Find and deploy utility mapping models

• 1: Example 1: Predict health utility from psychological and functional measures (PHQ-9 and SOFAS)
• 2: Example 2: Predict health utility from psychological measures (PHQ-9 and GAD-7)

1 - Example 1: Predict health utility from psychological and functional measures (PHQ-9 and SOFAS)

library(ready4)
library(ready4use)
library(youthu)

This vignette outlines a workflow for:

• Searching, selecting and retrieving transfer to utility models;
• Preparing a prediction dataset for use with a selected transfer to utility model; and
• Applying the selected transfer to utility model to a prediction dataset to predict Quality Adjusted Life Years (QALYs).

The practical value of implementing such a workflow is discussed in the economic analysis vignette and a scientific manuscript. Note, this example uses fake data - it should should not be used to inform decision making.

Search, select and retrieve transfer to utility models

To identify datasets that contain transfer to utility models compatible with youthu (ie those developped with the TTU package), you can use the get_ttu_dv_dss function. The function searches specified dataverses (in the below example, the TTU dataverse) for datasets containing output from the TTU package.

ttu_dv_dss_tb <- get_ttu_dv_dss("TTU")

The ttu_dv_dss_tb table summarises some pertinent details about each dataset containing TTU models found by the preceding command. These details include a link to any scientific summary (the “Article” column) associated with a dataset.

To identify models that predict a specified type of health utility from one or more of a specified subset of predictors, use:

mdls_lup <- get_mdls_lup(ttu_dv_dss_tb = ttu_dv_dss_tb,
                         utility_type_chr = "AQoL-6D",
                         mdl_predrs_in_ds_chr = c("PHQ9 total score",
                                                  "SOFAS total score"))

The preceding command will produce a lookup table with information that includes the catalogue names of models, the predictors used in each model and the analysis that generated each one.

To review the summary information about the predictive performance of a specific model, use:

get_dv_mdl_smrys(mdls_lup,
                 mdl_nms_chr = "PHQ9_SOFAS_1_OLS_CLL")
#> $PHQ9_SOFAS_1_OLS_CLL
#>        Parameter Estimate    SE          95% CI
#> 1 SD (Intercept)    0.348 0.017   0.312 , 0.382
#> 2      Intercept    0.428 0.129   0.174 , 0.686
#> 3  PHQ9 baseline   -9.115 0.249 -9.601 , -8.618
#> 4    PHQ9 change   -7.331 0.339 -8.007 , -6.665
#> 5 SOFAS baseline    0.960 0.172   0.616 , 1.292
#> 6   SOFAS change    1.146 0.235   0.674 , 1.607
#> 7             R2    0.767 0.012   0.743 , 0.788
#> 8           RMSE    0.925 0.004   0.922 , 0.928
#> 9          Sigma    0.406 0.012   0.384 , 0.429

More information about a selected model can be found in the online model catalogue, the link to which can be obtained with the following command:

get_mdl_ctlg_url(mdls_lup,
                 mdl_nm_1L_chr = "PHQ9_SOFAS_1_OLS_CLL")

Prepare a prediction dataset for use with a selected transfer to utility model

Import data

You can now import and inspect the dataset you plan on using for prediction. In the below example we use fake data.

data_tb <- make_fake_ds_one()

Confirm dataset can be used as a prediction dataset

The prediction dataset must contain variables that correspond to all the predictors of the model you intend to apply. The allowable range and required class of each predictor variable are described in the min_val_dbl, max_val_dbl and class_chr columns of the model predictors lookup table, which can be accessed with a call to the get_predictors_lup function.

predictors_lup <- get_predictors_lup(mdls_lup = mdls_lup,
                                     mdl_nm_1L_chr = "PHQ9_SOFAS_1_OLS_CLL")

