change text from purrr to simpler simulation

Author: avallecam

episodes/superspreading-simulate.Rmd

@@ -386,29 +386,31 @@ If you need help, return to the "Chain size and length" callout box from the beg
 ```{r,echo=FALSE}
 #### get simulated chain with more infections --------------------------------
 
-chains_subgroup <- simulated_chains_map %>%
+epichain_output <- multiple_epichains
+
+chains_subgroup <- epichain_output %>%
   as_tibble() %>%
-  group_by(simulation_id) %>%
+  group_by(chain) %>%
   distinct(infector) %>%
-  count(simulation_id) %>%
+  count(chain) %>%
   filter(n < 5, n >= 3) %>%
-  pull(simulation_id)
+  pull(chain)
 
-chain_to_observe <- simulated_chains_map %>%
+chain_to_observe <- epichain_output %>%
   as_tibble() %>%
-  count(simulation_id, sort = TRUE) %>%
+  count(chain, sort = TRUE) %>%
   filter(
     magrittr::is_in(
-      simulation_id, chains_subgroup
+      chain, chains_subgroup
     )
   ) %>%
-  filter(n < 10) %>%
+  # filter(n < 10) %>%
   filter(n == max(n)) %>%
-  slice_min(simulation_id) %>%
-  pull(simulation_id)
+  slice_min(chain) %>%
+  pull(chain)
 ```
 
-To explore the output format of the `<epichains>` class object of name `simulated_chains_map`, let's look at the simulated `simulation_id` number `r chain_to_observe`. 
+To explore the output format of the `<epichains>` class object of name `multiple_epichains`, let's look at the simulated `chain` number `r chain_to_observe`. 
 
 :::::::::::::::::::::::::::::::::
 
@@ -419,24 +421,27 @@ To explore the output format of the `<epichains>` class object of name `simulate
 Let's use `dplyr::filter()` for this:
 
 ```r
-chain_to_observe <- 806
+chain_to_observe <- 30
 ```
 
 ```{r}
 #### get epichain summary ----------------------------------------------------
 
-simulated_chains_map %>%
-  dplyr::filter(simulation_id == chain_to_observe)
+multiple_epichains %>%
+  dplyr::filter(chain == chain_to_observe)
 ```
 
-Key elements from this output are in the footer, the piece of text that appears at the bottom:
+This output contains two parts:
+
+- A `head()` print of the infector-infectee pairs __starting from the first known infector__.
+- A summary footer, the piece of text that appears at the bottom:
 
 ```output
 Number of infectors (known): 3
 Number of generations: 3
 ```
 
-The simulated `simulation_id` number `r chain_to_observe` has three known infectors and three generations. These numbers are more visible when reading the `<epichains>` objects as a data frame.
+The simulated `chain` number `r chain_to_observe` has three known infectors and three generations. These numbers are more visible when printing the `<epichains>` objects as a data frame (or `<tibble>`).
 
 :::::::::::::::::::::::::
 
@@ -447,15 +452,21 @@ The simulated `simulation_id` number `r chain_to_observe` has three known infect
 ```{r}
 #### infector-infectee data frame --------------------------------------------
 
-simulated_chains_map %>%
-  dplyr::filter(simulation_id == chain_to_observe) %>%
+multiple_epichains %>%
+  dplyr::filter(chain == chain_to_observe) %>%
   dplyr::as_tibble()
 ```
 
 Chain `r chain_to_observe` tells us a **story**: 
-"In the first transmission generation at `time = 0`, one index case (`infector = NA`) infected the first case with `infectee = 1`.
-Then, in the second transmission generation (between `time` 10 to 16), `infector = 1` infected five cases. 
-Later, in the third transmission generation (between `time` 26 to 30), `infector = 2` infected three new cases."
+
+"In the first transmission generation at `time = 0`, one subject (`ID = NA`) infected the subject with `ID = 1`.
+Subject `ID = 1` is the first known infector.
+
+"Then, in the second transmission generation, subject `ID = 1` infected seven subjects, from `ID = 2` to `ID = 8`. 
+These infections ocurred in `time` between day 9 and day 15, after the first known infection.
+
+"Later, in the third transmission generation, subject `ID = 4` infected six new subjects, from `ID = 9` to `ID = 14`.
+These infections ocurred in `time` between day 24 and day 31, after the first known infection."
 
 :::::::::::::::::::::::::
 
@@ -465,12 +476,12 @@ Later, in the third transmission generation (between `time` 26 to 30), `infector
 
 The output data frame collects **infectees** as the observation unit: 
 
-- Each infectee has a `infectee` "id". 
+- Each infectee has a `infectee` "ID". 
 - Each _infectee_ that behaved as an _infector_ is registered in the `infector` column using `infectee` "id". 
 - Each infectee got infected in a specific `generation` and (continuous) `time`. 
-- The simulation number is registered under the `simulation_id` column.
+- The simulation number is registered under the `chain` column.
 
-**Note:** The `Number of infectors (known)` includes the `NA` observation under the `infector` column. This refers to the infector specified as index case (in the `n_chains` argument), which started the transmission chain to the infectee of `sim_id = 1`, at `generation = 1`, and `time = 0`.
+**Note:** The `Number of infectors (known)` includes the subject `ID = NA` under the `infector` column. This refers to the infector specified as index case (in the `n_chains` argument), which started the transmission chain to the infectee of `ID = 1`, at `generation = 1`, and `time = 0`.
 
 :::::::::::::::::::::::::