adjusts to data curation template script, using iris data

data/raw_data/iris.csv

@@ -0,0 +1,151 @@
+Sepal.Length,Sepal.Width,Petal.Length,Petal.Width,Species
+5.1,3.5,1.4,0.2,setosa
+4.9,3,1.4,0.2,setosa
+4.7,3.2,1.3,0.2,setosa
+4.6,3.1,1.5,0.2,setosa
+5,3.6,1.4,0.2,setosa
+5.4,3.9,1.7,0.4,setosa
+4.6,3.4,1.4,0.3,setosa
+5,3.4,1.5,0.2,setosa
+4.4,2.9,1.4,0.2,setosa
+4.9,3.1,1.5,0.1,setosa
+5.4,3.7,1.5,0.2,setosa
+4.8,3.4,1.6,0.2,setosa
+4.8,3,1.4,0.1,setosa
+4.3,3,1.1,0.1,setosa
+5.8,4,1.2,0.2,setosa
+5.7,4.4,1.5,0.4,setosa
+5.4,3.9,1.3,0.4,setosa
+5.1,3.5,1.4,0.3,setosa
+5.7,3.8,1.7,0.3,setosa
+5.1,3.8,1.5,0.3,setosa
+5.4,3.4,1.7,0.2,setosa
+5.1,3.7,1.5,0.4,setosa
+4.6,3.6,1,0.2,setosa
+5.1,3.3,1.7,0.5,setosa
+4.8,3.4,1.9,0.2,setosa
+5,3,1.6,0.2,setosa
+5,3.4,1.6,0.4,setosa
+5.2,3.5,1.5,0.2,setosa
+5.2,3.4,1.4,0.2,setosa
+4.7,3.2,1.6,0.2,setosa
+4.8,3.1,1.6,0.2,setosa
+5.4,3.4,1.5,0.4,setosa
+5.2,4.1,1.5,0.1,setosa
+5.5,4.2,1.4,0.2,setosa
+4.9,3.1,1.5,0.2,setosa
+5,3.2,1.2,0.2,setosa
+5.5,3.5,1.3,0.2,setosa
+4.9,3.6,1.4,0.1,setosa
+4.4,3,1.3,0.2,setosa
+5.1,3.4,1.5,0.2,setosa
+5,3.5,1.3,0.3,setosa
+4.5,2.3,1.3,0.3,setosa
+4.4,3.2,1.3,0.2,setosa
+5,3.5,1.6,0.6,setosa
+5.1,3.8,1.9,0.4,setosa
+4.8,3,1.4,0.3,setosa
+5.1,3.8,1.6,0.2,setosa
+4.6,3.2,1.4,0.2,setosa
+5.3,3.7,1.5,0.2,setosa
+5,3.3,1.4,0.2,setosa
+7,3.2,4.7,1.4,versicolor
+6.4,3.2,4.5,1.5,versicolor
+6.9,3.1,4.9,1.5,versicolor
+5.5,2.3,4,1.3,versicolor
+6.5,2.8,4.6,1.5,versicolor
+5.7,2.8,4.5,1.3,versicolor
+6.3,3.3,4.7,1.6,versicolor
+4.9,2.4,3.3,1,versicolor
+6.6,2.9,4.6,1.3,versicolor
+5.2,2.7,3.9,1.4,versicolor
+5,2,3.5,1,versicolor
+5.9,3,4.2,1.5,versicolor
+6,2.2,4,1,versicolor
+6.1,2.9,4.7,1.4,versicolor
+5.6,2.9,3.6,1.3,versicolor
+6.7,3.1,4.4,1.4,versicolor
+5.6,3,4.5,1.5,versicolor
+5.8,2.7,4.1,1,versicolor
+6.2,2.2,4.5,1.5,versicolor
+5.6,2.5,3.9,1.1,versicolor
+5.9,3.2,4.8,1.8,versicolor
+6.1,2.8,4,1.3,versicolor
+6.3,2.5,4.9,1.5,versicolor
+6.1,2.8,4.7,1.2,versicolor
+6.4,2.9,4.3,1.3,versicolor
+6.6,3,4.4,1.4,versicolor
+6.8,2.8,4.8,1.4,versicolor
+6.7,3,5,1.7,versicolor
+6,2.9,4.5,1.5,versicolor
+5.7,2.6,3.5,1,versicolor
+5.5,2.4,3.8,1.1,versicolor
+5.5,2.4,3.7,1,versicolor
+5.8,2.7,3.9,1.2,versicolor
+6,2.7,5.1,1.6,versicolor
+5.4,3,4.5,1.5,versicolor
+6,3.4,4.5,1.6,versicolor
+6.7,3.1,4.7,1.5,versicolor
+6.3,2.3,4.4,1.3,versicolor
+5.6,3,4.1,1.3,versicolor
+5.5,2.5,4,1.3,versicolor
+5.5,2.6,4.4,1.2,versicolor
+6.1,3,4.6,1.4,versicolor
+5.8,2.6,4,1.2,versicolor
+5,2.3,3.3,1,versicolor
+5.6,2.7,4.2,1.3,versicolor
+5.7,3,4.2,1.2,versicolor
+5.7,2.9,4.2,1.3,versicolor
+6.2,2.9,4.3,1.3,versicolor
+5.1,2.5,3,1.1,versicolor
+5.7,2.8,4.1,1.3,versicolor
+6.3,3.3,6,2.5,virginica
+5.8,2.7,5.1,1.9,virginica
+7.1,3,5.9,2.1,virginica
+6.3,2.9,5.6,1.8,virginica
+6.5,3,5.8,2.2,virginica
+7.6,3,6.6,2.1,virginica
+4.9,2.5,4.5,1.7,virginica
+7.3,2.9,6.3,1.8,virginica
+6.7,2.5,5.8,1.8,virginica
+7.2,3.6,6.1,2.5,virginica
+6.5,3.2,5.1,2,virginica
+6.4,2.7,5.3,1.9,virginica
+6.8,3,5.5,2.1,virginica
+5.7,2.5,5,2,virginica
+5.8,2.8,5.1,2.4,virginica
+6.4,3.2,5.3,2.3,virginica
+6.5,3,5.5,1.8,virginica
+7.7,3.8,6.7,2.2,virginica
+7.7,2.6,6.9,2.3,virginica
+6,2.2,5,1.5,virginica
+6.9,3.2,5.7,2.3,virginica
+5.6,2.8,4.9,2,virginica
+7.7,2.8,6.7,2,virginica
+6.3,2.7,4.9,1.8,virginica
+6.7,3.3,5.7,2.1,virginica
+7.2,3.2,6,1.8,virginica
+6.2,2.8,4.8,1.8,virginica
+6.1,3,4.9,1.8,virginica
+6.4,2.8,5.6,2.1,virginica
+7.2,3,5.8,1.6,virginica
+7.4,2.8,6.1,1.9,virginica
+7.9,3.8,6.4,2,virginica
+6.4,2.8,5.6,2.2,virginica
+6.3,2.8,5.1,1.5,virginica
+6.1,2.6,5.6,1.4,virginica
+7.7,3,6.1,2.3,virginica
+6.3,3.4,5.6,2.4,virginica
+6.4,3.1,5.5,1.8,virginica
+6,3,4.8,1.8,virginica
+6.9,3.1,5.4,2.1,virginica
+6.7,3.1,5.6,2.4,virginica
+6.9,3.1,5.1,2.3,virginica
+5.8,2.7,5.1,1.9,virginica
+6.8,3.2,5.9,2.3,virginica
+6.7,3.3,5.7,2.5,virginica
+6.7,3,5.2,2.3,virginica
+6.3,2.5,5,1.9,virginica
+6.5,3,5.2,2,virginica
+6.2,3.4,5.4,2.3,virginica
+5.9,3,5.1,1.8,virginica