The prediction dataset must also include both a unique client identifier variable and a measurement time-point identifier variable (which must be a factor with two levels). The dataset also needs to be in long format (ie where measures at different time-points for the same individual are stacked on top of each other in separate rows). We can confirm these conditions hold by creating a dataset metadata object using the make_predn_metadata_ls function. In creating the metadata object, the function checks that the dataset can be used in conjunction with the model specified at the mdl_nm_1L_chr argument. If the prediction dataset uses different variable names for the predictors to those specified in the predictors_lup lookup table, a named vector detailing the correspondence between the two sets of variable names needs to be passed to the predr_vars_nms_chr argument. Finally, if you wish to specify a preferred variable name to use for the predicted utility values when applying the model, you can do this by passing this name to the utl_var_nm_1L_chr argument.

predn_ds_ls <- make_predn_metadata_ls(data_tb,
                                      id_var_nm_1L_chr = "UID",
                                      msrmnt_date_var_nm_1L_chr = "Date",
                                      predr_vars_nms_chr = c(PHQ9 = "PHQ_total",SOFAS = "SOFAS_total"),
                                      round_var_nm_1L_chr = "Timepoint",
                                      round_bl_val_1L_chr = "Baseline",
                                      utl_var_nm_1L_chr = "AQoL6D_HU",
                                      mdls_lup = mdls_lup,
                                      mdl_nm_1L_chr = "PHQ9_SOFAS_1_OLS_CLL")

Apply the selected transfer to utility model to a prediction dataset to predict Quality Adjusted Life Years (QALYs)

Predict health utility at baseline and follow-up timepoints

To generate utility predictions we use the add_utl_predn function. The function needs to be supplied with the prediction dataset (the value passed to argument data_tb) and the validated prediction metadata object we created in the previous step.

data_tb <- add_utl_predn(data_tb,
                         predn_ds_ls = predn_ds_ls)
#> Joining with `by = join_by(UID, Timepoint)`

By default the add_utl_predn function samples model parameter values based on a table of model coefficients when making predictions and constrains predictions to an allowed range. You can override these defaults by adding additional arguments new_data_is_1L_chr = "Predicted" (which uses mean parameter values), force_min_max_1L_lgl = F (removes range constraint) and (if the source dataset makes available downloadable model objects) make_from_tbl_1L_lgl = F. These settings will produce different predictions. It is strongly recommended that you consult the model catalogue (see above) to understand how such decisions may affect the validity of the predicted values that will be generated.

Our health utility predictions are now available for use and are summarised below.

summary(data_tb$AQoL6D_HU)
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#> 0.06525 0.42832 0.62654 0.62142 0.83585 0.99999

Calculate QALYs

The last step is to calculate Quality Adjusted Life Years, using a method assuming a linear rate of change between timepoints.

data_tb <- data_tb %>% add_qalys_to_ds(predn_ds_ls = predn_ds_ls,
                                       include_predrs_1L_lgl = F,
                                       reshape_1L_lgl = F)

2 - Example 2: Predict health utility from psychological measures (PHQ-9 and GAD-7)

This vignette article is abridged and modified version of another article on predicting Quality Adjusted Life Years with youthu.

Motivation

This article illustrates how to make QALY predictions using a dataset in wide format with no health-utility measures but containing two psychological measures (GAD-7 and PHQ-9).

Install youthu

If not already installed it will be necessary to install the youthu R library. As youthu is not yet available on CRAN, it will be necessary to install it directly from its GitHub repository using an R package like remotes or devtools.

# Uncomment and run if installation is required.
# utils::install.packages("devtools") 
# devtools::install_github("ready4-dev/youthu")

Load required packages

We now load the libraries we will be using in subsequent steps. Note, both the ready4, ready4show and ready4use ready4 framework libraries will have been installed automatically when youthu was installed. The specific readyforwhatsnext module library and dplyr, purrr, stringr and tidyr CRAN libraries will have been installed at the same time.

library(ready4)
library(ready4show)
library(ready4use)
library(specific)
library(youthu)

Specify data sources

We begin by specifying the sources for our data. In this example, our data sources are online repositories.

