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How to make graphs in R From default to publication-quality graphics @anchu 2th Hanoi UseRs Meetup

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Thank you for coming!

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About me

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Download this PDF https://speakerdeck.com/chuvanan

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This talk is . . .

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This talk is . . . not really for beginners

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This talk is . . . not really for beginners not really for experts either

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This talk is . . . not really for beginners not really for experts either not a comprehensive treatment of data visualization

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This talk is . . . not really for beginners not really for experts either not a comprehensive treatment of data visualization not about design

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This talk is . . . not really for beginners not really for experts either not a comprehensive treatment of data visualization not about design not about R’s ggplot2 (sorry ggplot2’s folks)

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This talk is . . .

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This talk is . . . a gentle introduction to graphing data with R

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This talk is . . . a gentle introduction to graphing data with R (mostly) about statistical graphics

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This talk is . . . a gentle introduction to graphing data with R (mostly) about statistical graphics (entirely) about R’s base graphics

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This talk is . . . a gentle introduction to graphing data with R (mostly) about statistical graphics (entirely) about R’s base graphics (hopefully) helping you to improve your visualization skills

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This talk is . . . a gentle introduction to graphing data with R (mostly) about statistical graphics (entirely) about R’s base graphics (hopefully) helping you to improve your visualization skills . . . . (hopefully) fun and entertaining

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Statistical Graphics

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Some (frequent) encounters from the web/publications

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Some (frequent) encounters from the web/publications

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Some (frequent) encounters from the web/publications

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Some (frequent) encounters from the web/publications

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Some (frequent) encounters from the web/publications

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We can do better

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We can do better with R

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Basic principles of visualization

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Visualization components Visual encodings Coordinate system Scale Context (Data Points, Nathan Yau)

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Decomposing visualization 5 10 15 20 25 0 20 40 60 80 100 120 Speed (mph) Stopping distance (ft) Source: Ezekiel, M. (1930). Wiley. Drivers: Keep your speed down! Higher speed, longer distance taken to stop

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Visual Cues Coordinate System 5 10 15 20 25 0 20 40 60 80 100 120 Scale Speed (mph) Stopping distance (ft) Source: Ezekiel, M. (1930). Wiley. Drivers: Keep your speed down! Higher speed, longer distance taken to stop Annotation

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Visual encodings Mapping data into visual properties

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Different methods of encoding the same data set A B C D E 0 10 20 30 A B C D E 0 5 15 25 A B C D E 15 20 25 30 A B C D E 15 25 A B C D E A B C D E

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Posi�on Length Angle Direc�on Shapes Area Color hue Color satura�on Shading

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How to Choose Appropriate Visual Encodings

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What is your question?

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Graphical perception

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Graphical perception

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Graphical perception 1. Position along a common scale 2. Position on identical but nonaligned scales 3. Length 4. Angle. Slope 5. Direction 6. Area 7. Volume. Density. Color saturation 8. Color hue (W. Clevelan and R. Mcgrill, 1985)

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Example

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Redesign Q1/ 2010 Q1/ '11 Q1/ '12 Q1/ '13 Q1/ '14 Q1/ '15 Q1/ '16 Q1/ '17 0% 5% 10% 15% 4.96% CPI quý I/2017 tăng cao nhất trong 3 năm qua Đo bằng sự thay đổi so vơí cùng kỳ năm trước (CPI) Nguồn: GSO

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Coordinate system x y Cartesian Polar Geographic r

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Scales

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1 2 3 4 5 Linear 1 10 100 1000 10000 Logarithmic A B C D E Categorical strongly disagree disagree neutral agree strongly agree Ordinal 0% 25% 50% 75% 100% Percent Jan Feb Mar Apr May Time

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Example

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87 88 89 90 91 92 93 94 Truncated axis Full-scale axis 0 20 40 60 80 100

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Example

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10k 12k 14k 16k 18k None-zero baseline 0 5k 10k 15k 20k Zero baseline

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20/09/16 05/10/16 20/10/16 04/11/16 19/11/16 20/12/16 18/02/17 06/03/17 21/03/17 05/04/17 16000 16500 17000 17500 18000 18500 19000 Biểu đồ giá xăng (VND)

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Annotation “The annotation layer is the most important thing we do. . . otherwise it’s a case of here it is, you go figure it out.” (Amanda Cox, Graphics Editor, NYTimes)

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Annotation Title Subtitle Axix labels Source User guide

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Example

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Example

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The R Plotting System

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R graphics system Cairo tkzDevice JavaGD lattice ggplot2 vcd grImport gridBase maps diagram plotrix gplots pixmap grid graphics grDevices

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R graphics system grDevices: graphics engine which provides facilities such as selecting colors, fonts and output formats. Two (largely incompatible) packages built on top of the graphics engine: graphics: (aka base graphics) S’s legacy. graphics provides both high-level and low-level functions for creating plots. grid: unique to R. grid offers low-level tools used for building ggplot2 and lattice.

