen * 0.38, 0))/1

session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.0 (2019-04-26)
#>  os       macOS High Sierra 10.13.6   
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2019-07-16                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────
#>  package       * version    date       lib source                            
#>  assertthat      0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                    
#>  backports       1.1.4      2019-04-10 [1] CRAN (R 3.6.0)                    
#>  base64enc       0.1-3      2015-07-28 [1] CRAN (R 3.6.0)                    
#>  bayesplot       1.6.0      2018-08-02 [1] CRAN (R 3.6.0)                    
#>  broom         * 0.5.1      2018-12-05 [1] CRAN (R 3.6.0)                    
#>  callr           3.2.0      2019-03-15 [1] CRAN (R 3.6.0)                    
#>  class           7.3-15     2019-01-01 [1] CRAN (R 3.6.0)                    
#>  cli             1.1.0      2019-03-19 [1] CRAN (R 3.6.0)                    
#>  codetools       0.2-16     2018-12-24 [1] CRAN (R 3.6.0)                    
#>  colorspace      1.4-1      2019-03-18 [1] CRAN (R 3.6.0)                    
#>  colourpicker    1.0        2017-09-27 [1] CRAN (R 3.6.0)                    
#>  crayon          1.3.4      2017-09-16 [1] CRAN (R 3.6.0)                    
#>  crosstalk       1.0.0      2016-12-21 [1] CRAN (R 3.6.0)                    
#>  Cubist        * 0.2.2      2018-05-21 [1] CRAN (R 3.6.0)                    
#>  dials         * 0.0.2.9000 2019-07-08 [1] local                             
#>  DiceDesign      1.8        2018-10-29 [1] CRAN (R 3.6.0)                    
#>  digest          0.6.20     2019-07-04 [1] CRAN (R 3.6.0)                    
#>  dplyr         * 0.8.3      2019-07-04 [1] CRAN (R 3.6.0)                    
#>  DT              0.5        2018-11-05 [1] CRAN (R 3.6.0)                    
#>  dygraphs        1.1.1.6    2018-07-11 [1] CRAN (R 3.6.0)                    
#>  evaluate        0.14       2019-05-28 [1] CRAN (R 3.6.0)                    
#>  furrr           0.1.0      2018-05-16 [1] CRAN (R 3.6.0)                    
#>  future          1.14.0     2019-07-02 [1] CRAN (R 3.6.0)                    
#>  generics        0.0.2      2018-11-29 [1] CRAN (R 3.6.0)                    
#>  ggplot2       * 3.2.0      2019-06-16 [1] CRAN (R 3.6.0)                    
#>  ggridges        0.5.1      2018-09-27 [1] CRAN (R 3.6.0)                    
#>  globals         0.12.4     2018-10-11 [1] CRAN (R 3.6.0)                    
#>  glue            1.3.1      2019-03-12 [1] CRAN (R 3.6.0)                    
#>  gower           0.2.0      2019-03-07 [1] CRAN (R 3.6.0)                    
#>  gridExtra       2.3        2017-09-09 [1] CRAN (R 3.6.0)                    
#>  gtable          0.3.0      2019-03-25 [1] CRAN (R 3.6.0)                    
#>  gtools          3.8.1      2018-06-26 [1] CRAN (R 3.6.0)                    
#>  highr           0.8        2019-03-20 [1] CRAN (R 3.6.0)                    
#>  htmltools       0.3.6      2017-04-28 [1] CRAN (R 3.6.0)                    
#>  htmlwidgets     1.3        2018-09-30 [1] CRAN (R 3.6.0)                    
#>  httpuv          1.5.1      2019-04-05 [1] CRAN (R 3.6.0)                    
#>  igraph          1.2.4      2019-02-13 [1] CRAN (R 3.6.0)                    
