The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

Controlling behavior of model fitting functions

library(postcard)
library(magrittr)
withr::local_seed(1395878)
withr::local_options(list(postcard.verbose = 0))

For introductory examples on how to use the package, see vignette("postcard").

In this vignette, we will explain how to alter the default behavior of the model fitting functions rctglm() and rctglm_with_prognosticscore().

Generating some data to run examples

As in vignette("postcard"), we simulate data using the glm_data() function from the package.

n <- 1000
b0 <- 1
b1 <- 3
b2 <- 2

dat_gaus <- glm_data(
  Y ~ b0+b1*sin(W)^2+b2*A,
  W = runif(n, min = -2, max = 2),
  A = rbinom(n, 1, prob = 1/2)
)

dat_gaus_hist <- glm_data(
  Y ~ b0+b1*sin(W)^2,
  W = runif(n, min = -2, max = 2)
)

dat_pois <- glm_data(
  Y ~ b0+b1*sin(W)^2+b2*A,
  W = runif(n, min = -2, max = 2),
  A = rbinom(n, 1, 1/2),
  family = poisson(link = "log")
)

Controlling verbosity

See package level options documentation in options(), giving information on how to change package behavior through options and environmental variables. Only option is verbose, which controls the amount of information printed to the console.

As a default, verbose = 2, meaning various information printed throughout the algorithm. Change to verbose = 1 for a little less information or verbose = 0 for no information.

Below we showcase the information that is printed with different specifications of verbosity.

 # Default amount of printing
ate <- rctglm(
  formula = Y ~ A + W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_gaus,
  verbose = 2)
#> 
#> ── Symbolic differentiation of estimand function ──
#> 
#> ℹ Symbolically deriving partial derivative of the function 'psi1 - psi0' with respect to 'psi0' as: '-1'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv0`
#> ℹ Symbolically deriving partial derivative of the function 'psi1 - psi0' with respect to 'psi1' as: '1'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv1`
ate_prog <- rctglm_with_prognosticscore(
  formula = Y ~ A + W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_gaus,
  data_hist = dat_gaus_hist,
  verbose = 2)
#> 
#> ── Fitting prognostic model ──
#> 
#> ℹ Created formula for fitting prognostic model as: Y ~ .
#> ℹ Fitting learners
#> • mod_mars
#> • mod_lm
#> • mod_gbt
#> i    No tuning parameters. `fit_resamples()` will be attempted
#> i 1 of 3 resampling: mod_mars
#> ✔ 1 of 3 resampling: mod_mars (680ms)
#> i    No tuning parameters. `fit_resamples()` will be attempted
#> i 2 of 3 resampling: mod_lm
#> ✔ 2 of 3 resampling: mod_lm (340ms)
#> i 3 of 3 tuning:     mod_gbt
#> ✔ 3 of 3 tuning:     mod_gbt (5.1s)
#> ℹ Model with lowest RMSE: mod_mars
#> ℹ Investigate trained learners and fitted model in `prognostic_info` list element
#> 
#> ── Symbolic differentiation of estimand function ──
#> 
#> ℹ Symbolically deriving partial derivative of the function 'psi1 - psi0' with respect to 'psi0' as: '-1'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv0`
#> ℹ Symbolically deriving partial derivative of the function 'psi1 - psi0' with respect to 'psi1' as: '1'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv1`
# At little less printing
ate <- rctglm(
  formula = Y ~ A + W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_gaus,
  verbose = 1)
#> 
#> ── Symbolic differentiation of estimand function ──
#> 
#> ℹ Symbolically deriving partial derivative of the function 'psi1 - psi0' with respect to 'psi0' as: '-1'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv0`
#> ℹ Symbolically deriving partial derivative of the function 'psi1 - psi0' with respect to 'psi1' as: '1'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv1`
ate_prog <- rctglm_with_prognosticscore(
  formula = Y ~ A + W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_gaus,
  data_hist = dat_gaus_hist,
  verbose = 1)
#> 
#> ── Fitting prognostic model ──
#> 
#> ℹ Created formula for fitting prognostic model as: Y ~ .
#> ℹ Fitting learners
#> • mod_mars
#> • mod_lm
#> • mod_gbt
#> ℹ Model with lowest RMSE: mod_gbt
#> 
#> ── Symbolic differentiation of estimand function ──
#> 
#> ℹ Symbolically deriving partial derivative of the function 'psi1 - psi0' with respect to 'psi0' as: '-1'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv0`
#> ℹ Symbolically deriving partial derivative of the function 'psi1 - psi0' with respect to 'psi1' as: '1'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv1`
# No printing
ate <- rctglm(
  formula = Y ~ A + W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_gaus,
  verbose = 0)
ate_prog <- rctglm_with_prognosticscore(
  formula = Y ~ A + W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_gaus,
  data_hist = dat_gaus_hist,
  verbose = 0)

Verbosity is suppressed in the rest of the vignette by setting option postcard.verbose to 0.