scripts/04_cleaning_curation/data_curation_template.R

@@ -2,8 +2,13 @@
 ## [email protected]
 ## This script provides a template of organization for reproducible workflows
 
+## BAD BAD BAD BAD BAD
+# setwd("Users/David/Desktop")
+
 ## 1. Workspace prep ##############
 
+# Where we load the dependencies of the script (software packages and data)
+
 ## Load packages
 # Workspace/system
 library(here)
@@ -13,23 +18,14 @@ library(tidyverse) # library() returns error, require() returns warning
 library(lubridate)
 # Spatial data
 library(raster)
-library(rgdal)
-
-
-## BAD BAD BAD BAD BAD
-# setwd("Users/David/Desktop")
 
 ## Read in data
-ameriflux_raw <- read_csv("data/raw_data/meteorology/ameriflux/BASE_MeasurementHeight_20190902.csv")
-ameriflux_raw <- read_csv(Sys.glob("*/*/*/*/*/*/BASE_MeasurementHeight_20190902.csv"))
-ameriflux_raw <- read_csv(grepl("BASE_MeasurementHeight_20190902.csv"), list.files)
-
-## Alt + O to collapse all headers
-
-## Load source functions
-source("scripts/01_data_selection/hello_world.R")
-source(Sys.glob("scripts/*_data_selection/hello_world.R"))
-source(here(Sys.glob("scripts/*_data_selection/hello_world.R")))
+iris_raw <- read_csv("data/raw_data/iris.csv") # Pretty standard
+iris_raw <- read_csv(Sys.glob("*/*/iris*.csv")) # Throw in wildcards
+# Harder to read, but possibly useful if you have tons of folders
+iris_raw <- read_csv(list.files(recursive = TRUE)[ # list all files in my project
+  grepl("iris.csv", list.files(recursive = TRUE)) # grepl to get those with "iris.csv"
+  ])
 
 # Written code should be within a margin that most users will be able to view 
 # without having to move their panes around or scroll. This text is cut off at
@@ -40,18 +36,31 @@ source(here(Sys.glob("scripts/*_data_selection/hello_world.R")))
 
 # Tools>Global Options>Code>Display>Show Margin> 60 or 80 are common
 
-
+## Load source functions
+source("scripts/00_source/hello_world.R")
+source(Sys.glob("scripts/*_source/hello_world.R"))
+source(here(Sys.glob("scripts/*_source/hello_world.R")))
 
 ## 2. Data curation #############
 
 ## Make some changes just in case
+
 ## 3. Data QA/QC ##############
 
 ## 4. Write out derived data ###########
 
 # Common practice stemming from when RStudio and other IDE's weren't as popular:
 ####################################################
-############# THIS IS A HEADER #####################
+############# THIS IS A HEADER LOOK AT ME #####################
 ####################################################
 
+## But this is also a header ############
+
+## And this is a header ---------------
+
+
+## Alt + O to collapse all headers on Windows & Linux
+## Alt + Cmd + O to collapse all headers on Mac
 
+## Shift + Alt + O to expand all headers on Windows & Linux
+## Shift + Alt + Cmd + O to collapse all headers on Mac