revisit docs on model formulas

man/rmd/gen_additive_mod_mgcv.Rmd

@@ -60,7 +60,7 @@ gen_additive_mod() %>%
 The smoothness of the terms will need to be manually specified (e.g., using `s(x, df = 10)`) in the formula. Tuning can be accomplished using the `adjust_deg_free` parameter. 
 
 
-However, when using a workflow, the best approach is to avoid using [workflows::add_formula()] and use [workflows::add_variables()] in conjunction with a model formula:
+When using a workflow, pass the _model formula_ to [add_model()]'s `formula` argument, and a simplified _preprocessing formula_ elsewhere.
 
 ```{r}
 spec <- 
@@ -69,13 +69,13 @@ spec <-
   set_mode("regression")
 
 workflow() %>% 
-  add_variables(outcomes = c(mpg), predictors = c(wt, gear, cyl, disp)) %>% 
   add_model(spec, formula = mpg ~ wt + gear + cyl + s(disp, k = 10)) %>% 
+  add_formula(mpg ~ wt + gear + cyl + disp) %>% 
   fit(data = mtcars) %>% 
   extract_fit_engine()
 ```
 
-The reason for this is that [workflows::add_formula()] will try to create the model matrix and fail to find/use `s()`.  
+To learn more about the differences between these formulas, see [`?model_formula`][parsnip::model_formula].
 
 ## Preprocessing requirements
 

man/rmd/gen_additive_mod_mgcv.md

@@ -96,7 +96,7 @@ gen_additive_mod() %>%
 The smoothness of the terms will need to be manually specified (e.g., using `s(x, df = 10)`) in the formula. Tuning can be accomplished using the `adjust_deg_free` parameter. 
 
 
-However, when using a workflow, the best approach is to avoid using [workflows::add_formula()] and use [workflows::add_variables()] in conjunction with a model formula:
+When using a workflow, pass the _model formula_ to [add_model()]'s `formula` argument, and a simplified _preprocessing formula_ elsewhere.
 
 
 ```r
@@ -106,8 +106,8 @@ spec <-
   set_mode("regression")
 
 workflow() %>% 
-  add_variables(outcomes = c(mpg), predictors = c(wt, gear, cyl, disp)) %>% 
   add_model(spec, formula = mpg ~ wt + gear + cyl + s(disp, k = 10)) %>% 
+  add_formula(mpg ~ wt + gear + cyl + disp) %>% 
   fit(data = mtcars) %>% 
   extract_fit_engine()
 ```
@@ -126,7 +126,7 @@ workflow() %>%
 ## GCV score: 4.225228
 ```
 
-The reason for this is that [workflows::add_formula()] will try to create the model matrix and fail to find/use `s()`.  
+To learn more about the differences between these formulas, see [`?model_formula`][parsnip::model_formula].
 
 ## Preprocessing requirements
 

man/rmd/glmnet-details.md

@@ -169,7 +169,7 @@ tidy(fit)
 ## 4 hp           -0.0101       1
 ## 5 drat          0            1
 ## 6 wt           -2.59         1
-## # … with 5 more rows
+## # ℹ 5 more rows
 ```
 
 Note that there is a `tidy()` method for `glmnet` objects in the `broom` package. If this is used directly on the underlying `glmnet` object, it returns _all of coefficients on the path_:
@@ -191,7 +191,7 @@ all_tidy_coefs
 ## 4 (Intercept)     4     24.7   3.89     0.347
 ## 5 (Intercept)     5     26.0   3.55     0.429
 ## 6 (Intercept)     6     27.2   3.23     0.497
-## # … with 634 more rows
+## # ℹ 634 more rows
 ```
 
 ```r

man/rmd/proportional_hazards_glmnet.Rmd

@@ -54,7 +54,7 @@ By default, [glmnet::glmnet()] uses the argument `standardize = TRUE` to center
 
 The model does not fit an intercept. 
 
-The model formula (which is required) can include _special_ terms, such as [survival::strata()]. This allows the baseline hazard to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. This is different than the syntax offered by the [glmnet::glmnet()] package (i.e., [glmnet::stratifySurv()]) which is not recommended here. 
+The model formula (which is required) can include _special_ terms, such as [survival::strata()]. This allows the baseline hazard to differ between groups contained in the function. (To learn more about using special terms in formulas with tidymodels, see [`?model_formula`][parsnip::model_formula].) The column used inside `strata()` is treated as qualitative no matter its type. This is different than the syntax offered by the [glmnet::glmnet()] package (i.e., [glmnet::stratifySurv()]) which is not recommended here.
 
 For example, in this model, the numeric column `rx` is used to estimate two different baseline hazards for each value of the column:
 

man/rmd/proportional_hazards_glmnet.md

@@ -61,7 +61,7 @@ By default, [glmnet::glmnet()] uses the argument `standardize = TRUE` to center
 
 The model does not fit an intercept. 
 
