Documentation fixes.

vignettes/cohortBuilder.Rmd

@@ -374,14 +374,15 @@ specific source (i.e. `dplyr` for `tblist` and `dbplyr` for `db` source):
 code(librarian_cohort)
 ```
 
-We can see above, the resulting code uses `source` object, which creation can be
+We can see above, the resulting code uses `source` object, which creation code can be
 defined separately while creating it:
 
 ```{r}
 librarian_source <- set_source(
   as.tblist(librarian),
   source_code = quote({
-    source <- list(attributes = list(datasets = librarian))
+    source <- list()
+    source$dtconn <- as.tblist(librarian)
   })
 )
 
@@ -409,7 +410,14 @@ librarian_cohort <- librarian_source %>%
 code(librarian_cohort)
 ```
 
-The second option allows to restore cohort configuration using its state.
+What's more, you can manipulate the output with additional arguments:
+
+- `include_methods` - list of methods names which definition should be printed in output,
+- `include_action` - list of actions names (such as "pre_filtering") that should be included in output,
+- `modifier` - a custom modifier of data.frame storing reproducible code parts,
+- `mark_step` - should step ID be presented in output.
+
+The second option for achieving reproducibility allows to restore cohort configuration using its state.
 The cohort state is a list (or json) storing information about all the steps and filters configuration.
 
 You may get the state with `get_state` method:

vignettes/managing-cohort.Rmd

@@ -148,21 +148,23 @@ See `vignette("cohort-configuration")`.
 The last Cohort configuration component - source, can be also managed within the Cohort itself.
 With `update_source` method you can change the source defined in the existing Cohort.
 
-Below we update cohort with Source having `source_code` parameter defined:
+Below we update cohort with Source having `source_code` parameter defined.
+The argument is responsible to generate `source` object definition printed in the reproducible code (you can use it when the default method doesn't print reasonable output).
+
 ```{r}
-code(librarian_cohort)
+code(librarian_cohort, include_methods = NULL)
 
 new_source <- set_source(
   as.tblist(librarian),
   source_code = quote({
-    source <- list(attributes = list(datasets = librarian))
+    source <- list()
+    source$dtconn <- as.tblist(librarian)
   })
 )
 
 update_source(librarian_cohort, new_source)
-code(librarian_cohort)
 sum_up(librarian_cohort)
-code(librarian_cohort)
+code(librarian_cohort, include_methods = NULL)
 ```
 
 Note that updating source doesn't remove Cohort configuration (steps and filters).
@@ -176,9 +178,12 @@ sum_up(librarian_cohort)
 You can also use `update_source` to add Source to an empty Cohort:
 
 ```{r}
+new_source <- set_source(
+  as.tblist(librarian)
+)
 empty_cohort <- cohort()
-update_source(librarian_cohort, new_source)
-sum_up(empty_cohort)
+update_source(empty_cohort, new_source)
+code(empty_cohort, include_methods = NULL)
 ```
 
 The `update_source` method can be also useful if you want to update source along with steps and filters configuration.