#>  infer         * 0.4.0      2018-11-15 [1] CRAN (R 3.6.0)                    
#>  inline          0.3.15     2018-05-18 [1] CRAN (R 3.6.0)                    
#>  ipred           0.9-8      2018-11-05 [1] CRAN (R 3.6.0)                    
#>  janeaustenr     0.1.5      2017-06-10 [1] CRAN (R 3.6.0)                    
#>  knitr           1.23       2019-05-18 [1] CRAN (R 3.6.0)                    
#>  later           0.8.0      2019-02-11 [1] CRAN (R 3.6.0)                    
#>  lattice       * 0.20-38    2018-11-04 [1] CRAN (R 3.6.0)                    
#>  lava            1.6.5      2019-02-12 [1] CRAN (R 3.6.0)                    
#>  lazyeval        0.2.2      2019-03-15 [1] CRAN (R 3.6.0)                    
#>  listenv         0.7.0      2018-01-21 [1] CRAN (R 3.6.0)                    
#>  lme4            1.1-20     2019-02-04 [1] CRAN (R 3.6.0)                    
#>  loo             2.0.0      2018-04-11 [1] CRAN (R 3.6.0)                    
#>  lubridate       1.7.4      2018-04-11 [1] CRAN (R 3.5.0)                    
#>  magrittr        1.5        2014-11-22 [1] CRAN (R 3.6.0)                    
#>  markdown        1.0        2019-06-07 [1] CRAN (R 3.6.0)                    
#>  MASS            7.3-51.4   2019-03-31 [1] CRAN (R 3.6.0)                    
#>  Matrix          1.2-17     2019-03-22 [1] CRAN (R 3.6.0)                    
#>  matrixStats     0.54.0     2018-07-23 [1] CRAN (R 3.6.0)                    
#>  mime            0.7        2019-06-11 [1] CRAN (R 3.6.0)                    
#>  miniUI          0.1.1.1    2018-05-18 [1] CRAN (R 3.6.0)                    
#>  minqa           1.2.4      2014-10-09 [1] CRAN (R 3.6.0)                    
#>  munsell         0.5.0      2018-06-12 [1] CRAN (R 3.6.0)                    
#>  nlme            3.1-139    2019-04-09 [1] CRAN (R 3.6.0)                    
#>  nloptr          1.2.1      2018-10-03 [1] CRAN (R 3.6.0)                    
#>  nnet            7.3-12     2016-02-02 [1] CRAN (R 3.6.0)                    
#>  parsnip       * 0.0.2.9000 2019-07-16 [1] local                             
#>  pillar          1.4.2      2019-06-29 [1] CRAN (R 3.6.0)                    
#>  pkgbuild        1.0.3      2019-03-20 [1] CRAN (R 3.6.0)                    
#>  pkgconfig       2.0.2      2018-08-16 [1] CRAN (R 3.6.0)                    
#>  plyr            1.8.4      2016-06-08 [1] CRAN (R 3.6.0)                    
#>  prettyunits     1.0.2      2015-07-13 [1] CRAN (R 3.6.0)                    
#>  pROC            1.14.0     2019-03-12 [1] CRAN (R 3.6.0)                    
#>  processx        3.4.0      2019-07-03 [1] CRAN (R 3.6.0)                    
#>  prodlim         2018.04.18 2018-04-18 [1] CRAN (R 3.6.0)                    
#>  promises        1.0.1      2018-04-13 [1] CRAN (R 3.6.0)                    
#>  ps              1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                    
#>  purrr         * 0.3.2      2019-03-15 [1] CRAN (R 3.6.0)                    
#>  R6              2.4.0      2019-02-14 [1] CRAN (R 3.6.0)                    
#>  Rcpp            1.0.1      2019-03-17 [1] CRAN (R 3.6.0)                    
#>  recipes       * 0.1.6      2019-07-02 [1] CRAN (R 3.6.0)                    
#>  reshape2        1.4.3      2017-12-11 [1] CRAN (R 3.6.0)                    