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Base graphics vs ggplot2

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Base graphics vs ggplot2 base graphics: Accpet many types of input (vectors, data frames, matrix,...) Quicker to get going (lots of single-call functions) Better performance (speedier) Easier to customize (mimics ’painters model’: output occurs in steps) Awkward workflow (sometimes) ggplot2: Dataframe-centerd Steeper learning curve (to master conceptual framework) Better default (generally) Highly extensible, more efficient in the long run (thanks to paradigm-based design) Seamlessly integration with tidyverse

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Why I choose base graphics Both packages are super! But, base graphics might be better for beginners to make graphs quickly with as little as mental efforts.

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Graphical Functions

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The base graphics model First, call a high-level funtions to make a complete plot. Then, call low-level functions to add more output (if necessary).

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plot(x = pressure$temperature, y = pressure$pressure, xlab = "temperature", ylab = "pressure") 0 50 100 150 200 250 300 350 0 200 400 600 800 temperature pressure

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plot(x = pressure$temperature, y = pressure$pressure, ann = F) text(150, 600, "Pressure (mmHg)\nvs.\nTemperature (Celsius)") 0 50 100 150 200 250 300 350 0 200 400 600 800 Pressure (mmHg) vs. Temperature (Celsius)

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High-level plotting functions plot() : scatterplot (lines plot) barplot() : bar chart pie() : pie chart boxplot : boxplot hist() : histogram stripchart() : 1-d scatterplot

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Visualizing distributions Demo visualize_distributions.R

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Revealing changes Demo reveal_changes.R:

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Showing relationships Demo show_relationships.R

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Making comparisions Demo make_comparisions.R

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Some arguments are accepted by many high-level functions: xlab: x-axis label ylab: y-axis label main: plot title sub: plot subtitle col: color lty: line type lwd: line width xlim: x-axis scale limits ylim: y-axis scale limits

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Going beyond the default

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The layout of graphics Plot Region Margin 1 Margin 2 Margin 3 Margin 4

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Control the margins par() is used to control low-level graphics by setting graphical parameters set the margin sizes in inches par(mai = c(2, 2, 1, 1)) set the margin sizes in lines of text par(mar = c(4, 4, 2, 2))

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line 1 line 2 line 3 line 4 line 1 line 2 line 3 line 4 line 1 line 2 line 1 line 2

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Multifigure layouts par can be used to set up multiple figures on the page. row-by-row: par(mfrow = c(2, 2)) column-by-column: par(mfcol = c(2, 2))

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figure 1 figure 2 figure 3 figure 4

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Draw axes axis() can be used to draw axes at any of the four side of a plot. This is a default call: axis(side) Possible values of side include: side = 1: bottom side = 2: left side = 3: top side = 4: right

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axis() example par(mfrow = c(2, 2)) plot(cars, ann = F, axes = F) axis(1) plot(cars, ann = F, axes = F) axis(2) plot(cars, ann = F, axes = F) axis(3) plot(cars, ann = F, axes = F) axis(4)

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5 10 15 20 25 5 10 15 20 25 0 20 40 60 80 120 0 20 40 60 80 120

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Axis customization axis(at = , labels = , las = , line = , cex.axis = , col.axis = ) at: tick marks position labels: texts are to be made the tick marks las: labels rotation (0, 1, 2, 3) line: the number of lines into the margin at which the axis line will be drawn cex.axis and col.axis: size and color of axis labels

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axis() example (cont) par(mfrow = c(2, 2), mar = c(2, 2, 2, 2)) plot(cars, ann = F, axes = F) axis(1, at = c(4, 12, 15, 15.4, 19, 25), labels = c("min", "1st Qu. ", "median", "mean", "3rd Qu.", "ma plot(cars, ann = F, axes = F) axis(3, cex.axis = 2) plot(cars, ann = F, axes = F) axis(2, las = 1) plot(cars, ann = F, axes = F) axis(4, col.axis = "gray40")

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min 1st Qu. 3rd Qu. max 5 10 15 20 25 0 20 40 60 80 100 120 0 20 40 60 80 120

