[R] glmer, Error: Downdated X'X is not positive definite,49
Annika
annika.opperbeck at jyu.fi
Tue Nov 16 10:25:12 CET 2010
Dear list,
I am new to this list and I am new to the world of R. Additionally I am not
very firm in statistics either but have to deal. So here is my problem:
I have a dataset (which I attach at the end of the post) with a binomial
response variable (alive or not) and three fixed factors
(trapping,treat,sex). I do have repeated measures and would like to include
one (enclosure) random factor.
I chose to use the glmer function (and tried the lmer as well).
m1<-glmer(alive~treat*sex*trapping*ID+(1|enclosure),family=binomial,data=survadult)
Both give the following error message:
Error in mer_finalize(ans) : Downdated X'X is not positive definite,
49.
Additionally: Warning:
glm.fit: fitted probabilities numerically 0 or 1 occurred
I get that there is something wrong in my dataframe, but I don`t understand
what and how I could change it.
If I run a glm without the random factor
m1<-glm(alive~treat*sex*trapping*ID,family=binomial,data=survadult)
it works out really fine, but is the wrong analysis in my opinion. (Does glm
actually consider the repeated measures? Does glmer?)
Is glmer the right function for me and how do I deal with the error I get?
Thanks for any help for a non-professional :)
Annika
trapping treat sex alive ID enclosure
trapping1 m/m f 1 400 1
trapping1 m/m f 1 401 1
trapping1 m/m f 1 402 1
trapping1 m/m m 0 403 1
trapping1 m/m m 1 404 1
trapping1 m/m m 1 405 1
trapping1 m/p f 1 406 2
trapping1 m/p f 1 407 2
trapping1 m/p f 1 408 2
trapping1 m/p m 1 409 2
trapping1 m/p m 1 410 2
trapping1 m/p m 1 411 2
trapping1 p/p f 1 412 3
trapping1 p/p f 1 413 3
trapping1 p/p f 1 414 3
trapping1 p/p m 1 415 3
trapping1 p/p m 1 416 3
trapping1 p/p m 1 417 3
trapping1 p/p f 1 418 4
trapping1 p/p f 1 419 4
trapping1 p/p f 1 420 4
trapping1 p/p m 1 421 4
trapping1 p/p m 1 422 4
trapping1 p/p m 1 423 4
trapping1 m/m f 1 424 5
trapping1 m/m f 1 425 5
trapping1 m/m f 1 426 5
trapping1 m/m m 1 427 5
trapping1 m/m m 1 428 5
trapping1 m/m m 1 429 5
trapping1 p/m f 1 430 6
trapping1 p/m f 1 431 6
trapping1 p/m f 1 432 6
trapping1 p/m m 1 433 6
trapping1 p/m m 1 434 6
trapping1 p/m m 1 435 6
trapping1 m/p f 1 436 7
trapping1 m/p f 1 437 7
trapping1 m/p f 1 438 7
trapping1 m/p m 1 439 7
trapping1 m/p m 1 440 7
trapping1 m/p m 1 441 7
trapping1 p/p f 1 442 8
trapping1 p/p f 1 443 8
trapping1 p/p f 1 444 8
trapping1 p/p m 1 445 8
trapping1 p/p m 1 446 8
trapping1 p/p m 1 447 8
trapping1 m/m f 1 448 9
trapping1 m/m f 1 449 9
trapping1 m/m f 1 450 9
trapping1 m/m m 1 451 9
trapping1 m/m m 1 452 9
trapping1 m/m m 1 453 9
trapping1 p/m f 1 454 10
trapping1 p/m f 1 455 10
trapping1 p/m f 1 456 10
trapping1 p/m m 1 457 10
trapping1 p/m m 1 458 10
trapping1 p/m m 1 459 10
trapping1 m/m f 1 460 11
