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Published 20 hours ago • verified publisher icon pbiecek

Help: Error in yhats[[which.min(yhats_diff)]]

Open Margarida-F opened this issue 5 years ago • 6 comments

Hi !

Can I have help to fix the error below?

Error in yhats[[which.min(yhats_diff)]] : attempt to select less than one element in get1index

I only code this:

contribution <- broken(model = model, new_observation = df[1,features], data = train[,features])

and my model is a randomForest.

It seems that is trying to access to the zero position, and it doesn't exist.

Thanks, Margarida

Margarida-F avatar Dec 06 '19 15:12 Margarida-F

Do you have a reproducible example that produces this error? And please try the iBreakDown package (https://github.com/ModelOriented/iBreakDown) with break_down) function, it's a newer version so maybe this problem is already solved there

pbiecek avatar Dec 06 '19 15:12 pbiecek

First of all, thanks for you answer.

I suppose I can't show the data but I guarantee the variables are all right. However, maybe the problem is the model...

I try this:

contribution <- break_down(model, new_observation = df[1,features], data = train[,features]) Error in colMeans(yhatpred) : 'x' must be numeric

And then, tried construct explainer first:

explainer <- explain(model,data=train[,features],y=train$Y) Error in UseMethod("explain") : no applicable method for 'explain' applied to an object of class "c('randomForest.formula', 'randomForest')"

My model is like: model

Can you help me, please?

Thank you, very much , Margarida

Margarida-F avatar Dec 06 '19 16:12 Margarida-F

Can you share devtools::session_info()? It is hard to suggest anything without knowing on which versions of DALEX/breakDown you are working. Try latest versions DALEX & iBreakDown from CRAN.

If this is not enough then try to change thy y variable from factor to numeric (as Y == "1")

pbiecek avatar Dec 07 '19 16:12 pbiecek

Hi, again. Thank you very much you're trying to help me.

My Session Information is:

  • Session info ----------------------------------------------------------------------------------------------------------------- setting value
    version R version 3.5.2 (2018-12-20) os Windows >= 8 x64
    system x86_64, mingw32
    ui RStudio
    language (EN)
    collate Portuguese_Portugal.1252
    ctype Portuguese_Portugal.1252
    tz Europe/London
    date 2019-12-09

