Tree phenology observations in Wauseon, Ohio

Using Shiny for R, explore dynamic visualizations of tree phenology recorded by Thomas Mikesell in Wauseon, Ohio between 1883 and 1912

Hometown specials

I often think that I know everything about my origins in rural Ohio. As a child, I constantly roamed the roads and trails of my quiet hometown on my bike, and I observed the rhythms of small town life marked by planting, harvest, small talk, and public school calendars. Outside of town, the land was shaped by generations of agriculture, and everyone experienced some form of hardship as the world around us changed. It was a quiet corner of the country where nothing remarkable happened.

Given my familiarity with the territory, I am rarely surprised by stories from my birthplace, but I recently discovered a person who lived a quiet life in the area with a remarkable legacy - Thomas Mikesell. Over several decades, he kept meticulous records about seasonal events in the natural world. A keen student of phenology, he made thousands of records of shoot expansion, flowering, fruiting, and leaf senescence for hundreds of commodity crops, specialty crops, trees, and ornamental plants around the turn of the 20th Century with accompanying notes about weather conditions. In 1914, a detailed report of Thomas Mikesell’s life and work was published in the Monthly Weather Review Supplement, and it offers some remarkable details about one man’s passionate side project:

The observer, Thomas Mikesell, was born on the farm 1 mile north of where Wauseon, Ohio, now stands in Fulton County but then Lucas County. His parents, William and Margaret (Boyes) Mikesell, came from western Pennsylvania in April, 1837, and settled in the forest.

He attended country schools until 14 years of age and then went to the high school at Wauseon, 1 mile distant. At that time the Wauseon High School had but two rooms. In June, 1863, he enlisted in Company H, Eighty-sixth Ohio Volunteer Infantry and served with it until February 10, 1864. After leaving the Army Mr. Mikesell resumed his high-school course and in 1866 his school days ended; not so his study of nature.

For several winters Mikesell taught elementary school in Ohio, Iowa, and northern Missouri; then he returned to Wauseon in the fall of 1869. From this time on he worked on the farm, retiring from active life in the spring of 1902. In November, 1873, he married Miss Martha Heniman, but no children have come to this union.

In 1889 he was elected secretary of the Fulton County Fair and for 16 consecutive years he continued to serve in that capacity. In 1902 he was appointed a corn and wheat region observer by the United States Weather Bureau and that same year, because of failing health, he was obliged to give up his farm and move to Wauseon, where he still resides.

The observations published in this present supplement are but a portion of the records that this one man maintained during his busy life. They constitute one of the most complete and reliable local records of which we have knowledge, as to the development of plant life and the migrations of birds and animals. Quietly, carefully, conscientiously, this man has merely kept his eyes open to see and systematically recorded the movements of nature about him year after year. He has done what thousands of other men might have done, but which no other one has done. The writer believes that science owes a great debt to such a man, that all honor is due him, and that the name of Thomas Mikesell should be set high among the faithful students of nature in this country.

Exploring tree phenology

Mikesell brought a level of commitment and dedication rarely matched to his hobby, and the biographer echoes the natural reaction of ordinary people to such an extraordinary accomplishment. I certainly appreciate the character required for such an undertaking. In life, we more often seek quick rewards from meager investments, and it’s always a pleasure to see someone creating enduring value without an expectation for immediate recognition. Similar examples of impressive amateur study, like Billy Barr at the Rocky Mountain Biological Laboratory, are rare. In recent decades, Mikesell’s valuable records have been discovered and used by many scientists studying changes in the pattern of natural events over time. I encountered the story and data in an article attempting to predict the timing of budburst for temperate tree species, and one interesting study compared Mikesell’s notes to more recent observations of trees on the same land. Notably, they discovered that delayed fall leaf drop was largely responsible for a longer growing season in recent years.

TipMore about phenophases

To aid observations, the USA National Phenology Network developed standardized definitions for some of the major phenophases (listed below). Mikesell’s protocol may not have been equally detailed, but he probably, like many people, intuitively recognized and enjoyed observing repeating patterns in nature, especially if they coincided with other seasonal milestones in life.

Breaking leaf buds: One or more breaking leaf buds are visible on the plant. A leaf bud is considered “breaking” once a green leaf tip is visible at the end of the bud but before the first leaf from the bud has unfolded to expose the leaf stalk (petiole) or leaf base.

Leaves: One or more live, unfolded leaves are visible on the plant. A leaf is considered “unfolded” once its entire length has emerged from a breaking bud, stem node, or growing stem tip so that the leaf stalk (petiole) or leaf base is visible at its point of attachment to the stem. Do not include any fully dried or dead leaves.

