[R-sig-ME] MCMCglmm predict failing with more than one fixed effect

[Tom Houslay]

Hi all,

Just closing the open question I had in case anyone else has had the same
issue using predict.MCMCglmm. Turns out that it didn't seem to like
predicting with a single value in any of the fixed effect terms - so even
if I just want to predict for a single value of something, I just have to
add in another value and then ignore those rows afterwards. I've appended a
little bit to the reproducible code from my last email to show how that's
working (see below).

Cheers

Tom

---

sleepstudy <- lme4::sleepstudy

# Basic model of sleepstudy with 1 fixed effect and simple random intercept
mcmc_ss_1 <- MCMCglmm(Reaction ~ Days,
                      random =~ Subject,
                      data = sleepstudy)

summary(mcmc_ss_1)

# Predicts fine on original data
predict(mcmc_ss_1)

# Create data on which to predict
df_ss_pred <- data.frame(Days = 0:9,
                         Subject = 350,
                         Reaction = 0)

# This prediction works
predict(mcmc_ss_1,
        newdata = df_ss_pred)

# Create new data frame with fake additional column
sleepstudy_2 <- cbind(sleepstudy,
                      extra = rnorm(nrow(sleepstudy)))

# Run model with additional fixed effect
mcmc_ss_2 <- MCMCglmm(Reaction ~ Days + extra,
                      random =~ Subject,
                      data = sleepstudy_2)

summary(mcmc_ss_2)

# Predict works fine from original data
predict(mcmc_ss_2)

# Create data frame on which to predict,
#  as before but now with new column added
df_ss_pred_2 <- as.data.frame(expand.grid(Reaction = 0,
                                          Days = 0:9,
                                          Subject = 350,
                                          extra = mean(sleepstudy_2$extra)))

# Prediction fails
predict(mcmc_ss_2,
        newdata = df_ss_pred_2)

# Check model formula
mcmc_ss_2$Fixed$formula

# Check variable names in data frame
str(sleepstudy_2)

# Check variable names in new data frame
str(df_ss_pred_2)


# Try adding another value for 'extra'
df_ss_pred_3 <- as.data.frame(expand.grid(Reaction = 0,
                                          Days = 0:9,
                                          Subject = 350,
                                          extra =
c(mean(sleepstudy_2$extra),

mean(sleepstudy_2$extra) + sd(sleepstudy_2$extra))))


# Prediction now works!
predict(mcmc_ss_2,
        newdata = df_ss_pred_3)

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