Error in eval(predvars, data, env) : object 'SEXC' not found

[JSC67]

I have a data frame in my environment called Covars, which has subject-level information pertinent to various subjects. From this I made a linear model for predicting missing weight and height values based on other, non-missing columns. All was well. Then I tried to use such columns and make a vector of predicted values for imputing missing creatinine values, just analogously to how I had imputed values for weight and height. However, now it complains that it can't find a variable that it had no trouble finding earlier.

# 3rd model: Weight as function of age, sex, patient, country
lm.Wt.vs.AgeSexPatientCountry <-
  lm(Covars$WEIGHT ~ Covars$AGE + Covars$SEXC + Covars$AGE*Covars$SEXC +
                     Covars$PATIENT + Covars$COUNTRY,
     na.action = na.exclude)
summary(lm.Wt.vs.AgeSexPatientCountry)       # adjusted R-squared: 0.3611
# I skip showing the output; all is well so far.

predWEIGHT <- predict.lm(object = lm.Wt.vs.AgeSexPatientCountry,
                         newdata = data.frame(Covars$AGE,    # no NA's in AGE
                                              Covars$SEXC,   # no NA's in SEXC
                                              Covars$PATIENT,  # no NA's
                                              Covars$COUNTRY) # no NA's
                         )  # 29295 large numeric named vector
#  predWEIGHT gets made, 29295 elements.  All is well still.
sum(is.na(predWEIGHT))   #  0
summary(Covars$WEIGHT - predWEIGHT)
#    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
# -60.324 -10.223  -1.444   0.000   8.461 118.908 

# Covars$SEXC clearly exists and was found above, but now this:

# Try both race and country.
lm.CREATvSexAge2.LBM.S_Lint.PatientRaceCountry <-
  lm(CREAT ~ SEXC + AGE + I(AGE^2) + LBM + SEXC:LBM + PATIENT + RACE2 + COUNTRY,
     data = Covars)
summary(lm.CREATvSexAge2.LBM.S_Lint.PatientRaceCountry)   # Adj. R^2:  0.2523
plot(x = lm.CREATvSexAge2.LBM.S_Lint.PatientRaceCountry$fitted.values,
          # SEXC + AGE + I(AGE^2) + LBM + SEXC:LBM + PATIENT + RACE2 + COUNTRY
     y = lm.CREATvSexAge2.LBM.S_Lint.PatientRaceCountry$residuals +
         lm.CREATvSexAge2.LBM.S_Lint.PatientRaceCountry$fitted.values,
          # CREAT itself
     panel.first = grid(8,8),
     ylim = c(0, 250),
     xlab = "model fitted values of SEX, AGE, LBM, PATIENT, RACE, COUNTRY",
     ylab = "creatinine (μmol/L)",
     #log = "y",
     pch = '.', cex = 0.1, col = "blue")
# The plot works fine.

# The summary on this linear model and the above plot work fine, but the predicted CREAT does not:
### Now impute CREAT values.
predCREAT <- predict.lm(object = lm.CREATvSexAge2.LBM.S_Lint.PatientRaceCountry,
                        newdata = data.frame(Covars$AGE,
                                             Covars$SEXC,
                                             Covars$LBM,
                                             Covars$PATIENT,
                                             Covars$RACE2,
                                             Covars$COUNTRY)
) 
# Error in eval(predvars, data, env) : object 'SEXC' not found

This error is very strange considering my successful predWEIGHT above. Can someone please help me?

[nirgrahamuk]

Hello.
Thanks for providing code , but you could take further steps to make it more convenient for other forum users to help you.

Share some representative data that will enable your code to run and show the problematic behaviour.

You might use tools such as the library datapasta, or the base function dput() to share a portion of data in code form, i.e. that can be copied from forum and pasted to R session.

Reprex Guide

Aside from that, I think its worth a comment that use of $ syntax within an lm() construction is a bad code smell, and you are best advised to use the data = param to stipulate where the lm should look for the variables (as you do further down in your code).