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Get individual predictions from a fitted aba model

Source: R/aba_predict.R
aba_predict.Rd

This function allows you to get the fitted/predicted values from data used to fit an aba model or from new data. This is essentially an extension of the broom::augment() function.

Usage

aba_predict(model, newdata = NULL, merge = TRUE, augment = FALSE)

Arguments

model

a fitted aba model. The model to get predictions from.

newdata

dataframe (optional). New data to get predictions from. If this is null, predictions will be provided for the data originally used to fit the aba model

merge

logical. Whether to merge all the predictions into the original dataset or to store the predictions for each group - outcome - stat combo in a dataframe separately.

augment

logical. Whether to include original data with predictions.

Value

a dataframe with original data and with fitted/predicted values added for each group-outcome-stat-predictor combination.

Examples

data <- adnimerge %>% dplyr::filter(VISCODE == 'bl')

model <- data %>% aba_model() %>%
  set_groups(
    everyone(),
    DX_bl %in% c('MCI', 'AD')
  ) %>%
  set_outcomes(CDRSB_bl, MMSE_bl) %>%
  set_predictors(
    PLASMA_PTAU181_bl, PLASMA_NFL_bl,
    c(PLASMA_PTAU181_bl, PLASMA_NFL_bl)
  ) %>%
  set_covariates(AGE, GENDER, EDUCATION) %>%
  set_stats('lm')

model <- model %>% fit()
#> [1] "CDRSB_bl ~ AGE + GENDER + EDUCATION"
#> [1] "CDRSB_bl ~ AGE + GENDER + EDUCATION + PLASMA_PTAU181_bl"
#> [1] "CDRSB_bl ~ AGE + GENDER + EDUCATION + PLASMA_NFL_bl"
#> [1] "CDRSB_bl ~ AGE + GENDER + EDUCATION + PLASMA_PTAU181_bl + PLASMA_NFL_bl"
#> [1] "MMSE_bl ~ AGE + GENDER + EDUCATION"
#> [1] "MMSE_bl ~ AGE + GENDER + EDUCATION + PLASMA_PTAU181_bl"
#> [1] "MMSE_bl ~ AGE + GENDER + EDUCATION + PLASMA_NFL_bl"
#> [1] "MMSE_bl ~ AGE + GENDER + EDUCATION + PLASMA_PTAU181_bl + PLASMA_NFL_bl"
#> [1] "CDRSB_bl ~ AGE + GENDER + EDUCATION"
#> [1] "CDRSB_bl ~ AGE + GENDER + EDUCATION + PLASMA_PTAU181_bl"
#> [1] "CDRSB_bl ~ AGE + GENDER + EDUCATION + PLASMA_NFL_bl"
#> [1] "CDRSB_bl ~ AGE + GENDER + EDUCATION + PLASMA_PTAU181_bl + PLASMA_NFL_bl"
#> [1] "MMSE_bl ~ AGE + GENDER + EDUCATION"
#> [1] "MMSE_bl ~ AGE + GENDER + EDUCATION + PLASMA_PTAU181_bl"
#> [1] "MMSE_bl ~ AGE + GENDER + EDUCATION + PLASMA_NFL_bl"
#> [1] "MMSE_bl ~ AGE + GENDER + EDUCATION + PLASMA_PTAU181_bl + PLASMA_NFL_bl"

# add model predictions to original data
data_augmented <- model %>% aba_predict()

# store predictions separately by group - outcome - stat combination
data_augmented2 <- model %>% aba_predict(merge = FALSE)