diff --git a/data/raw_data/iris.csv b/data/raw_data/iris.csv new file mode 100644 index 0000000..8b63930 --- /dev/null +++ b/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 diff --git a/scripts/04_cleaning_curation/data_curation_template.R b/scripts/04_cleaning_curation/data_curation_template.R index 4b15d0b..ab01655 100644 --- a/scripts/04_cleaning_curation/data_curation_template.R +++ b/scripts/04_cleaning_curation/data_curation_template.R @@ -2,8 +2,13 @@ ## dklinges@ufl.edu ## 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