Coxph Model Error: NA/NaN/Inf in foreign function call (arg 6)
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Entering edit mode
5 months ago
jack.henry ▴ 50

I have been trying to test a coxph model using the survival R package but I get an error saying:

Error in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6).

Could anyone help with trying to figure out why I am getting this error? Any help would be greatly appreciated.

I don't have any NA/NAN in my data. Arg 6 to coxph.fit looks like it is the "control" arg but I do not change this from the default so I don't see why it would be NA.

My call is:

coxph(Surv(time, status) ~ a + b + c + d + e + f + g + h + i + j, data = data)

An small sample of the data that still breaks coxph:

        patient status time          a           b           c           d           e           f            g           h           i           j
TCGA-KL-8329      0 2752  0.5959293 -0.32985431  0.01111783  1.10744153 -0.70773316  2.33015904  1.463100812 -0.58329411  1.20687773 -0.28295541
TCGA-KN-8434      0 1797 -0.6500944  0.25498091 -0.35169400  2.81911736 -0.74883154  0.02330166  0.433175800 -0.45768414 -0.89713134  0.18003018
TCGA-KL-8339      1   64  0.4846779 -0.75415243  3.50603746 -0.35936700  0.45428359 -0.29873596  0.208140421  0.24296338  2.75467922 -0.83665793
TCGA-KM-8639      0  953  1.2930386 -0.75202936 -1.00069583  0.06050088  0.87667520  0.47147489 -0.831912681  1.04654568 -0.92575102  1.09891592
TCGA-KO-8410      0 3136  1.8160216  0.51484920  0.68337395  0.74592256 -0.55317283  0.55056419 -1.633187319  0.42832081  1.36152850  1.21369366
TCGA-KL-8345      0 1665  0.3655134  3.23947546 -0.82069294 -0.35579843 -0.10348039 -0.82487417  0.013001415 -0.73867513  0.51427163  1.60462114
TCGA-KM-8440      0 1366  1.3503198  0.68554209 -0.96563911 -0.75209746 -1.08852060 -0.73716727  0.620474898 -0.62548400  1.01743809 -0.04577739
TCGA-KN-8421      0 2674 -0.5999773 -0.92812435 -1.29402171 -1.04209357 -0.36470615 -0.80856206  0.138467144  0.91260631 -0.48853208 -0.05385749
TCGA-KO-8408      1   46 -0.7966362 -0.11108162 -0.09734132 -0.38926814 -0.08648102 -0.61187352  1.512610975 -0.02434646 -0.74341457 -0.93328251
TCGA-KM-8441      1  876  1.2476346  0.43054579  1.53359773  0.75223889 -0.70809878  0.24186658 -0.715544302  2.06504650 -1.42195827  1.39850139
TCGA-KN-8429      1 1989  0.6442450  0.12417443 -0.35520555 -0.67192046 -1.18596161 -0.38605648 -0.137363593 -0.42482600 -0.03640180 -0.21118608
TCGA-KN-8436      0 1288 -0.6045523 -0.66475787 -0.83244185 -0.61951029 -0.91843257 -0.52746350 -0.936507918  0.11748090  0.52896542  3.44647470
TCGA-KL-8323      1  758 -0.2876298  1.33759944  0.16933643 -0.86583167 -0.54652573 -0.45429365  1.038946771 -0.45015524 -0.24543396 -0.72123023
TCGA-KL-8335      0 2815  0.4643741 -0.47734933 -0.04148033 -0.94716189 -0.28416727 -0.11869188  0.001081911 -0.55421354 -0.19709587 -0.25093850
TCGA-KL-8342      0 2248 -0.6811296  1.06989305 -0.49154196  0.63527974 -0.16349934  0.81882058  0.479408563 -0.67364006  0.52097891 -0.60018980
TCGA-KL-8341      1  175  2.2993460  0.97148499 -1.08338334 -0.92154221 -0.79875858 -0.77990396 -0.772255184 -0.12252440 -0.82129263  1.43929478
TCGA-KN-8418      0 3935  0.5880805 -0.48058398 -0.60444151 -0.54974512 -0.57916121 -0.76058574  0.079354544 -0.36879020  1.16583457 -0.74584643
TCGA-KN-8433      0  341 -0.4327167 -1.39590608 -0.13868336 -0.02066941  0.52908383  0.52553709  0.049420802 -0.60782703 -1.39598026 -0.97120928
TCGA-KN-8427      0   30 -1.5261003 -2.21321280  3.61366151 -0.51032389  2.86850530  3.08845149 -0.286512019  4.42491129 -1.43815488 -0.71139085
TCGA-KN-8424      0 1983  0.1435498  1.29565513 -0.66865805  0.46317412 -0.49096263 -0.02104489  0.199648419 -0.54121811 -0.03600989  0.09847712
TCGA-KO-8404      1  148 -2.0367819 -2.29722822  0.48869237  0.61002742  0.73853424  0.01084746  2.922209321  1.46432769 -1.67244955 -0.93391669
TCGA-KL-8340      0 2024 -0.1763127 -0.21485371 -0.47613539 -0.48815605 -0.64883055 -0.56352292  1.098792615 -0.50637297 -0.23458907 -0.76127933
TCGA-KL-8328      0 3127 -0.7045284 -0.20443384  0.29524477 -0.90285461  1.11553049 -0.87844712  1.163996186 -0.01651090  0.43666672 -0.37453769
TCGA-KN-8419      0  714  2.1128842 -0.28858802  0.07314872 -0.91032357  0.65266749  0.76179219 -1.539406675 -0.48882948 -0.95832164  2.16468136
TCGA-KL-8332      0 2582 -0.2857939 -0.27370677 -0.19269890  0.07785714 -0.12539035  0.10739666  0.156789028 -0.30346481 -0.10040207  0.08045569
TCGA-KN-8435      0 3498 -0.3589219  0.06624912 -0.90719877 -0.84942279 -0.82143889 -0.74310721 -0.141505591 -0.07659146  1.25014257 -0.76830040

Thanks in advance.

r coxph survival • 388 views
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Entering edit mode

Here is some points:

  • It complains about the model size: with the default setting it works fine with 8 features, but feeding the model with all 9 features (a+b+c.....) , returning the same error. Maybe tuning different coxph parameters , can help.

  • Here is a similar post that might give you some insights

  • you missed data, before = data in your code, but I assumed this is some thing related to pasting your code here.
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