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    Aswan introduces himself as a senior data analyst and instructor for data visualization and R. He then shares contact information. The document discusses the grammar of graphics and its key elements like data, mappings, scales and geometries. It provides an example of visualizing COVID-19 case data in Jakarta using R, calculating a 7-day amplification factor and plotting the results.

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    Data Visualization in Data Science using R

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    Aswan introduces himself as a senior data analyst and instructor for data visualization and R. He then shares contact information. The document discusses the grammar of graphics and its key elements like data, mappings, scales and geometries. It provides an example of visualizing COVID-19 case data in Jakarta using R, calculating a 7-day amplification factor and plotting the results.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    Download as pdf or txt
    155 views37 pages

    Data Visualization in Data Science Using R

    Uploaded by

    BomBom
    Aswan introduces himself as a senior data analyst and instructor for data visualization and R. He then shares contact information. The document discusses the grammar of graphics and its key elements like data, mappings, scales and geometries. It provides an example of visualizing COVID-19 case data in Jakarta using R, calculating a 7-day amplification factor and plotting the results.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
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    of 37

    >_dataviz with #rstats

    from table into canvas


    DTS X DQLab | 26 March 2021
    Hi, I'm Aswan!
    Senior Data analyst @ Jabar Digital Service
    Sensometrics specialist @ Sensolution.ID
    Initiator of Komunitas R Indonesia
    R instructor @ DQLab, R Academy Telkom
    University, and some universities
    Freelance data analyst & visualization designer
    Passionate about: Data carpentry and data
    visualization

    Twitter: @aswansyahputra_
    Telegram: @aswansyahputra
    Email:
    muhammadaswansyahputra@gmail.com

    2 / 15
    Grammar of graphics
    3 / 15
    "In order to build, rst we need to
    deconstruct."

    4 / 15
    Elements of graphics

    5 / 15
    Elements of graphics
    1. Data
    2. Mapping
    3. Statistic
    4. Scales
    5. Geometries
    6. Facets
    7. Coordinates
    8. Theme

    5 / 15
    Elements of graphics
    1. Data
    2. Mapping
    3. Statistic
    4. Scales
    5. Geometries
    6. Facets
    7. Coordinates
    8. Theme

    5 / 15
    The devil is in the detail
    6 / 15
    7 / 15
    8 / 15
    COVID-19 in Jakarta

    library(tidyverse)
    library(lubridate)
    library(slider)
    library(scales)

    load("data/cov_jakarta.rda")

    9 / 15
    COVID-19 in Jakarta

    library(tidyverse) cov_jakarta
    library(lubridate)
    library(slider)
    ## # A tibble: 306 x 4
    library(scales)
    ## date newcase death recovered
    load("data/cov_jakarta.rda") ## <date> <int> <int> <int>
    ## 1 2020-03-01 2 0 0
    ## 2 2020-03-02 2 0 0
    ## 3 2020-03-03 2 0 0
    ## 4 2020-03-04 2 0 0
    ## 5 2020-03-05 0 1 0
    ## 6 2020-03-06 0 0 0
    ## 7 2020-03-07 0 2 0
    ## 8 2020-03-08 0 0 0
    ## 9 2020-03-09 0 1 0
    ## 10 2020-03-10 0 0 0
    ## # … with 296 more rows

    9 / 15
    7-th day ampli cation factor preparation

    cov_jakarta_a7 <- cov_jakarta ## # A tibble: 306 x 4


    ## date newcase death recovered
    cov_jakarta_a7 ## <date> <int> <int> <int>
    ## 1 2020-03-01 2 0 0
    ## 2 2020-03-02 2 0 0
    ## 3 2020-03-03 2 0 0
    ## 4 2020-03-04 2 0 0
    ## 5 2020-03-05 0 1 0
    ## 6 2020-03-06 0 0 0
    ## 7 2020-03-07 0 2 0
    ## 8 2020-03-08 0 0 0
    ## 9 2020-03-09 0 1 0
    ## 10 2020-03-10 0 0 0
    ## # … with 296 more rows

    9 / 15
    7-th day ampli cation factor preparation

    cov_jakarta_a7 <- cov_jakarta %>% ## # A tibble: 306 x 4


    transmute( ## date infected infected_lastweek a7
    date, ## <date> <int> <int> <dbl>
    infected = cumsum(newcase), ## 1 2020-03-01 2 NA NA
    infected_lastweek = dplyr::lag(infected, 7), ## 2 2020-03-02 4 NA NA
    a7 = infected / infected_lastweek, ## 3 2020-03-03 6 NA NA
    a7 = slide_dbl(a7, mean, .before = 1, .after = 1 ## 4 2020-03-04 8 NA NA
    ) ## 5 2020-03-05 8 NA NA
    ## 6 2020-03-06 8 NA NA
    cov_jakarta_a7 ## 7 2020-03-07 8 NA NA
    ## 8 2020-03-08 8 2 NA
    ## 9 2020-03-09 8 4 2.44
    ## 10 2020-03-10 8 6 1.44
    ## # … with 296 more rows

    9 / 15
    7-th day ampli cation factor preparation

    cov_jakarta_a7 <- cov_jakarta %>% ## # A tibble: 306 x 4


    transmute( ## date infected infected_lastweek a7
    date, ## <date> <int> <int> <dbl>
    infected = cumsum(newcase), ## 1 2020-03-01 2 NA NA
    infected_lastweek = dplyr::lag(infected, 7), ## 2 2020-03-02 4 NA NA
    a7 = infected / infected_lastweek, ## 3 2020-03-03 6 NA NA
    a7 = slide_dbl(a7, mean, .before = 1, .after = 1 ## 4 2020-03-04 8 NA NA
    ) ## 5 2020-03-05 8 NA NA
    ## 6 2020-03-06 8 NA NA
    ## 7 2020-03-07 8 NA NA
    cov_jakarta_a7
    ## 8 2020-03-08 8 2 NA
    ## 9 2020-03-09 8 4 2.44
    ## 10 2020-03-10 8 6 1.44
    ## # … with 296 more rows

    9 / 15
    7-th day ampli cation factor visualization

    cov_jakarta_a7 ## # A tibble: 306 x 4


    ## date infected infected_lastweek a7
    ## <date> <int> <int> <dbl>
    ## 1 2020-03-01 2 NA NA
    ## 2 2020-03-02 4 NA NA
    ## 3 2020-03-03 6 NA NA
    ## 4 2020-03-04 8 NA NA
    ## 5 2020-03-05 8 NA NA
    ## 6 2020-03-06 8 NA NA
    ## 7 2020-03-07 8 NA NA
    ## 8 2020-03-08 8 2 NA
    ## 9 2020-03-09 8 4 2.44
    ## 10 2020-03-10 8 6 1.44
    ## # … with 296 more rows

    9 / 15
    7-th day ampli cation factor visualization

    cov_jakarta_a7 %>%
    ggplot(aes(date, a7))

    9 / 15
    7-th day ampli cation factor visualization

    cov_jakarta_a7 %>%
    ggplot(aes(date, a7)) +
    geom_col(fill = "#136F63", alpha = 0.8, colour = "

    9 / 15
    7-th day ampli cation factor visualization

    cov_jakarta_a7 %>%
    ggplot(aes(date, a7)) +
    geom_col(fill = "#136F63", alpha = 0.8, colour = "
    geom_hline(yintercept = 1, colour = "#D72638", typ

    9 / 15
    7-th day ampli cation factor visualization

    cov_jakarta_a7 %>%
    ggplot(aes(date, a7)) +
    geom_col(fill = "#136F63", alpha = 0.8, colour = "
    geom_hline(yintercept = 1, colour = "#D72638", typ
    scale_x_date(
    breaks = "1 month",
    labels = label_date(format = "%b"),
    expand = c(0.005, 0.005)
    )

    9 / 15
    7-th day ampli cation factor visualization

    cov_jakarta_a7 %>%
    ggplot(aes(date, a7)) +
    geom_col(fill = "#136F63", alpha = 0.8, colour = "
    geom_hline(yintercept = 1, colour = "#D72638", typ
    scale_x_date(
    breaks = "1 month",
    labels = label_date(format = "%b"),
    expand = c(0.005, 0.005)
    ) +
    labs(
    x = NULL,
    y = "A7",
    title = "Silent transmission in Jakarta",
    subtitle = "Red line segment indicates 7-day per
    caption = "Data source: covid.19.go.id"
    )

    9 / 15
    7-th day ampli cation factor visualization

    cov_jakarta_a7 %>%
    ggplot(aes(date, a7)) +
    geom_col(fill = "#136F63", alpha = 0.8, colour = "
    geom_hline(yintercept = 1, colour = "#D72638", typ
    scale_x_date(
    breaks = "1 month",
    labels = label_date(format = "%b"),
    expand = c(0.005, 0.005)
    ) +
    labs(
    x = NULL,
    y = "A7",
    title = "Silent transmission in Jakarta",
    subtitle = "Red line segment indicates 7-day per
    caption = "Data source: covid.19.go.id"
    ) +
    theme_xaringan()

