Row

Intro
The Isabella County Big Tree Project is an ongoing effort to identify the largest individual(s) of all tree species native to and common within Isabella County, Michigan (USA). The primary purpose is to build the database that exists here with the intended secondary public interface with this database in the form of mapping applications for desktop and mobile. The mobile map is designed to run on the Google Maps App but can also run on an internet browser. There is a known bug that effectively prevents interfacing between one of the recent ios updates (not sure which one) and Google maps; if you get a “Can’t open map” message, use the alt mobile map link to open the map in a browser. The “largest” trees in this project are determined by measuring trunk circumference at 4.5 feet above the ground. The database, dependent maps and visualizations, and quantitative statements below were last updated December 11, 2019.

(Tree) Growth
This project is a continuation of a similar mission originally completed in 1999 by Hud Keenan and currently, 24 of the trees from his list are still the largest known individuals in the county (green below). For 31 trees, new largest individuals have been identified (blue below) and 20 additional species have been added to the list, 13 of which have currently identified largest individuals. All of the individuals that have been located from the 1999 survey (green) have grown (no big surprise there) and most of the new individuals from the ongoing survey are larger than their 1999 survey counterparts- with the exception of the northern red oak, White ash, and sugar maple. Hover over points for common names and measurements of the trees; click on the key to remove a classification from the plot.


(Other) Michigan Trees The Michigan Botanical Club maintains a that was most recently updated November 4, 2019. A map of the tree locations from their database is contained in the desktop map mentioned above (toggle “Michigan Trees”). Their database is different from the Isabella County database in that contains information about trees and tree locations for trees on public land only. Not including roadways and open water, Isabella County is ~99% private land and the majority of the identified big trees in the county are on private property. A comparison of trunk circumferences from the Isabella County and Greater Michigan databases shows a larger circumference for two tree species in Isabella County, the Eastern Cottonwood and Swamp Cottonwood (both of which are on private land).

Michigan (x axis) data
Location Isabella County is mostly (~97%) rural with “urban” exceptions that include all of Mount Pleasant, Lake Isabella, Shepherd, Weidman, Coldwater Lake, Rosebush, Winn, Blanchard, and Beal City and the southern half of Clare. These “urban” areas (namely Mount Pleasant, Shepherd, and Blanchard) are overrepresented (17x) in with respect to big trees with 30 of 68 mapped trees (44%). Isabella county also contains at least 18 cemeteries (all but 5 of which are rural) which account for less than 0.04% of total county area but contain 5 big trees. The sankey diagram below shows categorical locations for the 68 big trees that are currently mapped in Isabella County; the number in parentheses is the number of trees at this location and the number in brackets is the proportional representation.


Contribute
This is a living database and if you think that you know of a tree that is larger than the ones on our list, please contact us using this form. Our database currently lacks individuals from the following species: red maple (Acer rubrum), swamp cottonwood (Populus heterophylla), swamp white oak (Quercus bicolor), tupelo (black gum) (Nyssa sylvatica), black ash (Fraxinus nigra), white fir (Abies concolor), norway maple (Acer platanoides), green ash (Fraxinus pennsylvanica), balm of gilead (balsam poplar) (Populus balsamifera), slippery elm (Ulmus rubra), rock elm (Ulmus thomasii), mountain maple (Acer spicatum), english oak (Quercus robur). Thanks!

