changing file paths and configuring local data reads with here()

How-to-Learn-to-Code · Jun 19, 2024 · 30e55fe · 30e55fe
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diff --git a/_quarto.yml b/_quarto.yml
@@ -76,9 +76,9 @@ book:
     - "class7.qmd"
     - part: "class8.qmd"
       chapters: 
-        - deprecates/scripts/04_projects/project-day-2-files/example-analyses/example-temperatures.qmd
-        - deprecates/scripts/04_projects/project-day-2-files/example-analyses/example-ebola.qmd
-        - deprecates/scripts/04_projects/project-day-2-files/example-analyses/example-avida.qmd
+        - examples/example-temperatures.qmd
+        - examples/example-ebola.qmd
+        - examples/example-avida.qmd
 
 
 

diff --git a/examples/example-avida.qmd b/examples/example-avida.qmd
@@ -7,9 +7,11 @@ format:
 
 ```{r setup, echo=FALSE, include=FALSE}
 library(tidyverse)
-wt <- read.csv("../datasets/avida/avida_wildtype.csv", header = TRUE, sep = ",")
-mut <- read.csv("../datasets/avida/avida_mutant.csv", header = TRUE, sep = ",")
-comp <- read.csv("../datasets/avida/avida_competition.csv", header = TRUE, sep = ",")
+library(here)
+data_path <- "data/project-day-2-files/datasets/avida"
+wt <- read.csv(here(data_path, "avida_wildtype.csv"), header = TRUE, sep = ",")
+mut <- read.csv(here(data_path, "avida_mutant.csv"), header = TRUE, sep = ",")
+comp <- read.csv(here(data_path, "avida_competition.csv"), header = TRUE, sep = ",")
 ```
 
 # Preamble

diff --git a/examples/example-ebola.qmd b/examples/example-ebola.qmd
@@ -7,7 +7,9 @@ format:
 
 ```{r setup, echo=FALSE, include=FALSE}
 library(tidyverse)
-ebola <- read.csv("../datasets/ebola.csv", header = TRUE, sep = ",")
+library(here)
+data_path <- "data/project-day-2-files/datasets"
+ebola <- read.csv(here(data_path, "ebola.csv"), header = TRUE, sep = ",")
 ```
 
 # Preamble

diff --git a/examples/example-temperatures.qmd b/examples/example-temperatures.qmd
@@ -7,7 +7,9 @@ format:
 
 ```{r setup, echo=FALSE, include=FALSE}
 library(tidyverse)
-temps <- read.csv("../datasets/temperatures.csv", header = TRUE, sep = ",")
+library(here)
+data_path <- "data/project-day-2-files/datasets"
+temps <- read.csv(here(data_path, "temperatures.csv"), header = TRUE, sep = ",")
 ```
 
 # Preamble