Specifying the estimand

The default estimand_fun in rctglm() and rctglm_with_prognosticscore() is the average treatment effect (ATE).

However, it’s possible to specify any estimand by giving any function with 2 named arguments, psi0 and psi1. Note that in addition to estimand_fun, the functions also take arguments estimand_fun_deriv0 and estimand_fun_deriv1, which is the derivative with respect to psi0 and psi1, respectively. As a default, these are NULL, which means symbolic differentiation is performed on the estimand_fun to derive them automatically.

Note that when verbose > 0, information is printed to the console about the results of the symbolic differentiation. We run the below code with verbose = 1 though otherwise muted in this vignette to showcase this.

Built-in estimands - average treatment effect and rate ratio

Built in is the ATE and rate ratio, which can be specified with character strings. As is apparent from the documentation of rctglm() and rctglm_with_prognosticscore(), the default of estimand_fun is "ate", and similarly the user can specify estimand_fun = "rate_ratio" to use the estimand function psi1 / psi0 as seen below:

rate_ratio <- rctglm(
  formula = Y ~ A + W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_pois,
  family = "poisson",
  estimand_fun = "rate_ratio",
  verbose = 1)
#> 
#> ── Symbolic differentiation of estimand function ──
#> 
#> ℹ Symbolically deriving partial derivative of the function 'psi1/psi0' with respect to 'psi0' as: '-(psi1/psi0^2)'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv0`
#> ℹ Symbolically deriving partial derivative of the function 'psi1/psi0' with respect to 'psi1' as: '1/psi0'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv1`
rate_ratio$estimand_funs
#> $f
#> function (psi1, psi0) 
#> psi1/psi0
#> <bytecode: 0x00000283dc9a80a0>
#> <environment: 0x00000283dcaa28d0>
#> 
#> $d0
#> function (psi1, psi0) 
#> -(psi1/psi0^2)
#> <environment: 0x00000283dcaa28d0>
#> 
#> $d1
#> function (psi1, psi0) 
#> 1/psi0
#> <environment: 0x00000283dcaa28d0>

Specifying any estimand

Below is an example showing the specification of a custom defined function with arguments psi0 and psi1.

nonsense_estimand_fun <- function(psi1, psi0) {
  psi1 / sqrt(psi0) * 2 - 1
}

nonsense_estimand <- rctglm(
  formula = Y ~ A * W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_pois,
  family = poisson(),
  estimand_fun = nonsense_estimand_fun,
  verbose = 1)
#> 
#> ── Symbolic differentiation of estimand function ──
#> 
#> ℹ Symbolically deriving partial derivative of the function '{     psi1/sqrt(psi0) * 2 - 1 }' with respect to 'psi0' as: '-(psi1/(psi0 * sqrt(psi0)))'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv0`
#> ℹ Symbolically deriving partial derivative of the function '{     psi1/sqrt(psi0) * 2 - 1 }' with respect to 'psi1' as: '2/sqrt(psi0)'.
#> • Alternatively, specify the derivative through the argument
#> `estimand_fun_deriv1`
nonsense_estimand$estimand_funs
#> $f
#> function(psi1, psi0) {
#>   psi1 / sqrt(psi0) * 2 - 1
#> }
#> 
#> $d0
#> function (psi1, psi0) 
#> -(psi1/(psi0 * sqrt(psi0)))
#> 
#> $d1
#> function (psi1, psi0) 
#> 2/sqrt(psi0)

Variance estimation using cross validation

The variance is estimated as the variance of the influence function of the marginal effect. During the calculation of this function, counterfactual predictions are made for all observations, using a GLM to predict their outcome in case they were in exposure group 0 and 1, respectively.

cv_variance is an argument in rctglm() and rctglm_with_prognosticscore() that enables obtaining these counterfactual predictions as out-of-sample (OOS) prediction by using cross validation.

Prognostic covariate adjustment

The rctglm_with_prognosticscore() uses the function fit_best_learner() to fit a prognostic model to the historical data, data_hist. Thereafter, the model is used to predict prognostic scores for all observations in data before using these scores as a covariate when performing plug-in estimation in a GLM using rctglm.

The behavior of fit_best_learner() and subsequently fitting the prognostic model on data_hist in rctglm_with_prognosticscore() is to fit a discrete super learner (discrete to avoid overfitting) by finding the model with the lowest RMSE among a list of models. The algorithm uses a default of 5 folds for cross validation (cv_prog_folds) and if no formula is given for the prognostic model (prog_formula), the function attempts to model a response with the same name as given in the formula using an intercept and main effect from all variables in data_hist.

Specifying learners

fit_best_learner has a list of default models to use for fitting the discrete super learner, which can be seen in the section below. However, it’s easy for the user to specify a list of other learners to train the discrete super learner. The package utilises the framework of tidymodels, and it can be seen below how the list of models can look like.

Default learners

Below we show the code of the unexported default_learners function, which creates a list of default learners that are used in fit_best_learner() and rctglm_with_prognosticscore().

