Introduction to Environmental Data Science

403 Pages·2023·76.715 MB·English

by  Jerry D. Davis

Introduction to Environmental
Data Science
Introduction to Environmental Data Science focuses on data science methods in the R language
applied to environmental research, with sections on exploratory data analysis in R including data
abstraction, transformation, and visualization; spatial data analysis in vector and raster models;
statistics & modelling ranging from exploratory to modelling, considering confirmatory statis-
tics and extending to machine learning models; time series analysis, focusing especially on car-
bon and micrometeorological flux; and communication. Introduction to Environmental Data
Science. It is an ideal textbook to teach undergraduate to graduate level students in environmen-
tal science, environmental studies, geography, earth science, and biology, but can also serve as a
reference for environmental professionals working in consulting, NGOs, and government agen-
cies at the local, state, federal, and international levels.
Features
•
Gives thorough consideration of the needs for environmental research in both spatial and
temporal domains.
•
Features examples of applications involving field-collected data ranging from individual ob-
servations to data logging.
•
Includes examples also of applications involving government and NGO sources, ranging
from satellite imagery to environmental data collected by regulators such as EPA.
•
Contains class-tested exercises in all chapters other than case studies. Solutions manual
available for instructors.
•
All examples and exercises make use of a GitHub package for functions and especially data.
Taylor & Francis
Taylor & Francis Group
http://taylorandfrancis.com
Introduction to Environmental
Data Science
Jerry D. Davis
Designed cover image: By Anna Studwell and Jerry D. Davis
First edition published 2023
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© 2023 Jerry D. Davis
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ISBN: 978-1-032-32218-6 (hbk)
ISBN: 978-1-032-33034-1 (pbk)
ISBN: 978-1-003-31782-1 (ebk)
DOI: 10.1201/9781003317821
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Contents
Author/editor biographies xiii
List of Figures xv
1 Background, Goals and Data 1
1.1 Environmental Data Science . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Environmental Data and Methods . . . . . . . . . . . . . . . . . . . . . . . 1
1.3 Goals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3.1 Some definitions: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.4 Exploratory Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.5 Software and Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.5.1 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.6 Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
I Exploratory Data Analysis 11
2 Introduction to R 13
2.1 Data Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.1.1 Scalars and assignment . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.2 Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.3 Expressions and Statements . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.4 Data Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.4.1 Integers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.5 Rectangular Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.6 Data Structures in R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.6.1 Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.6.2 Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.6.3 Matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.6.4 Data frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.6.5 Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
2.7 Accessors and Subsetting . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
2.7.1 [] Subsetting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
2.7.2 [[]] The mysterious double bracket . . . . . . . . . . . . . . . . . . 41
2.7.3 $ Accessing a vector from a data frame. . . . . . . . . . . . . . . . . 42
2.8 Programming scripts in RStudio . . . . . . . . . . . . . . . . . . . . . . . . 42
2.8.1 function : creating your own . . . . . . . . . . . . . . . . . . . . . . 43
2.8.2 if : conditional operations . . . . . . . . . . . . . . . . . . . . . . . . 44
2.8.3 for loops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
2.8.4 Subsetting with logic . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
2.8.5 Apply functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
2.9 RStudio projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
2.9.1 R Markdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
vii
viii Contents
2.10 Exercises: Introduction to R . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3 Data Abstraction 55
3.1 The Tidyverse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.2 Tibbles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.2.1 Building a tibble from vectors . . . . . . . . . . . . . . . . . . . . . . 57
3.2.2 tribble . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
3.2.3 read_csv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
3.3 Summarizing variable distributions . . . . . . . . . . . . . . . . . . . . . . 60
3.3.1 Stratifying variables by site using a Tukey box plot . . . . . . . . . . 62
3.4 Database operations with dplyr . . . . . . . . . . . . . . . . . . . . . . . . 63
3.4.1 Select, mutate, and the pipe . . . . . . . . . . . . . . . . . . . . . . . 63
3.4.2 filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
3.4.3 Writing a data frame to a csv . . . . . . . . . . . . . . . . . . . . . . 67
3.4.4 Summarize by group . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
3.4.5 Count . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