#>  rlang           0.4.0.9000 2019-07-09 [1] Github (r-lib/rlang@a3d7e47)      
#>  rmarkdown       1.14       2019-07-12 [1] CRAN (R 3.6.0)                    
#>  rpart           4.1-15     2019-04-12 [1] CRAN (R 3.6.0)                    
#>  rsample       * 0.0.5.9000 2019-07-12 [1] local                             
#>  rsconnect       0.8.13     2019-01-10 [1] CRAN (R 3.6.0)                    
#>  rstan           2.18.2     2018-11-07 [1] CRAN (R 3.6.0)                    
#>  rstanarm        2.18.2     2018-11-10 [1] CRAN (R 3.6.0)                    
#>  rstantools      1.5.1      2018-08-22 [1] CRAN (R 3.6.0)                    
#>  rstudioapi      0.10       2019-03-19 [1] CRAN (R 3.6.0)                    
#>  scales        * 1.0.0      2018-08-09 [1] CRAN (R 3.6.0)                    
#>  sessioninfo   * 1.1.1.9000 2019-03-26 [1] Github (r-lib/sessioninfo@dfb3ea8)
#>  shiny           1.2.0      2018-11-02 [1] CRAN (R 3.6.0)                    
#>  shinyjs         1.0        2018-01-08 [1] CRAN (R 3.6.0)                    
#>  shinystan       2.5.0      2018-05-01 [1] CRAN (R 3.6.0)                    
#>  shinythemes     1.1.2      2018-11-06 [1] CRAN (R 3.6.0)                    
#>  SnowballC       0.6.0      2019-01-15 [1] CRAN (R 3.6.0)                    
#>  StanHeaders     2.18.1     2019-01-28 [1] CRAN (R 3.6.0)                    
#>  stringi         1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                    
#>  stringr         1.4.0      2019-02-10 [1] CRAN (R 3.6.0)                    
#>  survival        2.44-1.1   2019-04-01 [1] CRAN (R 3.6.0)                    
#>  threejs         0.3.1      2017-08-13 [1] CRAN (R 3.6.0)                    
#>  tibble        * 2.1.3      2019-06-06 [1] CRAN (R 3.6.0)                    
#>  tidymodels    * 0.0.2      2019-07-03 [1] local                             
#>  tidyposterior   0.0.2      2018-11-15 [1] CRAN (R 3.6.0)                    
#>  tidypredict   * 0.4.2      2019-07-15 [1] local                             
#>  tidyr         * 0.8.3      2019-03-01 [1] CRAN (R 3.6.0)                    
#>  tidyselect      0.2.5      2018-10-11 [1] CRAN (R 3.6.0)                    
#>  tidytext        0.2.0      2018-10-17 [1] CRAN (R 3.6.0)                    
#>  timeDate        3043.102   2018-02-21 [1] CRAN (R 3.6.0)                    
#>  tokenizers      0.2.1      2018-03-29 [1] CRAN (R 3.6.0)                    
#>  vctrs           0.2.0.9000 2019-07-15 [1] Github (r-lib/vctrs@a8fb108)      
#>  withr           2.1.2      2018-03-15 [1] CRAN (R 3.6.0)                    
#>  xfun            0.8        2019-06-25 [1] CRAN (R 3.6.0)                    
#>  xtable          1.8-3      2018-08-29 [1] CRAN (R 3.6.0)                    
#>  xts             0.11-2     2018-11-05 [1] CRAN (R 3.6.0)                    
#>  yaml            2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                    
#>  yardstick     * 0.0.2      2018-11-05 [1] CRAN (R 3.6.0)                    
#>  zeallot         0.1.0      2018-01-28 [1] CRAN (R 3.6.0)                    
#>  zoo             1.8-6      2019-05-28 [1] CRAN (R 3.6.0)                    
#> 
#> [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

Created on 2019-07-16 by the reprex package (v0.2.1)
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