[R] Obtaining Complete Dataset with Imputed Values

Thu Aug 30 16:18:30 CEST 2018

Dear Paul and WHP,

My guess: Paul apparently has loaded the mice package after the mi package. Both packages have complete() functions, but for objects of different classes -- "mids" in the case of mice. Consquently, complete() in the mice package is shadowing complete() in the mi package.

The solution is not to load both packages unless you actually need to, load mi after mice (though then other similar problems might surface), or invoke mi::complete()  explicitly.

I hope this helps,
 John

-----------------------------------------------------------------
John Fox
Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
Web: https://socialsciences.mcmaster.ca/jfox/

> -----Original Message-----
> From: R-help [mailto:r-help-bounces using r-project.org] On Behalf Of Bill Poling
> Sent: Thursday, August 30, 2018 8:42 AM
> To: Paul Bernal <paulbernal07 using gmail.com>; r-help using r-project.org
> Subject: Re: [R] Obtaining Complete Dataset with Imputed Values
> 
> Good morning Paul.
> 
> I am unfamiliar with the package you are using but I have been working
> through the tutorial for this purpose using finalfit, if that is any help.
> 
> Cheers
> 
> WHP
> 
> http://www.datasurg.net/2018/08/29/five-steps-for-missing-data-with-
> finalfit/
> 
> 
> From: R-help <r-help-bounces using r-project.org> On Behalf Of Paul Bernal
> Sent: Friday, August 24, 2018 2:57 PM
> To: r-help using r-project.org
> Subject: [R] Obtaining Complete Dataset with Imputed Values
> 
> Dear friends, hope all is well with you,
> 
> I am working with package mi for data inputation. Currently working with R
> version 3.5.0 (64-bit).
> 
> Say my data is defined as dat, and I do the following:
> 
> datimputations <- mi(dat[2:5], n.iter=50) completedat <-
> complete(datimputations)
> 
> After using the complete function, I get the following error message:
> 
> Error in complete(datimputations, m = 1) : 'data' not of class 'mids'
> 
> How can I retrieve the processed dataframe (along with the imputed values)?
> 
> Here is my dput() for you to see
> 
> > dput(head(dat,100))
> structure(list(TransitDate = structure(c(496990800, 499669200, 502261200,
> 504939600, 507618000, 510037200, 512715600, 515307600, 517986000,
> 520578000, 523256400, 525934800, 528526800, 531205200, 533797200,
> 536475600, 539154000, 541573200, 544251600, 546843600, 549522000,
> 552114000, 554792400, 557470800, 560062800, 562741200, 565333200,
> 568011600, 570690000, 573195600, 575874000, 578466000, 581144400,
> 583736400, 586414800, 589093200, 591685200, 594363600, 596955600,
> 599634000, 602312400, 604731600, 607410000, 610002000, 612680400,
> 615272400, 617950800, 620629200, 623221200, 625899600, 628491600,
> 631170000, 633848400, 636267600, 638946000, 641538000, 644216400,
> 646808400, 649486800, 652165200, 654757200, 657435600, 660027600,
> 662706000, 665384400, 667803600, 670482000, 673074000, 675752400,
> 678344400, 681022800, 683701200, 686293200, 688971600, 691563600,
> 694242000, 696920400, 699426000, 702104400, 704696400, 707371200,
> 709963200, 712641600, 715320000, 717912000, 720590400, 723182400,
> 725860800, 728539200, 730958400, 733636800, 736232400, 738910800,
> 741502800, 744181200, 746859600, 749451600, 752130000, 754722000,
> 757400400), class = c("POSIXct", "POSIXt"), tzone = ""), Transits = c(14L, 14L,
> 13L, 10L, 11L, 14L, 14L, 14L, 16L, 6L, 8L, 6L, 6L, 7L, 7L, 9L, 7L, 9L, 3L, 12L, 7L,
> 8L, 10L, 9L, 10L, 11L, 9L, 9L, 5L, 11L, 12L, 7L, 12L, 10L, 9L, 13L, 7L, 7L, 8L, 4L,