---
title: "Isabella County Big Tree Project"
#author: "pLow"
output: 
  flexdashboard::flex_dashboard:
    vertical_layout: scroll
    #orientation: rows
    social: menu
    source_code: embed
#runtime: shiny
---
 
```{r global, include=FALSE}
library(dplyr)
library(rgdal)
library(leaflet)
library(rgeos)
library(raster)
library(splitstackshape)
library(plotly)

library(googlesheets)
library(gsheet)

#gs_auth() #authorize access to google sheet
#this <- gs_title("ICBTP") #get the google sheet
#that <- this %>% gs_read(ws = "ICBTP") # get the worksheet
#btpx <- as.data.frame(that)

btpx <- read.csv('E:/bigTrees/bigTreesBackUp.csv') #use this if the google token is being problematic...

btpx$circ1999 <- as.numeric(gsub("([0-9]+\\.?[0-9]+)|.", '\\1', btpx$Circ_1999))
btpx$circ2019 <- as.numeric(gsub("([0-9]+\\.?[0-9]+)|.", '\\1', btpx$Circ_2019))

gps19 <- cSplit(btpx, "GPS_2019", ",") 
btp <- cSplit(gps19, "GPS_1999", ",") 

btp$Coordinates19 <- paste(btp$GPS_2019_1,btp$GPS_2019_2)
btp$Coordinates99 <- paste(btp$GPS_1999_1,btp$GPS_1999_2)

btp2019t <- subset(btp, Typical=="Y")
btp2019a <- subset(btp, Typical=="N")

btp2019Yt <- subset(btp2019t, Status == "yes") #24 on 2019.12.02
btp2019Nt <- subset(btp2019t, Status == "no") #6 on 2019.12.02
btp2019Et <- subset(btp2019t, Status == "new") #25 on 2019.12.02
btp2019Wt <- subset(btp2019t, Status == "new19") #12 on 2019.12.02

btp2019Ya <- subset(btp2019a, Status == "yes") #0 on 2019.12.02
btp2019Na <- subset(btp2019a, Status == "no") #0 on 2019.12.02
btp2019Ea <- subset(btp2019a, Status == "new") #6 on 2019.12.02
btp2019Wa <- subset(btp2019a, Status == "new19") #1 on 2019.12.02

url <- 'docs.google.com/spreadsheets/d/1uH6l1s3Sn6lEUeZMJGkrN0I4PtzTVoqf0xt3vX2pJXM' #this is the public url for their database
MI <- gsheet2tbl(url) #read google sheet to data table
MI <- as.data.frame(MI)
MI$Common_Name <- MI[, 2]
MI$Scientific_Name <- MI[, 3]
MIs <-  as.data.frame(MI %>% group_by(Scientific_Name) %>% filter(Girth == max(Girth, na.rm = TRUE)))
MIc <-  as.data.frame(MI %>% group_by(Common_Name) %>% filter(Girth == max(Girth, na.rm = TRUE)))

mergedCom <- merge(btp, MIc, by="Common_Name", all=FALSE)
mergedCom$Circ <- ifelse(is.na(mergedCom$circ2019), mergedCom$circ1999, mergedCom$circ2019) 
mergedCom$q <- round(mergedCom$Circ / mergedCom$Girth,2)

mergedSci <- merge(btp, MIs, by="Scientific_Name", all=FALSE)
mergedSci$Circ<- ifelse(is.na(mergedSci$circ2019), mergedSci$circ1999, mergedSci$circ2019) 
mergedSci$q <- round(mergedSci$Circ / mergedSci$Girth,2)
maxG <- max(max(mergedCom$Girth, na.rm=TRUE),max(mergedSci$Girth, na.rm=TRUE))

one2one = data.frame(x=c(0,maxG), y=c(0,maxG))

treeMI <- plot_ly() %>%	  
	add_lines(data=one2one, x=~x, y = ~y, name = '1:1', line = list(shape = "linear"), hoverinfo='text', text = "1:1", color="black") %>%
  	add_trace(data=mergedCom, x=mergedCom$Girth, y=mergedCom$Circ, type="scatter",mode="markers", name = 'Common', legendgroup="Common", 
		marker = list(color = 'black', size = 20, line = list(color = 'rgba(0, 0, 0, .8)', width = 1)), opacity=0.75, 
		hoverinfo = "text", showlegend = TRUE, 
		text = ~paste('Common name: ',Name,'
County: ',County,'
Isabella Circ:',Circ,'in.
Michigan Circ: ',Girth,'in.
I/M: ',q)) %>%
  	add_trace(data=mergedSci, x=mergedSci$Girth, y=mergedSci$Circ, type="scatter",mode="markers", name = 'Scientific', legendgroup="Scientific", 
		marker = list(color = 'red', size = 16, line = list(color = 'rgba(0, 0, 0, .8)', width = 1)), opacity=0.75, 
		hoverinfo = "text", showlegend = TRUE, 
		text = ~paste('Name: ',Name,'
Scientific name: ',Scientific_Name,'
County: ',County,'
Isabella Circ:',Circ,'in.
Michigan Circ: ',Girth,'in.
I/M: ',q)) %>%
	layout(xaxis = list(title = "Circumference of Michigan Tree (inches)", showgrid = FALSE, zeroline = TRUE, showticklabels = TRUE),
         	yaxis = list(side = 'left', title = 'Circumference of Isabella County Tree (inches)', showgrid = FALSE, zeroline = TRUE))

###growth

btp2019Yt$growth <- (btp2019Yt$circ2019 - btp2019Yt$circ1999)
btp2019Et$growth <- (btp2019Et$circ2019 - btp2019Et$circ1999)
btp2019Wt$growth <- (btp2019Wt$circ2019 - btp2019Wt$circ1999)

growth <- plot_ly() %>%	  
	add_lines(data=one2one, x=~x, y = ~y, name = '1:1', line = list(shape = "linear"), hoverinfo='text', text = "1:1", color="black") %>%
  	add_trace(data=btp2019Yt, x=btp2019Yt$circ1999, y=btp2019Yt$circ2019, type="scatter",mode="markers", name = 'Old', legendgroup="Old", 
		marker = list(color = 'darkgreen', size = ~circ2019/6, line = list(color = 'rgba(0, 0, 0, .8)', width = 1)), opacity=0.75, 
		hoverinfo = "text", showlegend = TRUE, 
		text = ~paste('Common name: ',Common_Name,'
Circ in 1999:',circ1999,'in.
Circ in 2019: ',circ2019,'in.')) %>%
  	add_trace(data=btp2019Et, x=btp2019Et$circ1999, y=btp2019Et$circ2019, type="scatter",mode="markers", name = 'New', legendgroup="New", 
		marker = list(color = 'blue', size = ~circ2019/6, line = list(color = 'rgba(0, 0, 0, .8)', width = 1)), opacity=0.75, 
		hoverinfo = "text", showlegend = TRUE, 
		text = ~paste('Common name: ',Common_Name,'
Circ in 1999:',circ1999,'in.
Circ in 2019: ',circ2019,'in.')) %>%
	layout(xaxis = list(title = "Circumference in 1999 (inches)", showgrid = FALSE, zeroline = TRUE, showticklabels = TRUE),
         	yaxis = list(side = 'left', title = 'Circumference in 2019 (inches)', showgrid = FALSE, zeroline = TRUE))
```

Inputs {.sidebar}
-----------------------------------------------------------------------
Links:


[Desktop Map](http://rpubs.com/fecr2o4/btp){target="_blank"}


[Mobile Map](https://www.google.com/maps/d/viewer?mid=1nBuplq88ljTv8fI3djqfESVf6TaIEvdR&ll=43.631172061033176%2C-84.8870255&z=9){target="_blank"}


[Alt Mobile Map](https://drive.google.com/open?id=1nBuplq88ljTv8fI3djqfESVf6TaIEvdR&usp=sharing){target="_blank"}


[Public Database](https://tinyurl.com/t9ve93n){target="_blank"}



Row {.bgwhite} 
-----------------------------------------------------------------------

Intro

The Isabella County Big Tree Project is an ongoing effort to identify the largest individual(s) of all tree species native to and common within Isabella County, Michigan (USA). The primary purpose is to build the database that exists [here](https://tinyurl.com/t9ve93n){target="_blank"} with the intended secondary public interface with this database in the form of mapping applications for [desktop](http://rpubs.com/fecr2o4/btp){target="_blank"} and [mobile](https://drive.google.com/open?id=1nBuplq88ljTv8fI3djqfESVf6TaIEvdR&usp=sharing){target="_blank"}. The mobile map is designed to run on the Google Maps App but can also run on an internet browser. There is a known bug that effectively prevents interfacing between one of the recent ios updates (not sure which one) and Google maps; if you get a "Can't open map" message, use the [alt mobile map](https://drive.google.com/open?id=1nBuplq88ljTv8fI3djqfESVf6TaIEvdR&usp=sharing){target="_blank"} link to open the map in a browser. The "largest" trees in this project are determined by measuring trunk circumference at 4.5 feet above the ground. The database, dependent maps and visualizations, and quantitative statements below were last updated December 11, 2019.


(Tree) Growth

This project is a continuation of a similar mission originally completed in 1999 by Hud Keenan and currently, 24 of the trees from his list are still the largest known individuals in the county (green below). For 31 trees, new largest individuals have been identified (blue below) and 20 additional species have been added to the list, 13 of which have currently identified largest individuals. All of the individuals that have been located from the 1999 survey (green) have grown (no big surprise there) and most of the new individuals from the ongoing survey are larger than their 1999 survey counterparts- with the exception of the northern red oak, White ash, and sugar maple. Hover over points for common names and measurements of the trees; click on the key to remove a classification from the plot.

    
```{r}
growth
```

(Other) Michigan Trees
The Michigan Botanical Club maintains a that was most recently updated November 4, 2019. A map of the tree locations from their database is contained in the desktop map mentioned above (toggle "Michigan Trees"). Their database is different from the Isabella County database in that contains information about trees and tree locations for trees on public land only. Not including roadways and open water, Isabella County is ~99% private land and the majority of the identified big trees in the county are on private property. A comparison of trunk circumferences from the Isabella County and Greater Michigan databases shows a larger circumference for two tree species in Isabella County, the Eastern Cottonwood and Swamp Cottonwood (both of which are on private land).

```{r}
treeMI
```
[Michigan (x axis) data](http://www.michbotclub.org/big-tree-on-google){target="_blank"}

Location
Isabella County is mostly (~97%) rural with "urban" exceptions that include all of Mount Pleasant, Lake Isabella, Shepherd, Weidman, Coldwater Lake, Rosebush, Winn, Blanchard, and Beal City and the southern half of Clare. These "urban" areas (namely Mount Pleasant, Shepherd, and Blanchard) are overrepresented (17x) in with respect to big trees with 30 of 68 mapped trees (44%). Isabella county also contains at least 18 cemeteries (all but 5 of which are rural) which account for less than 0.04% of total county area but contain 5 big trees. The sankey diagram below shows categorical locations for the 68 big trees that are currently mapped in Isabella County; the number in parentheses is the number of trees at this location and the number in brackets is the proportional representation.


![](E:/bigTrees/bigTrees2.png){width=80%}


Contribute

This is a living database and if you think that you know of a tree that is larger than the ones on our list, please contact us using this [form](https://forms.gle/xi9x1SuxGAYewpWH9){target="_blank"}. Our database currently lacks individuals from the following species: red maple	(*Acer rubrum*), swamp cottonwood (Populus heterophylla), swamp white oak	(Quercus bicolor), tupelo (black gum)	(Nyssa sylvatica), black ash	(Fraxinus nigra), white fir	(Abies concolor), norway maple	(Acer platanoides), green ash	(Fraxinus pennsylvanica), balm of gilead (balsam poplar)	(Populus balsamifera), slippery elm	(Ulmus rubra), rock elm	(Ulmus thomasii), mountain maple	(Acer spicatum), english oak	(Quercus robur). Thanks!