  • Packages --------------------------------------------------------------------------------------------------------------------- package * version date lib source
    assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.5.3) backports 1.1.5 2019-10-02 [1] CRAN (R 3.5.3) callr 3.3.2 2019-09-22 [1] CRAN (R 3.5.3) caret * 6.0-84 2019-04-27 [1] CRAN (R 3.5.3) class 7.3-14 2015-08-30 [2] CRAN (R 3.5.2) cli 1.1.0 2019-03-19 [1] CRAN (R 3.5.3) codetools 0.2-15 2016-10-05 [2] CRAN (R 3.5.2) colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.5.3) crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.3) DALEX 0.4.9 2019-10-24 [1] CRAN (R 3.5.3) data.table * 1.12.2 2019-04-07 [1] CRAN (R 3.5.3) DBI 1.0.0 2018-05-02 [1] CRAN (R 3.5.3) dbplyr * 1.4.2 2019-06-17 [1] CRAN (R 3.5.3) desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.3) devtools 2.2.1 2019-09-24 [1] CRAN (R 3.5.2) digest 0.6.23 2019-11-23 [1] CRAN (R 3.5.3) dplyr * 0.8.3 2019-07-04 [1] CRAN (R 3.5.3) ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.5.3) foreach 1.4.7 2019-07-27 [1] CRAN (R 3.5.3) fs 1.3.1 2019-05-06 [1] CRAN (R 3.5.3) generics 0.0.2 2018-11-29 [1] CRAN (R 3.5.3) ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.5.3) glue 1.3.1 2019-03-12 [1] CRAN (R 3.5.3) gower 0.2.1 2019-05-14 [1] CRAN (R 3.5.3) gtable 0.3.0 2019-03-25 [1] CRAN (R 3.5.3) iBreakDown 0.9.9 2019-08-26 [1] CRAN (R 3.5.3) ipred 0.9-9 2019-04-28 [1] CRAN (R 3.5.3) iterators 1.0.12 2019-07-26 [1] CRAN (R 3.5.3) lattice * 0.20-38 2018-11-04 [2] CRAN (R 3.5.2) lava 1.6.6 2019-08-01 [1] CRAN (R 3.5.3) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.5.3) lubridate * 1.7.4 2018-04-11 [1] CRAN (R 3.5.3) magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.3) MASS 7.3-51.1 2018-11-01 [2] CRAN (R 3.5.2) Matrix 1.2-15 2018-11-01 [2] CRAN (R 3.5.2) memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.3) ModelMetrics 1.2.2 2018-11-03 [1] CRAN (R 3.5.3) munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.3) nlme 3.1-137 2018-04-07 [2] CRAN (R 3.5.2) nnet 7.3-12 2016-02-02 [2] CRAN (R 3.5.2) pillar 1.4.2 2019-06-29 [1] CRAN (R 3.5.3) pkgbuild 1.0.5 2019-08-26 [1] CRAN (R 3.5.3) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.5.3) pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.3) plyr 1.8.4 2016-06-08 [1] CRAN (R 3.5.3) prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.3) processx 3.4.1 2019-07-18 [1] CRAN (R 3.5.3) prodlim 2018.04.18 2018-04-18 [1] CRAN (R 3.5.3) ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.3) purrr 0.3.2 2019-03-15 [1] CRAN (R 3.5.3) R6 2.4.0 2019-02-14 [1] CRAN (R 3.5.3) randomForest * 4.6-14 2018-03-25 [1] CRAN (R 3.5.3) Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.5.3) recipes 0.1.7 2019-09-15 [1] CRAN (R 3.5.2) remotes 2.1.0 2019-06-24 [1] CRAN (R 3.5.3) reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.3) rlang 0.4.1 2019-10-24 [1] CRAN (R 3.5.3) rpart 4.1-13 2018-02-23 [2] CRAN (R 3.5.2) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.3) rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.5.2) scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.3) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.3) stringi 1.4.3 2019-03-12 [1] CRAN (R 3.5.3) stringr 1.4.0 2019-02-10 [1] CRAN (R 3.5.3) survival 2.43-3 2018-11-26 [2] CRAN (R 3.5.2) testthat 2.2.1 2019-07-25 [1] CRAN (R 3.5.3) tibble 2.1.3 2019-06-06 [1] CRAN (R 3.5.3) tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.3) timeDate 3043.102 2018-02-21 [1] CRAN (R 3.5.3) usethis 1.5.1 2019-07-04 [1] CRAN (R 3.5.3) withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.3) yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.3)

[1] C:/Users/Margarida Ferreira/Documents/R/win-library/3.5 [2] C:/Program Files/R/R-3.5.2/library

Change Y to numeric doesn't works because Y isn't an argument of break_down().

Should I download the code and run each code block to debug?

Thanks for everything, Margarida

Margarida-F avatar Dec 09 '19 10:12 Margarida-F

Hi, again.

Just to close this issue:

I'm now using some code of iBreakDown. It's normal that it take too long (around 8 minutes) to calculate contributions of 13 variables and 1 row?

Thanks very much. I promise I close this issue before your answer.

Margarida

Margarida-F avatar Dec 12 '19 15:12 Margarida-F

Hi, busy time ar university, sorry for late response.

iBreakDown is much faster than breakDown. For FIFA data (200k cases, ~100 variables) calculation of break down is below a minute, do for 13 variables it shall be seconds at most.

Here you will find how to use the most recent version of iBreakDown https://pbiecek.github.io/PM_VEE/breakDown.html#BDR

pbiecek avatar Dec 19 '19 23:12 pbiecek