The body of the function thus represents a valid way of specifying the learners argument.

default_learners
#> function () 
#> {
#>     list(mars = list(model = parsnip::mars(mode = "regression", 
#>         prod_degree = 3) %>% parsnip::set_engine("earth")), lm = list(model = parsnip::linear_reg() %>% 
#>         parsnip::set_engine("lm")), gbt = list(model = parsnip::boost_tree(mode = "regression", 
#>         trees = parsnip::tune("trees"), tree_depth = parsnip::tune("tree_depth"), 
#>         learn_rate = 0.1) %>% parsnip::set_engine("xgboost"), 
#>         grid = data.frame(trees = seq(from = 25, to = 500, by = 25), 
#>             tree_depth = 3)))
#> }
#> <bytecode: 0x00000283dcb5d9e8>
#> <environment: namespace:postcard>

Creating own list of learners

A listing of models is available at the tidymodels website, and the user can specify a list of any of those models as the learners argument.

Below is an example of fitting the prognostic model as a discrete super learner with the best RMSE among a random forest and linear support vector machines model.

learners <- list(
  rf = list(
    model = parsnip::rand_forest(
      mode = "regression",
      trees = 500,
      min_n = parsnip::tune("min_n")
    ) %>% 
      parsnip::set_engine("ranger"),
    grid = data.frame(
      min_n = 1:10
    )
  ),
  svm.linear = list(
    model = parsnip::svm_linear(
      mode = "regression",
      cost = parsnip::tune("cost"),
      margin = parsnip::tune("margin")) %>% 
      parsnip::set_engine("LiblineaR"),
    grid = data.frame(
      cost = 1:5,
      margin = seq(0.1, 0.5, 0.1)
    )
  )
)

model_own_learners <- rctglm_with_prognosticscore(
  formula = Y ~ A * W,
  exposure_indicator = A,
  exposure_prob = 1/2,
  data = dat_gaus,
  data_hist = dat_gaus_hist,
  learners = learners)

Inspecting the prognostic model

It’s possible to view information regarding the fit of the prognostic model in the rctglm_prog class object that rctglm_with_prognosticscore() returns by looking at the list element prognostic_info. A shorthand way of doing this is using the method prog().

Inside this list element are elements

Note that we change the value of data to only show the first rows to not take up too much space when printing in the vignette.

prog_info <- prog(model_own_learners)
prog_info$data <- head(prog_info$data)
prog_info
#> $formula
#> Y ~ .
#> <environment: 0x00000283f01895f0>
#> 
#> $model_fit
#> ══ Workflow [trained] ══════════════════════════════════════════════════════════
#> Preprocessor: Formula
#> Model: rand_forest()
#> 
#> ── Preprocessor ────────────────────────────────────────────────────────────────
#> Y ~ .
#> 
#> ── Model ───────────────────────────────────────────────────────────────────────
#> Ranger result
#> 
#> Call:
#>  ranger::ranger(x = maybe_data_frame(x), y = y, num.trees = ~500,      min.node.size = min_rows(~10L, x), num.threads = 1, verbose = FALSE,      seed = sample.int(10^5, 1)) 
#> 
#> Type:                             Regression 
#> Number of trees:                  500 
#> Sample size:                      1000 
#> Number of independent variables:  1 
#> Mtry:                             1 
#> Target node size:                 10 
#> Variable importance mode:         none 
#> Splitrule:                        variance 
#> OOB prediction error (MSE):       1.383821 
#> R squared (OOB):                  0.3918115 
#> 
#> $learners
#> $learners$rf
#> $learners$rf$model
#> Random Forest Model Specification (regression)
#> 
#> Main Arguments:
#>   trees = 500
#>   min_n = parsnip::tune("min_n")
#> 
#> Computational engine: ranger 
#> 
#> 
#> $learners$rf$grid
#>    min_n
#> 1      1
#> 2      2
#> 3      3
#> 4      4
#> 5      5
#> 6      6
#> 7      7
#> 8      8
#> 9      9
#> 10    10
#> 
#> 
#> $learners$svm.linear
#> $learners$svm.linear$model
#> Linear Support Vector Machine Model Specification (regression)
#> 
#> Main Arguments:
#>   cost = parsnip::tune("cost")
#>   margin = parsnip::tune("margin")
#> 
#> Computational engine: LiblineaR 
#> 
#> 
#> $learners$svm.linear$grid
#>   cost margin
#> 1    1    0.1
#> 2    2    0.2
#> 3    3    0.3
#> 4    4    0.4
#> 5    5    0.5
#> 
#> 
#> 
#> $cv_folds
#> [1] 5
#> 
#> $data
#>           Y          W
#> 1 4.0429142  1.8336410
#> 2 5.1553821  1.8259065
#> 3 4.5318651 -1.0377573
#> 4 4.1458895 -1.5460878
#> 5 2.2437462  0.3011256
#> 6 0.5276273  0.5514324

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.