-The model formula (which is required) can include _special_ terms, such as [survival::strata()]. This allows the baseline hazard to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. This is different than the syntax offered by the [glmnet::glmnet()] package (i.e., [glmnet::stratifySurv()]) which is not recommended here. 
+The model formula (which is required) can include _special_ terms, such as [survival::strata()]. This allows the baseline hazard to differ between groups contained in the function. (To learn more about using special terms in formulas with tidymodels, see [`?model_formula`][parsnip::model_formula].) The column used inside `strata()` is treated as qualitative no matter its type. This is different than the syntax offered by the [glmnet::glmnet()] package (i.e., [glmnet::stratifySurv()]) which is not recommended here.
 
 For example, in this model, the numeric column `rx` is used to estimate two different baseline hazards for each value of the column:
 
@@ -89,10 +89,10 @@ predict(mod, pred_data, type = "survival", time = 500) %>%
 
 ```
 ## # A tibble: 2 × 5
-##   .time .pred_survival   age ecog.ps    rx
-##   <dbl>          <dbl> <dbl>   <dbl> <dbl>
-## 1   500          0.666    50       1     1
-## 2   500          0.769    50       1     2
+##   .eval_time .pred_survival   age ecog.ps    rx
+##        <dbl>          <dbl> <dbl>   <dbl> <dbl>
+## 1        500          0.666    50       1     1
+## 2        500          0.769    50       1     2
 ```
 
 Note that columns used in the `strata()` function _will_ also be estimated in the regular portion of the model (i.e., within the linear predictor).

man/rmd/proportional_hazards_survival.Rmd

@@ -26,7 +26,7 @@ The model does not fit an intercept.
 
 The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
 
-The model formula can include _special_ terms, such as [survival::strata()]. The allows the baseline hazard to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. 
+The model formula can include _special_ terms, such as [survival::strata()]. The allows the baseline hazard to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. To learn more about using special terms in formulas with tidymodels, see [`?model_formula`][parsnip::model_formula].
 
 For example, in this model, the numeric column `rx` is used to estimate two different baseline hazards for each value of the column:
 

man/rmd/proportional_hazards_survival.md

@@ -37,7 +37,7 @@ The model does not fit an intercept.
 
 The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
 
-The model formula can include _special_ terms, such as [survival::strata()]. The allows the baseline hazard to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. 
+The model formula can include _special_ terms, such as [survival::strata()]. The allows the baseline hazard to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. To learn more about using special terms in formulas with tidymodels, see [`?model_formula`][parsnip::model_formula].
 
 For example, in this model, the numeric column `rx` is used to estimate two different baseline hazards for each value of the column:
 

man/rmd/surv_reg_survival.Rmd

@@ -38,7 +38,7 @@ Note that `model = TRUE` is needed to produce quantile predictions when there is
 
 The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
 
-The model formula can include _special_ terms, such as [survival::strata()]. The allows the model scale parameter to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. 
+The model formula can include _special_ terms, such as [survival::strata()]. The allows the model scale parameter to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. To learn more about using special terms in formulas with tidymodels, see [`?model_formula`][parsnip::model_formula].
 
 For example, in this model, the numeric column `rx` is used to estimate two different scale parameters for each value of the column:
 

man/rmd/surv_reg_survival.md

@@ -40,7 +40,7 @@ Note that `model = TRUE` is needed to produce quantile predictions when there is
 
 The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
 
-The model formula can include _special_ terms, such as [survival::strata()]. The allows the model scale parameter to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. 
+The model formula can include _special_ terms, such as [survival::strata()]. The allows the model scale parameter to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. To learn more about using special terms in formulas with tidymodels, see [`?model_formula`][parsnip::model_formula].
 
 For example, in this model, the numeric column `rx` is used to estimate two different scale parameters for each value of the column:
 

man/rmd/survival_reg_survival.Rmd

@@ -42,7 +42,7 @@ In the translated syntax above, note that `model = TRUE` is needed to produce qu
 
 The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
 
-The model formula can include _special_ terms, such as [survival::strata()]. The allows the model scale parameter to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. 
+The model formula can include _special_ terms, such as [survival::strata()]. The allows the model scale parameter to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. To learn more about using special terms in formulas with tidymodels, see [`?model_formula`][parsnip::model_formula].
 
 For example, in this model, the numeric column `rx` is used to estimate two different scale parameters for each value of the column:
 

man/rmd/survival_reg_survival.md

@@ -44,7 +44,7 @@ In the translated syntax above, note that `model = TRUE` is needed to produce qu
 
 The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
 
-The model formula can include _special_ terms, such as [survival::strata()]. The allows the model scale parameter to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. 
+The model formula can include _special_ terms, such as [survival::strata()]. The allows the model scale parameter to differ between groups contained in the function. The column used inside `strata()` is treated as qualitative no matter its type. To learn more about using special terms in formulas with tidymodels, see [`?model_formula`][parsnip::model_formula].
 
 For example, in this model, the numeric column `rx` is used to estimate two different scale parameters for each value of the column: