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Multipanel plotting in Rwith base graphics
Sean Anderson Nov 2011 [email protected]
Compared to what?- Tufte
by handggplot2lattice
par(mfrow)layout()
split.screen()
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John et al. 1988, Science, 239, p162and reprinted in Tufte, Envisioning Information, p78
par(mfrow)
www.biosciencemag.org July 2011 / Vol. 61 No. 7
Articles
Figure 1. Beanplots of potential correlates of extinction risk for five groups of vertebrate species in Canada. The short vertical lines indicate species for which data are available. The estimated density of the distribution of values is shown for at-risk (white) and not-at-risk (gray) species in the form of curved polygons (beans). The median of each distribution is shown with a long vertical black line. Note the log-distributed horizontal axes. Missing plots were either data deficient (depth midpoint for freshwater fishes, range area for terrestrial and marine mammals, life span and maximum size for birds) or not applicable (all others). Relative age at maturity is the age at maturity divided by life span. Relative size at maturity is the size at maturity divided by maximum size. Abbreviations: g, grams; m, meters; mm, millimeters; m ! km –2, meters per square kilometer; °, degrees.
Anderson et al. 2011, Bioscience, 61, p538
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log(mean)
log(
varia
nce)
Anderson et al. In Prep.
par(mfrow)
layout()
Year that recent fishery began
Tim
e to p
eak (
years
)
Australia
Egypt
Fiji
Indonesia
MadagascarMalaysia
MaldivesMexico
New Caledonia
Papua New Guinea
Philippines
Republic of Korea
Seychelles
Solomon Islands
Tanzania
USA − California
USA − Washington State
(a)
1950 1960 1970 1980 1990 2000
010
20
30
40
50
60
Dis
tance fro
m H
ong K
ong (
km
)
Australia
Canada − East
Canada − West
Chile
Egypt
Fiji
Indonesia
Japan
Madagascar
Malaysia
Maldives
Mexico
New Caledonia
Papua New Guinea
Philippines
Republic of Korea
Solomon Islands
Sri Lanka
Tanzania
US − Alaska
USA − California
USA − Maine
USA − Washington State
(b)
1950 1960 1970 1980 1990 2000
05000
10000
15000
20000
(c)
1960
1970
1980
1990
2000
Year
that re
cent fishery
began
1950
Anderson et al. 2011, Fish. Fish, 12, p317
layout()
Year that recent fishery began
Tim
e to p
eak (
years
)
Australia
Egypt
Fiji
Indonesia
MadagascarMalaysia
MaldivesMexico
New Caledonia
Papua New Guinea
Philippines
Republic of Korea
Seychelles
Solomon Islands
Tanzania
USA − California
USA − Washington State
(a)
1950 1960 1970 1980 1990 2000
010
20
30
40
50
60
Dis
tance fro
m H
ong K
ong (
km
)
Australia
Canada − East
Canada − West
Chile
Egypt
Fiji
Indonesia
Japan
Madagascar
Malaysia
Maldives
Mexico
New Caledonia
Papua New Guinea
Philippines
Republic of Korea
Solomon Islands
Sri Lanka
Tanzania
US − Alaska
USA − California
USA − Maine
USA − Washington State
(b)
1950 1960 1970 1980 1990 2000
05000
10000
15000
20000
(c)
1960
1970
1980
1990
2000
Year
that re
cent fishery
began
1950
Anderson et al. 2011, Fish. Fish, 12, p317
1 2
3
layout()
050
010
0015
00
Eastern NewfoundlandSPA (1000 t)
Cod
05
1015
Commercial CPUE (kg/trap)
Cra
b
−1.0
−0.5
0.0
1970 1980 1990 2000 2010
Tem
pera
ture��$
C
010
020
030
040
0
Southern Gulf of St. LawrenceSPA (1000 t)
020
4060
Commercial CPUE (kg/trap)
0.0
0.5
1.0
1.5
1970 1980 1990 2000 2010
050
010
0015
00
Northern NewfoundlandSPA (1000 t)
05
1015
Commercial CPUE (kg/trap)
0.0
1.0
2.0
1970 1980 1990 2000 2010
05
1015
2025
Western Cape BretonRS (1000 t)
020
4060
80
Commercial CPUE (kg/trap)
0.5
1.5
2.5
1970 1980 1990 2000 2010
010
020
030
040
0 Northern Gulf of St. LawrenceSPA (1000 t)
05
1020
Commercial CPUE (kg/trap)
1.0
1.5
2.0
2.5
1970 1980 1990 2000 2010
050
000
1500
00
Eastern Scotian ShelfSPA (1000 t)
Cod
020
6010
0
Commercial CPUE (kg/trap)
Cra
b
1.5
2.5
3.5
1970 1980 1990 2000 2010
Tem
pera
ture��$
C
010
2030
40
Northern Cape BretonRS/SPA (1000 t)
020
4060
80
Commercial CPUE (kg/trap)
2.0
2.5
3.0
3.5
1970 1980 1990 2000 2010
0.0
1.0
2.0
3.0
Southern NewfoundlandRS (Biomass index)
05
1015
Commercial CPUE (kg/trap)
23
45
6
1970 1980 1990 2000 2010
010
2030
40
Gulf of MaineSPA (1000 t)
0.00
00.
004
0.00
8
RS (kg/trap)
4.5
5.5
6.5
1970 1980 1990 2000 2010
010
2030
40
Flemish CapSPA (1000 t)
050
100
150
RS (t)
67
89
11
1970 1980 1990 2000 2010
Year
Boudreau et al. 2011, MEPS, 429, p169
layout()
050
010
0015
00
Eastern NewfoundlandSPA (1000 t)
Cod
05
1015
Commercial CPUE (kg/trap)
Cra
b
−1.0
−0.5
0.0
1970 1980 1990 2000 2010
Tem
pera
ture��$
C
010
020
030
040
0
Southern Gulf of St. LawrenceSPA (1000 t)
020
4060
Commercial CPUE (kg/trap)
0.0
0.5
1.0
1.5
1970 1980 1990 2000 2010
050
010
0015
00
Northern NewfoundlandSPA (1000 t)
05
1015
Commercial CPUE (kg/trap)
0.0
1.0
2.0
1970 1980 1990 2000 2010
05
1015
2025
Western Cape BretonRS (1000 t)
020
4060
80
Commercial CPUE (kg/trap)
0.5
1.5
2.5
1970 1980 1990 2000 2010
010
020
030
040
0 Northern Gulf of St. LawrenceSPA (1000 t)
05
1020
Commercial CPUE (kg/trap)
1.0
1.5
2.0
2.5
1970 1980 1990 2000 2010
050
000
1500
00
Eastern Scotian ShelfSPA (1000 t)
Cod
020
6010
0
Commercial CPUE (kg/trap)
Cra
b
1.5
2.5
3.5
1970 1980 1990 2000 2010
Tem
pera
ture��$
C
010
2030
40
Northern Cape BretonRS/SPA (1000 t)
020
4060
80
Commercial CPUE (kg/trap)
2.0
2.5
3.0
3.5
1970 1980 1990 2000 2010
0.0
1.0
2.0
3.0
Southern NewfoundlandRS (Biomass index)
05
1015
Commercial CPUE (kg/trap)
23
45
6
1970 1980 1990 2000 2010
010
2030
40
Gulf of MaineSPA (1000 t)
0.00
00.
004
0.00
8
RS (kg/trap)
4.5
5.5
6.5
1970 1980 1990 2000 2010
010
2030
40
Flemish CapSPA (1000 t)
050
100
150
RS (t)
67
89
11
1970 1980 1990 2000 2010
Year
Boudreau et al. 2011, MEPS, 429, p169
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
4041
42
43
44
45
46
47
48
49
50
layout()
split.screen()
Taylor et al. 1982, J. Anim. Ecol., 51, p879
split.screen()
0
20
40
60
80
100(a) Original
Perc
enta
ge o
f fish
erie
s
(b) Original static method
Year1960 1970 1960 1970 1980
(d) Revised robust−dynamic method
Collapsed
Overexploited
Fully exploited
Developing
or closed
1990 2000
(c) Revised
0
20
40
60
80
100
Anderson et al. In Review
split.screen()
METHODS SUMMARYEach taxon in the analysis was assigned a diet-based fractional trophic level, mostlyfrom the online database FishBase24. Primary producers are trophic level one bydefinition, and were not included in our analyses; herbivores and filter feeders aretrophic level two; and omnivores and carnivores are at higher trophic levels. MTLis the catch- or biomass-weighted average of trophic levels of taxa recorded in aparticular year. Ecopath with Ecosim models21 were compiled from well-docu-mented sources and run for 100 years with zero catch to reach unfished states, andthen four main scenarios of fishery development (fishing down3, fishing through6,based on availability19, and increase to overfishing) were applied during years 101to 200. Global catch data were obtained from the United Nations Food andAgriculture Organization (FAO), while catch data for individual Large Marine
Ecosystems came from the Sea Around Us Project of the University of BritishColumbia; trends in catch MTL from these two sources are nearly identical. Long-term scientific trawl surveys from 15 Large Marine Ecosystems provide biomassestimates for regularly recorded taxa, and were obtained from a variety of sources.Biomass estimates for individual taxa were typically not corrected for differentialcatchability among taxa; furthermore, invertebrate biomass estimates were seldomincluded in the provided data. MTL time series from individual surveys werecombined into a single global time series using a linear mixed effects model with‘Large Marine Ecosystem’ modelled as a random effect. Stock assessment biomassvalues were obtained from the RAM Legacy database; total biomass was preferen-tially used in the analysis unless spawning biomass was the only time seriesavailable. Pearson correlations (r) were used to assess whether MTL followed
3.5
4.0
1
2
a Eastern Bering Sea
3.0
3.5
4.0
3
4
5
b Gulf of Alaska
3.0
3.5
4.0 6
c California Current
2.5
3.0
3.5 7
8
d Gulf of Mexico
1950 1965 1980 1995
2.5
3.0
3.5
4.0e Southeast USA
2.5
3.0
3.5
4.0
4.5
910
11
12
13
f Northeast USA
3.0
3.5
4.01415
g Scotian Shelf
3.0
3.5
4.0
4.5
161718h Newfoundland!Labrador
3.5
4.019
20
21
i North Sea
1950 1965 1980 1995
3.5
4.0
22
23j Celtic!Biscay
3.5
4.0
24k Canary Current
3.0
3.5
4.0
4.525
l Benguela Current
3.0
3.5 26mGulf of Thailand
3.0
3.5
4.027
n Northwest Australia
3.5
4.0 o Southeast Australia
1950 1965 1980 1995
3.5
4.0
4.5
2829
p New Zealand
Year
Mea
n tr
ophi
c le
vel
c
a
i
b jh
fe
g97
65
43
12
2321
1716
8
22 2019
1815
141210 1311
k
d
n
m 26
24
p
l
o 2928
27
25
Figure 4 | MTL for each Large Marine Ecosystem. The MTL is shown foreach Large Marine Ecosystem from catches (black lines), assessments (greylines) and surveys (colours). The map shows the location of each Large Marine
Ecosystem, highlighting those with data from all three sources (blue), fromcatches and surveys (red), and from catches and assessments (purple).Numbers on the map reflect the approximate centre of each survey.
RESEARCH LETTER
4 3 4 | N A T U R E | V O L 4 6 8 | 1 8 N O V E M B E R 2 0 1 0
Macmillan Publishers Limited. All rights reserved©2010
Branch et al. 2010, Nature, 468, p431
split.screen()
r = −0.1
0.5
1.5 a
r = 0
b
r = 0.1
k=
2
c
0.5
1.5 d e
k=
16
f
r = −0.5
0.5
1.0
g
r = 0
h
r = 0.5
µ2µ
1=
1
i
0.5
1.0
1.0 1.5 2.0 2.5
j
1.0 1.5 2.0 2.5
k
µ2µ
1=
16
1.0 1.5 2.0 2.5
l
Taylor's power law z−value
Portf
olio
effe
ct
Anderson et al. In Prep.
split.screen()
split.screen()
0, 0.46 1, 0.461, 0.44
0.75, 0.44
0.75, 0 1, 00.72, 00.37, 0
0.37, 0.44 0.72, 0.440.35, 0.44
0.34, 0
0, 0.43
0, 0
1, 10, 1
http://xkcd.com/323/
0, 0.46 1, 0.461, 0.44
0.75, 0.44
0.75, 0 1, 00.72, 00.37, 0
0.37, 0.44 0.72, 0.440.35, 0.44
0.34, 0
0, 0.43
0, 0
1, 10, 1
split.screen()