Open flowers: One or more open, fresh flowers are visible on the plant. Flowers are considered “open” when the reproductive parts (male stamens or female pistils) are visible between or within unfolded or open flower parts (petals, floral tubes, or sepals). Do not include wilted or dried flowers.

Ripe fruit: One or more ripe fruits are visible on the plant.

Colored leaves: One or more leaves show some of their typical late-season color, or yellow or brown due to drought or other stresses. Do not include small spots of color due to minor leaf damage or dieback on branches that have broken. Do not include any fully dried or dead leaves that remain on the plant.

Falling leaves: One or more leaves with typical late-season color, or yellow or brown due to other stresses, are falling or have recently fallen from the plant. Do not include fully dried or dead leaves that remain on the plant for many days before falling.

After discovering the data, I wanted to develop a new resource for my arboriculture course showing the sequence of major phenophases among various tree species. In my class, I often emphasize the importance of informed expectations about seasonal tree growth and development. The northern catalpa (Catalpa speciosa), for example, produces new leaves very late in the spring, and one could easily assume, without knowing the tree, that the delay was a serious concern. In becoming familiar with a tree, it’s also helpful to know the time it typically flowers, develops fall color, or, perhaps, fruits. In Colorado, we often receive heavy snow in the late spring and fall, and it isn’t always desirable for trees to hold leaves when the storms typically occur. The Mikesell records contain information about many of the trees grown in Colorado landscapes, and, although the historical observations from Ohio may not accurately predict contemporary tree phenology in Colorado, the data contains many useful insights for anyone interested in the subject.

Interactive Quarto documents with Shinylive

After digitizing the records for 26 woody species, I explored visualizations of the data using violin plots, ensuring the observations were properly formatted. Assuming it would be easier to plot a continuous variable, I originally coded the Mikesell observations using Julian days starting January 1 each year, but I converted them to standard dates for readability, since ggplot accepts dates on an axis. Next, I overlayed a jittered plot of individual observations using small circle markers with opacity corresponding to the year of observation. If the phenophases were consistently happening earlier or later each year, the opacity mapping should produce an obvious color gradient, but the gray colors for individual markers were clearly unorganized and showed stochastic variation in the timing of events each year. Last, I added a large circle marker depicting the median date of the phenophase for each species. After creating the basic plot elements, I edited the plot style to improve its appearance, and I reordered the display of species on the y-axis by sorting the median phenophase date from earliest to latest.

library(tidyverse)

data <- read.csv("Mikesell_Phenology_Data.csv", header = TRUE, na.strings = "999") |>
  mutate(bud_burst = as.Date(bud_burst,format="%j"),
         first_leaf = as.Date(first_leaf,format="%j"),
         full_leaf = as.Date(full_leaf,format="%j"),
         open_flowers = as.Date(open_flowers,format="%j"),
         ripe_fruit = as.Date(ripe_fruit,format="%j"),
         colored_leaves = as.Date(colored_leaves,format="%j"),
         leaves_dropped = as.Date(leaves_dropped,format="%j"))

ggplot(data, aes(bud_burst,reorder(species, bud_burst, FUN = median, na.rm = TRUE))) +
  geom_violin(aes(fill = reorder(species, bud_burst, FUN = median, na.rm = TRUE)), show.legend = FALSE, na.rm = TRUE) +
  stat_summary(fun = "median", size = 3.5, geom = "point", na.rm = TRUE) +
  geom_jitter(aes(alpha = year), height = 0, width = 0.2, na.rm = TRUE) +
  labs(
    x = "Date",
    y = "Species",
    alpha = "Year"
  ) +
  scale_y_discrete(limits=rev) +
  theme(axis.text.y = element_text(face="italic",size=12),
        axis.text.x = element_text(size=12),
        axis.title = element_text(face="bold",size=13),
        legend.text = element_text(size=12),
        legend.title = element_text(size=13),
        panel.background = element_rect(fill="white"),
        panel.grid.major = element_line(color="gray93"))

Figure 1: Calendar dates Thomas Mikesell observed breaking leaf buds for various tree species in Wauseon, Ohio.

Although I liked the presentation of information in the figure, I would need a lot of room for visual summaries of all seven phenophases for 26 different species. Instead, I thought it would be better to display everything dynamically in a single interactive plot based on a user-selected phenophase. Although I had never developed such an application in R, I wanted to use this as a reason to learn more about Shiny apps. Shiny, developed in 2013, creates reactive web applications in R, and, with some direction from other R users in my department, I used Posit’s Shiny tutorial to learn the basic principles. Essentially, there are three components of a Shiny app:

• a user-interface (ui) object defines the app’s layout and appearance
• a server (server) function contains instructions for rendering app components
• a call to the shinyApp function builds the app using ui and server as inputs

library(shiny)

ui <- ...

server <- ...

shinyApp(ui, server)

The Posit tutorial gives a detailed summary of the process for building a local app with everything contained in a single app.R script. With the file in its own directory, you can run the app by giving the name of the directory to the runApp function or, in RStudio, you can simply click on the Run App button at the top of the script editor window.

Creating a user interface

Although the Shiny package contains functions for controlling the appearance of an app, often relying on the fluidPage and related layout functions, most now recommend using the bslib package for its superior style themes and interactive features. For my user interface, I chose a standard sidebar layout with a collapsible sidebar on the left for user input and a larger main area on the right for displaying the main app content. In my code, the page_sidebar function requires three main arguments, including a display name for the Shiny app (title), control widgets for handling user input in the sidebar (sidebar), and an unassigned R object for rendering the plot in the main area (plotOutput). Notably, the first argument of the plotOutput function specifies the name of the object generated by the server function ("phenophasePlot") for display in the app.

library(bslib)
library(shiny)

ui <- page_sidebar(
  title = "Mikesell Phenology Data",
  sidebar = radioButtons("radio","Select phenophase",
                         choices = c("Breaking leaf buds" = "bud_burst",
                                     "First leaf" = "first_leaf",
                                     "Full leaf" = "full_leaf",
                                     "Open flowers" = "open_flowers",
                                     "Ripe fruit" = "ripe_fruit",
                                     "Colored leaves" = "colored_leaves",
                                     "Leaves dropped" = "leaves_dropped"),
                         selected = "bud_burst"),
  plotOutput("phenophasePlot",width="100%")
)

For a control widget, I used radio buttons to let users select a phenophase to display in the plot. In general, the widget functions require two mandatory arguments, including a name ("radio") and a display label ("Select phenophase"), both specified as character strings, for the user interface, and a number of additional inputs depending on the type of widget. In my case, I specified the list of possible choices for the radio buttons with the displayed names matched to values (i.e., variable names) used in the code, and I set the first choice as the initially selected value. The Shiny function reference contains extensive and detailed documentation related to Shiny UI layout and inputs.

Server structure and logic

The server function uses two list-like main arguments, input and output. The input object stores the current value of control widgets used by the app, accessed using the names assigned in the ui object. For example, I can access the user-selected phenophase using input$radio, and I used a switch function to match the input to a list of possible values. The switch function executes the code statements corresponding to the matching case, which, in my case, simply selects the variables needed to create the figure. I assigned the output to a new variable dataInput, and I made the entire statement a reactive expression to ensure the code section will be executed every time the control widget changes.

After creating the input data set, I assigned the output of the code previously developed for the figure to an element in the output object (phenophasePlot). The name of the element matches the one listed for display in the ui object. To create the type of reactive output expected, I wrapped the ggplot and related statements with the renderPlot function, and I had to define the plot variables implicitly in the corresponding lines of code to make everything work dynamically. For the input data, I called the reactive expression as a function, and I changed the statements corresponding to the phenophase observations to the current value stored in the control widget.

library(shiny)
library(tidyverse)

server <- function(input, output) {
  
  dataInput <- reactive({
    switch(input$radio,
           bud_burst = phenoData[,c("year","species","bud_burst")],
           first_leaf = phenoData[,c("year","species","first_leaf")],
           full_leaf = phenoData[,c("year","species","full_leaf")],
           open_flowers = phenoData[,c("year","species","open_flowers")],
           ripe_fruit = phenoData[,c("year","species","ripe_fruit")],
           colored_leaves = phenoData[,c("year","species","colored_leaves")],
           leaves_dropped = phenoData[,c("year","species","leaves_dropped")])
  })
  
  output$phenophasePlot <- renderPlot({
    ggplot(dataInput(), aes(.data[[input$radio]],reorder(species, .data[[input$radio]], FUN = median, na.rm = TRUE))) +
      geom_violin(aes(fill = reorder(species, .data[[input$radio]], FUN = median, na.rm = TRUE)), show.legend = FALSE, na.rm = TRUE) +
      stat_summary(fun = "median", size = 3.5, geom = "point", na.rm = TRUE) +
      geom_jitter(aes(alpha = year), height = 0, width = 0.2, na.rm = TRUE) +
      labs(
        x = "Date",
        y = "Species",
        alpha = "Year"
      ) +
      scale_y_discrete(limits=rev) +
      theme(axis.text.y = element_text(face="italic",size=12),
            axis.text.x = element_text(size=12),
            axis.title = element_text(face="bold",size=13),
            legend.text = element_text(size=12),
            legend.title = element_text(size=13),
            panel.background = element_rect(fill="white"),
            panel.grid.major = element_line(color="gray93"))
  })
}