trapping1 m/m f 1 461 11
trapping1 m/m f 1 462 11
trapping1 m/m m 1 463 11
trapping1 m/m m 1 464 11
trapping1 m/m m 0 465 11
trapping1 p/p f 1 466 12
trapping1 p/p f 1 467 12
trapping1 p/p f 1 468 12
trapping1 p/p m 1 469 12
trapping1 p/p m 0 470 12
trapping1 p/p m 1 471 12
trapping1 m/p f 1 472 13
trapping1 m/p f 1 473 13
trapping1 m/p f 1 474 13
trapping1 m/p m 1 475 13
trapping1 m/p m 1 476 13
trapping1 m/p m 1 477 13
trapping2 m/m f 1 478 1
trapping2 m/m f 1 479 1
trapping2 m/m f 1 480 1
trapping2 m/m m 1 481 1
trapping2 m/m m 1 482 1
trapping2 m/m m 1 483 1
trapping2 m/p f 1 484 2
trapping2 m/p f 1 485 2
trapping2 m/p f 1 486 2
trapping2 m/p m 0 487 2
trapping2 m/p m 1 488 2
trapping2 m/p m 1 489 2
trapping2 p/p f 1 490 3
trapping2 p/p f 1 491 3
trapping2 p/p f 1 492 3
trapping2 p/p m 1 493 3
trapping2 p/p m 1 494 3
trapping2 p/p m 1 495 3
trapping2 p/p f 1 496 4
trapping2 p/p f 1 497 4
trapping2 p/p f 1 498 4
trapping2 p/p m 1 499 4
trapping2 p/p m 1 500 4
trapping2 p/p m 1 501 4
trapping2 m/m f 1 502 5
trapping2 m/m f 1 503 5
trapping2 m/m f 1 504 5
trapping2 m/m m 1 505 5
trapping2 m/m m 1 506 5
trapping2 m/m m 1 507 5
trapping2 p/m f 1 508 6
trapping2 p/m f 1 509 6
trapping2 p/m f 1 510 6
trapping2 p/m m 1 511 6
trapping2 p/m m 1 512 6
trapping2 p/m m 1 513 6
trapping2 m/p f 1 514 7
trapping2 m/p f 1 515 7
trapping2 m/p f 1 516 7
trapping2 m/p m 1 517 7
trapping2 m/p m 1 518 7
trapping2 m/p m 1 519 7
trapping2 p/p f 1 520 8
trapping2 p/p f 1 521 8
trapping2 p/p f 1 522 8
trapping2 p/p m 1 523 8
trapping2 p/p m 1 524 8
trapping2 p/p m 1 525 8
trapping2 m/m f 1 526 9
trapping2 m/m f 1 527 9
trapping2 m/m f 1 528 9
trapping2 m/m m 1 529 9
trapping2 m/m m 1 530 9
trapping2 m/m m 1 531 9
trapping2 p/m f 1 532 10
trapping2 p/m f 1 533 10
trapping2 p/m f 1 534 10
trapping2 p/m m 1 535 10
trapping2 p/m m 1 536 10
trapping2 p/m m 0 537 10
trapping2 m/m f 1 538 11
trapping2 m/m f 1 539 11
trapping2 m/m f 1 540 11
trapping2 m/m m 1 541 11
trapping2 m/m m 0 542 11
trapping2 m/m m 1 543 11
trapping2 p/p f 1 544 12
trapping2 p/p f 1 545 12
trapping2 p/p f 1 546 12
trapping2 p/p m 0 547 12
trapping2 p/p m 1 548 12
trapping2 p/p m 1 549 12
trapping2 m/p f 1 550 13
trapping2 m/p f 1 551 13
trapping2 m/p f 1 552 13
trapping2 m/p m 1 553 13
trapping2 m/p m 1 554 13
trapping2 m/p m 1 555 13
trapping3 m/m f 1 556 1
trapping3 m/m f 1 557 1
trapping3 m/m f 1 558 1
trapping3 m/m m 1 559 1
trapping3 m/m m 1 560 1
trapping3 m/m m 1 561 1
trapping3 m/p f 1 562 2
trapping3 m/p f 1 563 2
trapping3 m/p f 1 564 2
trapping3 m/p m 1 565 2
trapping3 m/p m 1 566 2
trapping3 m/p m 0 567 2
trapping3 p/p f 1 568 3
trapping3 p/p f 1 569 3
trapping3 p/p f 1 570 3
trapping3 p/p m 1 571 3
trapping3 p/p m 1 572 3
trapping3 p/p m 1 573 3
trapping3 p/p f 1 574 4
trapping3 p/p f 1 575 4
trapping3 p/p f 1 576 4