X <- Ready4useRepos(dv_nm_1L_chr = "fakes", dv_ds_nm_1L_chr = "https://doi.org/10.7910/DVN/HJXYKQ", 
                    dv_server_1L_chr = "dataverse.harvard.edu",
                    gh_repo_1L_chr = "ready4-dev/youthu", gh_tag_1L_chr = "v0.0.0.91125")

Inspect dataset

We can now inspect the dataset we will be using to make predictions. As this is a demonstration article we are going to create a custom synthetic dataset. Our first step in doing so is to ingest a preexisting synthetic dataset (in long format) using the method explained in another vignette article

data_tb <- ingest(X, fls_to_ingest_chr = c("ymh_phq_gad_tb"), metadata_1L_lgl = F)

Our resulting dataset has unique IDs for each participant (character class), timestamps for each data collection timepoint (Date class variables) and GAD-7 and PHQ-9 scores for each timepoint (integer class).

data_tb %>% head() %>% ready4show::print_table(caption_1L_chr = "Dataset", output_type_1L_chr = "HTML") 

Get mapping models

We retrieve details of relevant AQoL-6D mapping models for wither of the predictors we plan on using. How these models were derived is described in a pre-print and details of model performance is included in catalogues available in an open access data repository.

mdls_lup <- get_mdls_lup(ttu_dv_dss_tb = get_ttu_dv_dss("TTU"),
                         utility_type_chr = "AQoL-6D",
                         mdl_predrs_in_ds_chr = c("GAD7 total score", "PHQ9 total score"))

mdls_lup[,c(1,2,5)] %>% 
  ready4show::print_table(caption_1L_chr = "Available models", output_type_1L_chr = "HTML") 

We select our preferred model and retrieve summary data about the model’s predictor variables.

predictors_lup <- get_predictors_lup(mdls_lup = mdls_lup, mdl_nm_1L_chr = "GAD7_PHQ9_1_OLS_CLL")

exhibit(predictors_lup)

Transform prediction dataset

To be used with the mapping models available to us, our prediction dataset needs to be in long format. We perform the necessary transformation.

data_tb <- transform_ds_to_long(data_tb, predictors_chr = c("gad7", "phq9"),
                             msrmnt_date_var_nm_1L_chr = "d_interview_date", round_var_nm_1L_chr = "When")
#> Joining with `by = join_by(case_id, fkClientID, When)`
#> Joining with `by = join_by(case_id, fkClientID, When)`

We drop records where we are missing data for either GAD7 or PHQ9 at either timepoint.

data_tb <- transform_ds_to_drop_msng(data_tb, predictors_chr = c("gad7", "phq9"), 
                                      uid_var_nm_1L_chr = "fkClientID")

We now predict AQoL-6D health utility for each case with complete data.

predn_ds_ls <- make_predn_metadata_ls(data_tb,
                                      id_var_nm_1L_chr = "fkClientID",
                                      msrmnt_date_var_nm_1L_chr = "d_interview_date",
                                      predr_vars_nms_chr = c(GAD7 = "gad7", PHQ9 = "phq9"),
                                      round_var_nm_1L_chr = "When",
                                      round_bl_val_1L_chr = "t1",
                                      utl_var_nm_1L_chr = "AQoL6D_HU",
                                      mdls_lup = mdls_lup,
                                      mdl_nm_1L_chr = "GAD7_PHQ9_1_OLS_CLL")
data_tb <- add_utl_predn(data_tb, new_data_is_1L_chr = "Predicted", predn_ds_ls = predn_ds_ls)
#> Joining with `by = join_by(fkClientID, When)`

Finally, we derive QALY predictions from the health utility measures at both time-points.

data_tb <- data_tb %>% add_qalys_to_ds(predn_ds_ls = predn_ds_ls, include_predrs_1L_lgl = F, reshape_1L_lgl = T)

data_tb %>% head() %>%
  ready4show::print_table(caption_1L_chr = "Final dataset", output_type_1L_chr = "HTML",
                          scroll_box_args_ls = list(width = "100%"))