Deploying the app

Now, the app worked well locally, but I wanted to find a reliable workflow for deploying the app to the web, since I want to share the app with people unfamiliar with R. As it turns out, the options for web deployment (e.g., shinyapps.io, Shiny Server) all require hosting the app on a web server running R. Since server administration is a complex task, I prefer to avoid it, if possible. Fortunately, several brilliant developers have recently created tools allowing anyone to run R in the browser! By some unfathomable magic, the shinylive package, relying on WebR, can be used to create serverless Shiny apps. That’s right - no server needed! Since I use Quarto markdown, I had to install the Quarto Extension for shinylive by running quarto add quarto-ext/shinylive in the terminal. To insert a Shiny app in an interactive Quarto document, I added a filter key for shinylive in the document’s YAML header, and I added a code block marked with {shinylive-r} and a #| standalone: true option. Below, you can explore the code and interactive Shiny app in adjacent windows. If you’d like, you can also edit the code and restart the app using the play button at the top. Try it out for yourself!

I hope you’re proud, Thomas Mikesell.

#| '!! shinylive warning !!': |
#|   shinylive does not work in self-contained HTML documents.
#|   Please set `embed-resources: false` in your metadata.
#| standalone: true
#| viewerHeight: 750
#| components: [editor, viewer]
#| layout: vertical

# Load packages
library(bslib)
library(shiny)
library(tidyverse)

# Import and wrangle data
download.file("https://raw.githubusercontent.com/danielburcham/arbdatascience/master/Mikesell_Phenology_Data.csv", "Mikesell_Phenology_Data.csv")
phenoData <- read.csv("Mikesell_Phenology_Data.csv", header = TRUE, na.strings = "999") |>
  mutate(bud_burst = as.Date(bud_burst,format="%j"),
         first_leaf = as.Date(first_leaf,format="%j"),
         full_leaf = as.Date(full_leaf,format="%j"),
         open_flowers = as.Date(open_flowers,format="%j"),
         ripe_fruit = as.Date(ripe_fruit,format="%j"),
         colored_leaves = as.Date(colored_leaves,format="%j"),
         leaves_dropped = as.Date(leaves_dropped,format="%j"))

# Define user interface
ui <- page_sidebar(
  title = "Mikesell Phenology Data",
  sidebar = radioButtons("radio","Select phenophase",
                         choices = c("Breaking leaf buds" = "bud_burst",
                                     "First leaf" = "first_leaf",
                                     "Full leaf" = "full_leaf",
                                     "Open flowers" = "open_flowers",
                                     "Ripe fruit" = "ripe_fruit",
                                     "Colored leaves" = "colored_leaves",
                                     "Leaves dropped" = "leaves_dropped"),
                         selected = "bud_burst"),
  plotOutput("phenophasePlot",width="100%")
)

# Define server function
server <- function(input, output) {
  
  dataInput <- reactive({
    switch(input$radio,
           bud_burst = phenoData[,c("year","species","bud_burst")],
           first_leaf = phenoData[,c("year","species","first_leaf")],
           full_leaf = phenoData[,c("year","species","full_leaf")],
           open_flowers = phenoData[,c("year","species","open_flowers")],
           ripe_fruit = phenoData[,c("year","species","ripe_fruit")],
           colored_leaves = phenoData[,c("year","species","colored_leaves")],
           leaves_dropped = phenoData[,c("year","species","leaves_dropped")])
  })
  
  output$phenophasePlot <- renderPlot({
    ggplot(dataInput(), aes(.data[[input$radio]],reorder(species, .data[[input$radio]], FUN = median, na.rm = TRUE))) +
      geom_violin(aes(fill = reorder(species, .data[[input$radio]], FUN = median, na.rm = TRUE)), show.legend = FALSE, na.rm = TRUE) +
      stat_summary(fun = "median", size = 3.5, geom = "point", na.rm = TRUE) +
      geom_jitter(aes(alpha = year), height = 0, width = 0.2, na.rm = TRUE) +
      labs(
        x = "Date",
        y = "Species",
        alpha = "Year"
      ) +
      scale_y_discrete(limits=rev) + 
      theme(axis.text.y = element_text(face="italic",size=12),
            axis.text.x = element_text(size=12),
            axis.title = element_text(face="bold",size=13),
            legend.text = element_text(size=12),
            legend.title = element_text(size=13),
            panel.background = element_rect(fill="white"),
            panel.grid.major = element_line(color="gray93"))
  }, res=75)
}

# Create Shiny App
shinyApp(ui, server)