add new data read

episodes/data/ebola_cases_2.csv

@@ -0,0 +1,121 @@
+year,month,day,confirm
+2014,5,18,1
+2014,5,20,2
+2014,5,21,4
+2014,5,22,6
+2014,5,23,1
+2014,5,24,2
+2014,5,26,10
+2014,5,27,8
+2014,5,28,2
+2014,5,29,12
+2014,5,30,7
+2014,5,31,2
+2014,6,1,5
+2014,6,2,2
+2014,6,3,1
+2014,6,5,3
+2014,6,6,7
+2014,6,7,4
+2014,6,8,6
+2014,6,9,1
+2014,6,10,29
+2014,6,11,1
+2014,6,12,10
+2014,6,13,20
+2014,6,14,17
+2014,6,15,4
+2014,6,16,1
+2014,6,17,4
+2014,6,18,8
+2014,6,19,11
+2014,6,20,9
+2014,6,21,3
+2014,6,22,3
+2014,6,23,2
+2014,6,24,9
+2014,6,25,9
+2014,6,26,14
+2014,6,27,15
+2014,6,28,21
+2014,6,29,9
+2014,6,30,15
+2014,7,1,12
+2014,7,2,11
+2014,7,3,4
+2014,7,4,11
+2014,7,5,17
+2014,7,6,9
+2014,7,7,18
+2014,7,8,11
+2014,7,9,8
+2014,7,10,14
+2014,7,11,8
+2014,7,12,7
+2014,7,13,4
+2014,7,14,7
+2014,7,15,5
+2014,7,16,7
+2014,7,17,8
+2014,7,18,10
+2014,7,19,13
+2014,7,20,13
+2014,7,21,18
+2014,7,22,9
+2014,7,23,13
+2014,7,24,10
+2014,7,25,40
+2014,7,26,8
+2014,7,27,7
+2014,7,28,14
+2014,7,29,9
+2014,7,30,14
+2014,7,31,12
+2014,8,1,12
+2014,8,2,15
+2014,8,3,14
+2014,8,4,5
+2014,8,5,13
+2014,8,6,8
+2014,8,7,8
+2014,8,8,13
+2014,8,9,8
+2014,8,10,13
+2014,8,11,4
+2014,8,12,9
+2014,8,13,6
+2014,8,14,8
+2014,8,15,5
+2014,8,16,1
+2014,8,17,5
+2014,8,18,17
+2014,8,19,18
+2014,8,20,35
+2014,8,21,18
+2014,8,22,16
+2014,8,23,18
+2014,8,24,38
+2014,8,25,25
+2014,8,26,42
+2014,8,27,16
+2014,8,28,26
+2014,8,29,30
+2014,8,30,23
+2014,8,31,24
+2014,9,1,29
+2014,9,2,29
+2014,9,3,43
+2014,9,4,41
+2014,9,5,15
+2014,9,6,44
+2014,9,7,30
+2014,9,8,42
+2014,9,9,38
+2014,9,10,21
+2014,9,11,39
+2014,9,12,37
+2014,9,13,38
+2014,9,14,49
+2014,9,15,68
+2014,9,16,84
+2014,9,17,56

episodes/read-cases.Rmd

@@ -60,7 +60,7 @@ This help us remember package functions and avoid namespace conflicts.
 
 - Create an RStudio project. If needed, follow this [how-to guide on "Hello RStudio Projects"](https://docs.posit.co/ide/user/ide/get-started/#hello-rstudio-projects) to create one.
 - Inside the RStudio project, create the `data/` folder.
-- Inside the `data/` folder, save the [ebola_cases.csv](https://epiverse-trace.github.io/tutorials-early/data/ebola_cases.csv) and [marburg.zip](https://epiverse-trace.github.io/tutorials-early/data/Marburg.zip) files.
+- Inside the `data/` folder, save the [ebola_cases_2.csv](https://epiverse-trace.github.io/tutorials-early/data/ebola_cases_2.csv) and [marburg.zip](https://epiverse-trace.github.io/tutorials-early/data/Marburg.zip) files.
 
 ::::::::::
 
@@ -72,9 +72,9 @@ The below example shows how to import a `csv` file into `R` environment using `{
 
 ```{r,eval=FALSE,echo=TRUE}
 # read data
-# e.g., the path to our file is data/raw-data/ebola_cases.csv then:
+# e.g., the path to our file is data/raw-data/ebola_cases_2.csv then:
 ebola_confirmed <- rio::import(
-  here::here("data", "ebola_cases.csv")
+  here::here("data", "ebola_cases_2.csv")
 ) %>%
   dplyr::as_tibble() # for a simple data frame output
 
@@ -87,7 +87,7 @@ ebola_confirmed
 # internal for DBI::dbWriteTable()
 # read data
 ebola_confirmed <- rio::import(
-  file.path("data", "ebola_cases.csv")
+  file.path("data", "ebola_cases_2.csv")
 ) %>%
   dplyr::as_tibble() # for a simple data frame output
 
@@ -105,7 +105,7 @@ The `{here}` package is designed to simplify file referencing in R projects by p
 
 - **Relative Paths**: Allows you to use relative file paths with respect to the `R` Project, making your code more portable and less error-prone.
 
-- **Cross-Environment Compatibility**: Works across different operating systems (Windows, Mac, Linux) without needing to adjust file paths. This notation `here::here("data", "ebola_cases.csv")` avoids using `"data\ebola_cases.csv"` in some and `"data/ebola_cases.csv"` in others!
+- **Cross-Environment Compatibility**: Works across different operating systems (Windows, Mac, Linux) without needing to adjust file paths. This notation `here::here("data", "ebola_cases_2.csv")` avoids using `"data\ebola_cases_2.csv"` in some and `"data/ebola_cases_2.csv"` in others!
 
 - **Reduces Errors**: Avoids the need to use `setwd()` or absolute paths, reducing errors in scripts shared across machines. This avoids notations like `"C:/Users/mycomputer/Documents/projects/helloworld"`.
 

learners/setup.md

@@ -37,13 +37,13 @@
 + **Challenges**: complete challenges to test your understanding.
 + **Explainers**: add to your understanding of mathematical and modelling concepts with the explainer boxes.
 
 Also check out the [glossary](../reference.md) for any terms you may be unfamiliar with.
 
 ### Epiverse-TRACE R packages
 
 Our strategy is to gradually incorporate specialised **R packages** into a traditional analysis pipeline. These packages should fill the gaps in these epidemiology-specific tasks in response to outbreaks.
 
 ![I](episodes/fig/pkgs-hexlogos-2.png).
 
 <p><figure>
     <img src="episodes/fig/pkgs-hexlogos-2.png"
@@ -281,7 +281,7 @@
 
 The data files for the tutorial can be downloaded manually here: 
 
-- <https://epiverse-trace.github.io/tutorials-early/data/ebola_cases.csv>
+- <https://epiverse-trace.github.io/tutorials-early/data/ebola_cases_2.csv>
 - <https://epiverse-trace.github.io/tutorials-early/data/Marburg.zip>
 - <https://epiverse-trace.github.io/tutorials-early/data/simulated_ebola_2.csv>