From 30e55fea16888c60c09623b1cc448f85fa158877 Mon Sep 17 00:00:00 2001
From: jtlandis <jtlandis314@gmail.com>
Date: Wed, 19 Jun 2024 15:25:17 -0400
Subject: [PATCH] changing file paths and configuring local data reads with
 `here()`

---
 _quarto.yml                       | 6 +++---
 examples/example-avida.qmd        | 8 +++++---
 examples/example-ebola.qmd        | 4 +++-
 examples/example-temperatures.qmd | 4 +++-
 4 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/_quarto.yml b/_quarto.yml
index 6bc84f4..9a020e2 100644
--- 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
index d78aade..7f22c9a 100644
--- 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
index ac4b46e..ff7eee8 100644
--- 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
index 085d6ef..d690bc4 100644
--- 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