> 4L, 7L, 5L, 7L, 7L, 6L, 9L, 4L, 7L, 9L, 5L, 5L, 10L, 6L, 6L, 13L, 6L, 7L, 10L, 7L, 8L,
> 5L, 6L, 7L, 6L, 9L, 8L, 10L, 9L, 9L, 12L, 5L, 9L, 6L, 7L, 10L, 10L, 9L, 14L, 14L, 15L,
> 14L, 16L, 17L, 18L, 11L, 15L, 14L, 8L, 13L, 10L, 9L, 12L, 8L, 12L, 10L, 11L, 10L,
> 9L, 10L), CargoTons = c(154973L, 129636L, 136884L, 86348L, 109907L,
> 154506L, 144083L, 152794L, 124861L, 60330L, 65221L, 61718L, 53997L,
> 83536L, 63218L, 98222L, 54719L, 98470L, 18263L, 104255L, 62869L, 62523L,
> 75344L, 81476L, 92818L, 87457L, 85231L, 77897L, 57699L, 96989L, 109361L,
> 59799L, 91116L, 82241L, 74251L, 124361L, 68751L, 61719L, 68017L, 37760L,
> 32513L, 56359L, 51333L, 80859L, 75852L, 65760L, 96043L, 38820L, 63202L,
> 102647L, 49104L, 53482L, 121305L, 71795L, 76704L, 146097L, 73047L,
> 68557L, 110642L, 77616L, 97767L, 52059L, 58658L, 66350L, 69303L, 76013L,
> 91909L, 108445L, 94454L, 101249L, 112131L, 56290L, 118342L, 70618L,
> 64783L, 112839L, 120506L, 94243L, 130768L, 133643L, 146321L, 140736L,
> 147234L, 158953L, 189888L, 93819L, 130021L, 130124L, 55088L, 114783L,
> 95184L, 82205L, 80321L, 65422L, 98933L, 93713L, 98417L, 97210L, 88464L,
> 94659L), RcnstPCUMS = c(229914L, 214547L, 215890L, 158695L, 173125L,
> 222533L, 212490L, 222125L, 266913L, 94268L, 112967L, 95480L, 87654L,
> 108996L, 97973L, 139247L, 93817L, 133197L, 40020L, 169749L, 102590L,
> 112121L, 140241L, 122989L, 144592L, 144979L, 123748L, 123249L, 70081L,
> 155218L, 168096L, 104743L, 163384L, 142648L, 129188L, 183170L, 99299L,
> 99873L, 111648L, 55890L, 59183L, 95568L, 72550L, 104562L, 100478L,
> 92665L, 130625L, 54786L, 105900L, 135833L, 70932L, 73247L, 149632L,
> 94317L, 87926L, 181989L, 92778L, 107097L, 153246L, 105175L, 126393L,
> 81976L, 95518L, 109019L, 95370L, 140492L, 125795L, 157978L, 138424L,
> 138160L, 180320L, 78757L, 135860L, 85921L, 114847L, 151965L, 152561L,
> 132841L, 204839L, 209567L, 224436L, 210209L, 227143L, 245968L, 264969L,
> 158648L, 222251L, 194335L, 111618L, 189643L, 137438L, 124953L, 163155L,
> 107633L, 164525L, 135102L, 152072L, 126636L, 121008L, 137824L), TotalToll
> = c(420742L, 392621L, 395078L, 290411L, 316818L, 407235L, 388856L,
> 406488L, 482774L, 172510L, 206729L, 174728L, 160406L, 199462L, 179290L,
> 254822L, 171685L, 243750L, 73236L, 310640L, 187739L, 205181L, 249438L,
> 225069L, 264603L, 265311L, 226458L, 225545L, 128248L, 284048L, 296023L,
> 184934L, 298992L, 261045L, 236414L, 335201L, 181717L, 182767L, 204315L,
> 102278L, 108304L, 174889L, 132766L, 191348L, 183874L, 169576L, 239043L,
> 100258L, 212859L, 273024L, 142573L, 147226L, 300760L, 189577L, 176731L,
> 365797L, 186483L, 215264L, 308024L, 211401L, 254049L, 164771L, 191991L,
> 219128L, 191693L, 282388L, 252847L, 317535L, 278232L, 277701L, 356022L,
> 158301L, 273078L, 172701L, 230842L, 305449L, 306647L, 267010L, 406202L,
> 421229L, 451116L, 422520L, 456557L, 494395L, 582202L, 350612L, 491174L,
> 429480L, 239858L, 419111L, 303737L, 276146L, 360572L, 237868L, 358627L,
> 298575L, 336079L, 279865L, 267427L, 304591L)), row.names = c(NA, 100L),
> class = "data.frame")
> 
> [[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help using r-project.org<mailto:R-help using r-project.org> mailing list -- To
> UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-
> help<https://stat.ethz.ch/mailman/listinfo/r-help>
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html<http://www.R-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
> 
> Confidentiality Notice This message is sent from Zelis. ...{{dropped:15}}
> 
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.