Hello,
I am attempting to create a multiple imputation model using the mice package in R. Here are some details about what I am specifically trying to do, and below is a subset of the data I am working with, the code I have tried, and the error that I am getting. In the dataset, labelled 'mturk.all', there are ~300 variables and around 1300 cases. For the multiple imputation model, I am trying to use only 33 of the ~300 variables; these 33 variables are dichotomous (coded as 0 and 1 in the dataset). Following the mice code provided at https://stefvanbuuren.name/fimd/sec-toomany.html (see section 9.1.6 on the linked website), I have tried the following code, which resulted in an error (also shown below): ``` >library(mice) >pred <- quickpred(mturk.all, mincor = .1, minpuc = 0, inc=c("TSHS_1R", "TSHS_2R", "TSHS_3R", "TSHS_4R", "TSHS_5R", "TSHS_6R", "TSHS_7R", "TSHS_8R", "TSHS_9R", "TSHS_10R", "TSHS_11R", "TSHS_12R", "TSHS_13R", "TSHS_14R", "TSHS_15R", "TSHS_16R", "TSHS_17R", "TSHS_18R", "TSHS_19R", "TSHS_20R", "TSHS_21R", "TSHS_22R", "TSHS_23R", "TSHS_24R", "TSHS_25R", "TSHS_26R", "TSHS_27R", "TSHS_28R", "TSHS_29R", "TSHS_30R", "TSHS_31R", "TSHS_32R", "TSHS_33R")) There were 14 warnings (use warnings() to see them) > warnings() Warning messages: 1: In data.matrix(data) : NAs introduced by coercion 2: In data.matrix(data) : NAs introduced by coercion 3: In data.matrix(data) : NAs introduced by coercion 4: In data.matrix(data) : NAs introduced by coercion 5: In data.matrix(data) : NAs introduced by coercion 6: In data.matrix(data) : NAs introduced by coercion 7: In data.matrix(data) : NAs introduced by coercion 8: In data.matrix(data) : NAs introduced by coercion 9: In data.matrix(data) : NAs introduced by coercion 10: In data.matrix(data) : NAs introduced by coercion 11: In data.matrix(data) : NAs introduced by coercion 12: In data.matrix(data) : NAs introduced by coercion 13: In data.matrix(data) : NAs introduced by coercion 14: In data.matrix(data) : NAs introduced by coercion >mturk.all.imp <- mice(mturk.all, m = 40, method = 'logreg', pred = pred) Error in parse(text = x, keep.source = FALSE) : <text>:1:1: unexpected '<' 1: < ^ ``` Alternatively, I tried the following: ``` >inlist <- mturk.all[c("TSHS_1R", "TSHS_2R", "TSHS_3R", "TSHS_4R", "TSHS_5R", "TSHS_6R", "TSHS_7R", "TSHS_8R", "TSHS_9R", "TSHS_10R", "TSHS_11R", "TSHS_12R", "TSHS_13R", "TSHS_14R", "TSHS_15R", "TSHS_16R", "TSHS_17R", "TSHS_18R", "TSHS_19R", "TSHS_20R", "TSHS_21R", "TSHS_22R", "TSHS_23R", "TSHS_24R", "TSHS_25R", "TSHS_26R", "TSHS_27R", "TSHS_28R", "TSHS_29R", "TSHS_30R", "TSHS_31R", "TSHS_32R", "TSHS_33R")] >pred <- quickpred(mturk.all, mincor = .1, minpuc = 0, inc=inlist) >mturk.all.imp <- mice(mturk.all, m = 40, method = 'logreg', pred = pred) Error in parse(text = x, keep.source = FALSE) : <text>:1:1: unexpected '<' 1: < ^ ``` I have also switched out the 'logreg' imputation method with 'pmm' and received the same error message. Here is a subset of the dataset, mturk.all, and the version of R Studio I am using, plus the version of mice I am using. ``` > dput(mturk.all[425:434, 1:33]) structure(list(TSHS_1R = c(0, 1, 1, 0, 0, 0, 1, 1, 0, 1), TSHS_2R = c(0, 0, 0, 1, 0, 0, 0, 0, 0, 0), TSHS_3R = c(0, 1, 0, 0, 0, 0, 0, 0, 1, 0), TSHS_4R = c(0, 1, 0, 0, 0, 0, 1, 0, 1, 0), TSHS_5R = c(0, 0, 0, 1, 0, 0, 0, 0, 1, 0), TSHS_6R = c(0, 0, NA, NA, 0, 0, 1, 0, 0, 0), TSHS_7R = c(0, 0, 0, 1, 0, 1, 1, 0, 0, 0), TSHS_8R = c(1, 1, 0, 0, 1, 1, 1, 1, 0, 1), TSHS_9R = c(0, 0, 0, 0, 0, 0, 0, 1, 1, 0), TSHS_10R = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), TSHS_11R = c(0, 0, NA, 0, 0, 0, 0, 1, 0, 0), TSHS_12R = c(1, 0, 1, 0, 1, 0, 0, 0, 0, 0), TSHS_13R = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 1), TSHS_14R = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), TSHS_15R = c(0, 0, 1, 0, 0, 0, 0, 0, 0, 0), TSHS_16R = c(0, 0, 1, 0, 0, 0, 0, 0, 0, 0), TSHS_17R = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), TSHS_18R = c(0, 0, 0, 0, 1, 0, 0, 0, 0, 0), TSHS_19R = c(0, 0, 0, NA, 0, 0, 0, 0, 0, 0), TSHS_20R = c(0, 0, 0, 1, 0, 0, 0, 0, 0, 0), TSHS_21R = c(0, 0, 0, 0, 1, 0, 0, 0, 0, 0), TSHS_22R = c(0, 1, 0, 0, NA, 1, 0, 0, 0, 0), TSHS_23R = c(0, 0, 0, 0, NA, 1, 0, 0, 0, 1), TSHS_24R = c(0, 0, 0, 1, NA, 1, 0, 1, 1, 0), TSHS_25R = c(1, 1, 1, 0, 1, 1, 1, 1, 1, 1), TSHS_26R = c(1, 0, 1, 0, 0, 0, 0, 1, 0, 1), TSHS_27R = c(1, 0, 0, 1, 0, 1, 1, 0, 0, 1), TSHS_28R = c(0, 0, 0, 0, 0, 0, 0, 0, 1, 0), TSHS_29R = c(1, 0, 0, 0, 1, 0, 0, 0, 0, 0), TSHS_30R = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), TSHS_31R = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), TSHS_32R = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), TSHS_33R = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA, -10L), class = c("tbl_df", "tbl", "data.frame")) > rstudioapi::versionInfo() $`citation` To cite RStudio in publications use: RStudio Team (2018). RStudio: Integrated Development for R. RStudio, Inc., Boston, MA URL http://www.rstudio.com/. A BibTeX entry for LaTeX users is @Manual{, title = {RStudio: Integrated Development Environment for R}, author = {{RStudio Team}}, organization = {RStudio, Inc.}, address = {Boston, MA}, year = {2018}, url = {http://www.rstudio.com/}, } $`mode` [1] "desktop" $version [1] ‘1.2.1335’ > packageVersion("mice") [1] ‘3.8.0’ ``` Any help identifying what I am doing wrong in the code would be appreciated! Ian -- Ian McPhail, M.A. Clinical Psychology Graduate Student Department of Psychology, University of Saskatchewan [[alternative HTML version deleted]] ______________________________________________ [email protected] 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.