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Plot annotation mtext() function can be used to place labels in the margins of a plot. mtext(text = , side = ) side: on which side of the plot (1=b, 2=l, 3=t, 4=r)

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mtext() example par(mar = c(4, 4, 4, 4)) plot(1:10, 1:10, ann = F) mtext("X-axis label", side = 1, line = 2) mtext("Y-axis label", side = 2, line = 2) mtext("Title", side = 3, line = 3) mtext("Subtitle", side = 3, line = 1.5) mtext("Source", side = 1, line = 3)

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2 4 6 8 10 2 4 6 8 10 X−axis label Y−axis label Title Subtitle Source

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Customizng plot annotation line: the number of lines into the margin at which the axis line will be drawn adj: adjustment direction [0, 1] outer: use outer margins if available (TRUE or FALSE) cex: size (expansion factor) col: color font: 1=regular, 2=bold, 3=itali, 4=bold-itatlic

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Recap Setting margins by par(mar) Draw axes by axis() Add annotation by mtext()

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Special topic: Color

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Choosing color is hard

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Choosing color is hard R has: 657 named colors (run: colors())

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Choosing color is hard R has: 657 named colors (run: colors()) 7 default color sets (rainbow(), heat.colors(), terrain.colors(), topo.colors(), cm.colors(), gray.colors())

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Choosing color is hard R has: 657 named colors (run: colors()) 7 default color sets (rainbow(), heat.colors(), terrain.colors(), topo.colors(), cm.colors(), gray.colors()) and a bunch of color packages (viridis, RColorBrewer, colorspace,. . . )

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When choosing color: Above all, do no harm. (Edward R. Tufte)

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Think carefully what you are using color for Fundamental use of color in visualization: to label (color as noun) to measure (color as quantity) to represent and imitate reality (color as representation) to decorate (color as beauty) (Edward R. Tufte)

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8h 10h 12h 14h 16h 18h 20h 22h 24h more submissions less submissions rtLab R&A rtSolu�on When do you submit your daily report? A survey of RTA's employees Source: Form RTA_Daily_Report rtLab's guys did it pre�y early

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Consult experts:

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Consult experts:

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Going beyond the default Demo customize_traditional_graphics.R

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Adding details with graphical primitives

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Some functions for drawing basic graphical primitives points(): draw data symbols at (x, y) lines(): draw lines between locations (x, y) abline(): draw straight lines segments(): draw line segments between (x0, y0) and (x1, y1) arrows(): draw line segments with arrowheads rect(): draw rectangles polygon(): draw one or more polygons text(): draw text at locations (x, y) legends(): draw legends

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Drawing points Basic call: points(x, y, pch = , col = ) pch: plotting symbols col: color of point

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Plotting symbols pch = 1 pch = 2 pch = 3 pch = 4 pch = 5 pch = 6 pch = 7 pch = 8 pch = 9 pch = 10 pch = 11 pch = 12 pch = 13 pch = 14 pch = 15 pch = 16 pch = 17 pch = 18 pch = 19 pch = 20 pch = 21

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Drawing connected line Basic call: lines(x, y, lty = , lwd = , col =, type = ) lty: line texture (“blank”, “solid”, “dashed”, “dotted”, “dotdash”, “longdash”, “twodash”) lwd: line width col: color of lines type: type of lines

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Line texture lty = 1 lty = 2 lty = 3 lty = 4 lty = 5 lty = 6

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Line graph variations Other forms can be made by lines(): type="l": line graph (default) type="s": step - horizontal first type="S": step - vertical first type="h": high density plot type="b": both points and lines type="o": over-plotting of points and lines

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type = l type = s type = S type = h type = b type = o

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Drawing straight lines Basic calls: abline(a = , b = ) abline(h = ) abline(v = ) a and b: specifies a line intercept and slope h: horizontal lines v: vertical lines Other arguments: lty, col, lwd

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Drawing line segments Basic call: segments(x0, y0, x1, y1) (x0, y0, x1, y1) gives the locations of the star and end point of the segments. Other arguments: lty, col, lwd

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Drawing arrows Basic calls: arrows(x0, y0, x1, y1, code = , length = , angle = ) (x0, y0, x1, y1) gives the locations of the star and end point of the arrows. head=1: head at the start; head=2: head at the end and head=3: head at both ends. length: length of arrow head. angle: angle to the shaft.