3.4.6 Sorting after summarizing . . . . . . . . . . . . . . . . . . . . . . . . 69
3.4.7 The dot operator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
3.5 String abstraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
3.5.1 Detecting matches . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
3.5.2 Subsetting strings . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
3.5.3 String length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
3.5.4 Replacing substrings with other text (“mutating” strings) . . . . . . 73
3.5.5 Concatenating and splitting . . . . . . . . . . . . . . . . . . . . . . . 74
3.6 Dates and times with lubridate . . . . . . . . . . . . . . . . . . . . . . . . 76
3.7 Calling functions explicitly with :: . . . . . . . . . . . . . . . . . . . . . . 77
3.8 Exercises: Data Abstraction . . . . . . . . . . . . . . . . . . . . . . . . . . 77
4 Visualization 79
4.1 plot in base R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.2 ggplot2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
4.3 Plotting one variable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
4.3.1 Histogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
4.3.2 Density plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.3.3 Boxplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
4.4 Plotting Two Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
4.4.1 Two continuous variables . . . . . . . . . . . . . . . . . . . . . . . . 90
4.4.2 Two variables, one discrete . . . . . . . . . . . . . . . . . . . . . . . 92
4.4.3 Color systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
4.4.4 Trend line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
4.5 General Symbology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
4.5.1 Categorical symbology . . . . . . . . . . . . . . . . . . . . . . . . . . 99
4.5.2 Log scales instead of transform . . . . . . . . . . . . . . . . . . . . . 99
4.6 Graphs from Grouped Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
4.6.1 Faceted graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
4.7 Titles and Subtitles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
4.8 Pairs Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
4.9 Exercises: Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
5 Data Transformation 107
5.1 Data joins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Contents ix
5.2 Set operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
5.3 Binding rows and columns . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
5.4 Pivoting data frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.4.1 pivot_longer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.4.2 pivot_wider . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
5.4.3 A free_y faceted graph using a pivot . . . . . . . . . . . . . . . . . . 116
5.5 Exercise: Transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
II Spatial 121
6 Spatial Data and Maps 123
6.1 Spatial Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
6.1.1 Simple geometry building in sf . . . . . . . . . . . . . . . . . . . . . 125
6.1.2 Building points from a data frame . . . . . . . . . . . . . . . . . . . 128
6.1.3 SpatVectors in terra . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
6.1.4 Creating features from shapefiles . . . . . . . . . . . . . . . . . . . . 133
6.2 Coordinate Referencing Systems . . . . . . . . . . . . . . . . . . . . . . . . 135
6.3 Creating sf Data from Data Frames . . . . . . . . . . . . . . . . . . . . . . 137
6.3.1 Removing geometry . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.4 Base R’s plot() with terra . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
6.4.1 Using maptiles to create a basemap . . . . . . . . . . . . . . . . . . 139
6.5 Raster data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
6.5.1 Building rasters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
6.5.2 Vector to raster conversion . . . . . . . . . . . . . . . . . . . . . . . 143
6.6 ggplot2 for Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
6.6.1 Rasters in ggplot2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
6.7 tmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
6.8 Interactive Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
6.8.1 Leaflet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
6.8.2 Mapview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
6.8.3 tmap (view mode) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
6.8.4 Interactive mapping of individual penguins abstracted from a big
dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
6.9 Exercises: Spatial Data and Maps . . . . . . . . . . . . . . . . . . . . . . . 159
6.9.1 Project preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
7 Spatial Analysis 163
7.1 Data Frame Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
7.1.1 Using grouped summaries, and filtering by a selection . . . . . . . . 165
7.2 Spatial Analysis Operations . . . . . . . . . . . . . . . . . . . . . . . . . . 168
7.2.1 Using topology to subset. . . . . . . . . . . . . . . . . . . . . . . . . 168
7.2.2 Centroid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
7.2.3 Distance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
7.2.4 Buffers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
7.2.5 Spatial overlay: union and intersection . . . . . . . . . . . . . . . . . 179
7.2.6 Clip with st_crop . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
7.2.7 Spatial join with st_join . . . . . . . . . . . . . . . . . . . . . . . . 183
7.2.8 Further exploration of spatial analysis . . . . . . . . . . . . . . . . . 184
7.3 Exercises: Spatial Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
8 Raster Spatial Analysis 187