    9 / 15
    7-th day ampli cation factor visualization

    cov_jakarta_a7 %>%
    ggplot(aes(date, a7)) +
    geom_col(fill = "#136F63", alpha = 0.8, colour = "
    geom_hline(yintercept = 1, colour = "#D72638", typ
    scale_x_date(
    breaks = "1 month",
    labels = label_date(format = "%b"),
    expand = c(0.005, 0.005)
    ) +
    labs(
    x = NULL,
    y = "A7",
    title = "Silent transmission in Jakarta",
    subtitle = "Red line segment indicates 7-day per
    caption = "Data source: covid.19.go.id"
    ) +
    theme_xaringan() +
    theme(
    panel.grid.major.x = element_blank(),
    panel.grid.minor = element_blank(),
    axis.text.x = element_text(size = rel(0.5))
    )

    9 / 15
    Adding annotation (1)

    cov_jakarta_a7_plot

    9 / 15
    Adding annotation (1)

    cov_jakarta_a7_plot +
    annotate(
    geom = "label",
    x = min(cov_jakarta$date),
    y = 1,
    label = "A7 = 1.0",
    fontface = "italic",
    size = 4,
    colour = "#D72638",
    alpha = 0.8
    )

    9 / 15
    Adding annotation (1)

    cov_jakarta_a7_plot +
    annotate(
    geom = "label",
    x = min(cov_jakarta$date),
    y = 1,
    label = "A7 = 1.0",
    fontface = "italic",
    size = 4,
    colour = "#D72638",
    alpha = 0.8
    ) +
    geom_curve(
    x = as.Date("2020-04-16"),
    xend = as.Date("2020-04-9"),
    y = 5,
    yend = subset(cov_jakarta_a7, date == "2020-04-9
    arrow = arrow(length = unit(0.07, "inch")),
    size = 0.025,
    color = "gray40",
    curvature = 0.3
    )

    9 / 15
    Adding annotation (1)

    cov_jakarta_a7_plot +
    annotate(
    geom = "label",
    x = min(cov_jakarta$date),
    y = 1,
    label = "A7 = 1.0",
    fontface = "italic",
    size = 4,
    colour = "#D72638",
    alpha = 0.8
    ) +
    geom_curve(
    x = as.Date("2020-04-16"),
    xend = as.Date("2020-04-9"),
    y = 5,
    yend = subset(cov_jakarta_a7, date == "2020-04-9
    arrow = arrow(length = unit(0.07, "inch")),
    size = 0.025,
    color = "gray40",
    curvature = 0.3
    ) +
    annotate(
    geom = "label",
    x = as.Date("2020-04-16"),
    y = 5,
    label = "First PSBB\n(9 April)",
    size = 5,
    colour = "gray30",
    alpha = 1
    ) 9 / 15
    Adding annotation (2)

    cov_jakarta_a7_plot

    9 / 15
    Adding annotation (2)

    cov_jakarta_a7_plot +
    annotate(
    geom = "text",
    x = as.Date("2020-08-31"),
    y = 12,
    label = str_wrap("A7 is the ratio of total confi
    fontface = "italic",
    size = 3.5,
    colour = "gray30"
    )

    9 / 15
    Adding annotation (2)

    cov_jakarta_a7_plot +
    annotate(
    geom = "text",
    x = as.Date("2020-08-31"),
    y = 12,
    label = str_wrap("A7 is the ratio of total confi
    fontface = "italic",
    size = 3.5,
    colour = "gray30"
    ) +
    geom_segment(
    x = as.Date("2020-04-9"),
    xend = as.Date("2020-04-9") + 7,
    y = 2,
    yend = 2,
    arrow = arrow(length = unit(0.05, "inch"), type
    size = 0.025,
    colour = "#D72638"
    )

    9 / 15
    Adding annotation (2)

    cov_jakarta_a7_plot +
    annotate(
    geom = "text",
    x = as.Date("2020-08-31"),
    y = 12,
    label = str_wrap("A7 is the ratio of total confi
    fontface = "italic",
    size = 3.5,
    colour = "gray30"
    ) +
    geom_segment(
    x = as.Date("2020-04-9"),
    xend = as.Date("2020-04-9") + 7,
    y = 2,
    yend = 2,
    arrow = arrow(length = unit(0.05, "inch"), type
    size = 0.025,
    colour = "#D72638"
    ) +
    coord_cartesian(clip = "off")

    9 / 15
    Some practical tips
    10 / 15
    11 / 15
    12 / 15
    13 / 15
    Learn from re-viz, demo time!
    14 / 15
    Thank you!

    Contact me!
    muhammadaswansyahputra@gmail.com

    15 / 15

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