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Drawing rectangles Basic call: rect(x0, y0, x1, y1, col = , border = ) (x0, y0, x1, y1) gives the locations of opposite corners of the rectangles. col and border give color of the interior and border. Others: lty and lwd

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Drawing polygon Basic call: polygon(x, y, col = , border = ) x, y gives the coordinates of the polygon vertexes. col and border give color of the interior and border. Others: lty and lwd.

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Drawing text text(x, y, labels) x, y: locations of the text labels: actual strings Others: font, col, adj

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Drawing legend Basic form: legend(x, y, legend = ,...)

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Adding details Demo add_details.R

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Practice

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“Critique by redesign”

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Case 1

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Case 1 - Redesign Cornell Darthmouth Upenn Brown Yale Princeton Columbia Harvard 12.5% 10.4% 9.2% 8.3% 6.9% 6.1% 5.8% 5.2% Các trường đại học cạnh tranh nhất nước Mỹ So sánh dựa trên tỷ lệ trúng tuyển niên khóa 2017-2021 Nguồn: Business Insider

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Case 2

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Case 2 - Redesign 2011 2012 2013 2014 2015 Hải Phòng Hà Nội Cần Thơ Sài Gòn Đà Nẵng 36 24 45 28 5 1 20 6 16 14 Thứ hạng PCI của 5 thành phố trực thuộc TW Chỉ số PCI đo lường chất lượng môi trường kinh doanh, điều hành kinh tế và cải cách hành chính của chính quyền 63 tỉnh/thành phố Nguồn: VCCI

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Case 3

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Case 3 - Redesign 20,000$ 40,000$ 60,000$ 80,000$ 100,000$ 120,000$ 140,000$ Hungary Slovak Republic Estonia Poland Colombia Czech Republic Chile Greece Israel Mexico Slovenia Iceland Turkey Scotland Japan England Korea New Zealand Italy France Portugal OECD Average Sweden Belgium Austria Finland Ireland Netherlands Australia Canada Spain Norway United States Denmark Germany Luxembourg lương khởi điểm lương tối đa Cách biệt về lương giáo viên các quốc gia OECD So sánh lương khởi điểm và lương tối đa của giáo viên trung học cơ sở, 2013 Nguồn: OECD

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Where to go from here

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Blogs to follow http://flowingdata.com/, Nathan Yau (lots of R tutorials) https://eagereyes.org/, Robert Kosara http://junkcharts.typepad.com/, Kaiser Fung http://www.perceptualedge.com/library.php, Stephen Few http://www.thefunctionalart.com/, Alberto Cairo http://www.visualisingdata.com/, Andy Kirk http://www.randalolson.com/blog/, Randal S. Olson

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Books to read. Classic The Visual Display Of Quantitative Information, Edward R.Tufte Visual Explanations, Edward R.Tufte Envisioning Information, Edward R.Tufte Beautiful Evidence, Edward R.Tufte The Elements of Graphing Data, William Cleveland Visualizing Data, William Cleveland Semiology of Graphics, Jacques Bertin Exploratory Data Analysis, John W. Tukey

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Books to read. Accessible and Recent The Truthful Art, Albert Cairo The Functional Art, Albert Cairo Visualize This, Nathan Yau Data Points, Nathan Yau Information Dashboard Design, Stephen Few Show Me The Numbers, Stephen Few Now you see it, Stephen Few Signal, Stephen Few Storytelling With Data, Cole Nussbaumer Knaflic Creating More Effective Graphs, Naomi B. Robbins The Wall Street Journal Guide to Information Graphics, Dona M. Wong

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Books to read. R-centric R Graphics, Paul Murrell ggplot2 - Elegant Graphics for Data Analysis, Hadley Wickham lattice - Multivariate Data Visualization with R, Deepayan Sarkar R Graphics Cookbook: Practical Recipes for Visualizing Data, Winston Chang Data Visualisation with R - 100 Examples, Thomas Rahlf Graphing Data With R, John Jay Hilfiger Graphics for Statistics and Data Analysis with R, Kevin J. Keen Graphical Data Analysis with R, Antony Unwin

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Books to read. Design Data Visualisation: A Handbook for Data Driven Design, Andy Kirk Data Visualization: A Successful Design Process, Andy Kirk Information Visualization: Perception for Design, Colin Ware Visual Thinking for Design, Colin Ware Designing Data Visualizations: Representing Informational Relationships, Noah Iliinsky Visualization Analysis and Design, Tamara Munzner Design for Information, Isabel Meirelles The Non-designer’s Design Book, Robin Williams