gg_error is not showing anything

[jgarces02]

Hi @ehrlinger,

Thanks for make easier working with radomForestSRC, you saved me a lot time! After calculating a rfsrc object with the following code...

> rfs <- rfsrc(Surv(time, event) ~ ., data = mydata, nsplit = NULL, ntree = 100, importance = T)
> rfs
                         Sample size: 99
                    Number of deaths: 35
                     Number of trees: 100
           Forest terminal node size: 15
       Average no. of terminal nodes: 9.44
No. of variables tried at each split: 4
              Total no. of variables: 12
       Resampling used to grow trees: swor
    Resample size used to grow trees: 63
                            Analysis: RSF
                              Family: surv
                      Splitting rule: logrank
                          Error rate: 28.85%

... I'm trying to obtain the OOB plot for each tree but I'm having this (uninformative) error and a empty plot appears:

> plot(gg_error(rfs))
Warning message:
Removed 9 rows containing missing values (geom_path).

Any idea about what I'm doing wrong, please? Thanks in advance.

[ehrlinger]

I think there is a new rfsrc argument that turns the error calculation on. Look for that and the error plot will work.... I do have to revisit this package... soon. I might update the docs to include this information. Hope it works. John

…

On Mon, Apr 6, 2020 at 6:39 AM jgarces ***@***.***> wrote: Hi @ehrlinger <https://github.com/ehrlinger>, Thanks for make easier working with radomForestSRC, you saved me a lot time! After calculating a rfsrc object with the following code... > rfs <- rfsrc(Surv(time, event) ~ ., data = mydata, nsplit = NULL, ntree = 100, importance = T) > rfs Sample size: 99 Number of deaths: 35 Number of trees: 100 Forest terminal node size: 15 Average no. of terminal nodes: 9.44 No. of variables tried at each split: 4 Total no. of variables: 12 Resampling used to grow trees: swor Resample size used to grow trees: 63 Analysis: RSF Family: surv Splitting rule: logrank Error rate: 28.85% ... I'm trying to obtain the OOB plot for each tree but I'm having this (uninformative) error and a empty plot appears: > plot(gg_error(rfs)) Warning message: Removed 9 rows containing missing values (geom_path). Any idea about what I'm doing wrong, please? Thanks in advance. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#35>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIPFFGR5AFW4BYYZFFMOKTRLGWOHANCNFSM4MCFBFZQ> .

[ehrlinger]

Corrected in v2.1.0. rfsrc no longer returns ntree information since it is the index. Create a new ntree column, and na.omit to allow the figure creation.