trapping3 p/p m 1 577 4
trapping3 p/p m 1 578 4
trapping3 p/p m 1 579 4
trapping3 m/m f 1 580 5
trapping3 m/m f 1 581 5
trapping3 m/m f 1 582 5
trapping3 m/m m 1 583 5
trapping3 m/m m 0 584 5
trapping3 m/m m 1 585 5
trapping3 p/m f 1 586 6
trapping3 p/m f 1 587 6
trapping3 p/m f 1 588 6
trapping3 p/m m 0 589 6
trapping3 p/m m 1 590 6
trapping3 p/m m 1 591 6
trapping3 m/p f 1 592 7
trapping3 m/p f 1 593 7
trapping3 m/p f 1 594 7
trapping3 m/p m 1 595 7
trapping3 m/p m 1 596 7
trapping3 m/p m 1 597 7
trapping3 p/p f 1 598 8
trapping3 p/p f 1 599 8
trapping3 p/p f 1 600 8
trapping3 p/p m 1 601 8
trapping3 p/p m 1 602 8
trapping3 p/p m 1 603 8
trapping3 m/m f 1 604 9
trapping3 m/m f 1 605 9
trapping3 m/m f 1 606 9
trapping3 m/m m 0 607 9
trapping3 m/m m 1 608 9
trapping3 m/m m 1 609 9
trapping3 p/m f 1 610 10
trapping3 p/m f 0 611 10
trapping3 p/m f 1 612 10
trapping3 p/m m 1 613 10
trapping3 p/m m 1 614 10
trapping3 p/m m 0 615 10
trapping3 m/m f 1 616 11
trapping3 m/m f 1 617 11
trapping3 m/m f 1 618 11
trapping3 m/m m 0 619 11
trapping3 m/m m 0 620 11
trapping3 m/m m 0 621 11
trapping3 p/p f 1 622 12
trapping3 p/p f 0 623 12
trapping3 p/p f 1 624 12
trapping3 p/p m 0 625 12
trapping3 p/p m 0 626 12
trapping3 p/p m 0 627 12
trapping3 m/p f 1 628 13
trapping3 m/p f 1 629 13
trapping3 m/p f 1 630 13
trapping3 m/p m 1 631 13
trapping3 m/p m 1 632 13
trapping3 m/p m 0 633 13
trapping4 m/m f 1 634 1
trapping4 m/m f 1 635 1
trapping4 m/m f 1 636 1
trapping4 m/m m 1 637 1
trapping4 m/m m 1 638 1
trapping4 m/m m 1 639 1
trapping4 m/p f 1 640 2
trapping4 m/p f 1 641 2
trapping4 m/p f 0 642 2
trapping4 m/p m 1 643 2
trapping4 m/p m 1 644 2
trapping4 m/p m 0 645 2
trapping4 p/p f 1 646 3
trapping4 p/p f 0 647 3
trapping4 p/p f 1 648 3
trapping4 p/p m 1 649 3
trapping4 p/p m 0 650 3
trapping4 p/p m 1 651 3
trapping4 p/p f 1 652 4
trapping4 p/p f 1 653 4
trapping4 p/p f 1 654 4
trapping4 p/p m 1 655 4
trapping4 p/p m 1 656 4
trapping4 p/p m 1 657 4
trapping4 m/m f 1 658 5
trapping4 m/m f 1 659 5
trapping4 m/m f 1 660 5
trapping4 m/m m 1 661 5
trapping4 m/m m 0 662 5
trapping4 m/m m 0 663 5
trapping4 p/m f 1 664 6
trapping4 p/m f 1 665 6
trapping4 p/m f 1 666 6
trapping4 p/m m 1 667 6
trapping4 p/m m 0 668 6
trapping4 p/m m 0 669 6
trapping4 m/p f 0 670 7
trapping4 m/p f 0 671 7
trapping4 m/p f 0 672 7
trapping4 m/p m 0 673 7
trapping4 m/p m 0 674 7
trapping4 m/p m 0 675 7
trapping4 p/p f 1 676 8
trapping4 p/p f 1 677 8
trapping4 p/p f 0 678 8
trapping4 p/p m 1 679 8
trapping4 p/p m 1 680 8
trapping4 p/p m 1 681 8
trapping4 m/m f 1 682 9
trapping4 m/m f 1 683 9
trapping4 m/m f 1 684 9
trapping4 m/m m 1 685 9
trapping4 m/m m 1 686 9
trapping4 m/m m 0 687 9
trapping4 p/m f 0 688 10
trapping4 p/m f 1 689 10
trapping4 p/m f 1 690 10
trapping4 p/m m 0 691 10
--
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