Type:	Package
Title:	Retrieve Data from MacLeish Field Station
Version:	0.3.9
Description:	Download data from the Ada and Archibald MacLeish Field Station in Whately, MA. The Ada and Archibald MacLeish Field Station is a 260-acre patchwork of forest and farmland located in West Whately, MA that provides opportunities for faculty and students to pursue environmental research, outdoor education, and low-impact recreation (see https://www.smith.edu/about-smith/sustainable-smith/macleish for more information). This package contains weather data over several years, and spatial data on various man-made and natural structures.
License:	CC0
LazyData:	TRUE
Imports:	dplyr, lubridate, phenocamr, readr, rvest, sf, stringr, xml2
Depends:	R (≥ 3.5), etl
Suggests:	ggplot2, dbplyr, RSQLite, broom, knitr, leaflet, purrr, rmarkdown, markdown, mgcv, clifro, testthat
URL:	https://github.com/beanumber/macleish
BugReports:	https://github.com/beanumber/macleish/issues
RoxygenNote:	7.2.0
Encoding:	UTF-8
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2022-07-06 20:11:41 UTC; bbaumer
Author:	Benjamin S. Baumer [aut, cre], Rose Goueth [aut], Wencong Li [aut], Weijia Zhang [ctb], Nicholas Horton [ctb], Dominique Kelly [aut], Albert Y. Kim [aut]
Maintainer:	Benjamin S. Baumer <ben.baumer@gmail.com>
Repository:	CRAN
Date/Publication:	2022-07-06 20:30:07 UTC

Extract weather data

Description

Retrieve data from the Macleish Field Station weather monitors

Usage

## S3 method for class 'etl_macleish'
etl_extract(obj, ...)

## S3 method for class 'etl_macleish'
etl_transform(obj, ...)

etl_transform_help(obj, ...)

Arguments

Examples

macleish <- etl("macleish")
str(macleish)

## Not run: 
macleish %>%
  etl_extract() %>%
  etl_transform() %>%
  etl_load()
whately <- macleish %>%
  tbl("whately") 
orchard <- macleish %>%
  tbl("orchard") 
  
whately %>%
  summarize(N = n(), avg_temp = mean(temperature))
orchard %>%
  summarize(N = n(), avg_temp = mean(temperature))
  
# check data types
whately %>%
  glimpse()

# if using SQLite, datetimes will get converted to integers
whately <- whately %>%
  mutate(when_datetime = datetime(when, 'unixepoch'))
whately %>%
  glimpse()

# show the most recent data -- should be within the past hour
whately %>%
  collect() %>%
  tail()

# show that no time-shifting is happening
if (require(ggplot2)) {
macleish %>%
  tbl("whately") %>%
  collect() %>%
  mutate(when = lubridate::ymd_hms(when)) %>%
  filter(lubridate::year(when) == 2012 & month(when) == 12 & day(when) == 20) %>%
  ggplot(aes(x = when, y = temperature)) + geom_line()
}

## End(Not run)

MacLeish spatial data

Description

Shapefiles from the MacLeish Field Station. The field station itself is located at lat = 42.449167, lon = -72.679389. These data contain information about various man-made and natural structures surrounding the field station.

Usage

macleish_layers

Format

A list of sf::sf() objects, each providing a different layer.

landmarks

Landmarks

forests

Type of dominant tree in individual forests, as noted by Jesse Bellemare

streams

local streams

challenge_courses

Challenge courses on the property

buildings

Buildings at MacLeish

wetlands

Wetland areas

boundary

the property boundary

research

research plots

soil

soil deposits used by Amy Rhodes

trails

Hiking trails

camp_sites

Two camp sites

elevation

30 foot elevation contours

Details

Each of the sf::sf() objects are projected in epsg:4326 for easy integration with Google Maps or leaflet::leaflet() objects.

Examples

names(macleish_layers)
macleish_layers[["buildings"]]

if (require(sf)) {
 plot(macleish_layers[["buildings"]])
}

Maple sap collection at MacLeish

Description

Maple sap collection at MacLeish

Usage

maple_sap

Format

when

the date of collection

sap

how much sap was collected, in gallons

Comments

comments

People

who was there?

Retrieve elevation layers from MassGIS

Description

Retrieve elevation layers from MassGIS

Usage

mass_gis(layer = "contours250k")

macleish_intersect(x)

Arguments

Details

This function will download shapefiles from MassGIS, unzip them, transform the projection to EPSG:4326, compute their intersection with the boundary of the MacLeish property, and return the resulting sf::sf() object.

Intersect a spatial layer with the MacLeish boundary layer

Source

https://www.mass.gov/info-details/massgis-data-layers

Examples

## Not run: 
# have to download the shapefiles...could take a while...
elevation <- mass_gis()
macleish_elevation <- macleish_intersect(elevation)
if (require(sf)) {
  plot(macleish_elevation)
}

dcr_trails <- mass_gis("dcrtrails")


## End(Not run)

Retrieve images from Phenocam

Description

Phenocam contains over 70,000 images taken from MacLeish. Photos have been taken every 30 minutes since February 2017.

Usage

phenocam_image_url(when = NULL, ...)

phenocam_read_day_urls(x = Sys.Date())

phenocam_read_monthly_midday_urls(x = Sys.Date())

phenocam_image_url_midday(x = Sys.Date())

phenocam_info()

phenocam_download(...)

Arguments

References

https://phenocam.nau.edu/webcam/sites/macleish/

See Also

download_phenocam

Examples

phenocam_image_url()
phenocam_image_url("2021-12-25 12:05:05")
## Not run: 
phenocam_read_day_urls()

## End(Not run)
## Not run: 
phenocam_read_monthly_midday_urls()

## End(Not run)
## Not run: 
phenocam_image_url_midday(Sys.Date() - 3)
phenocam_image_url_midday(Sys.Date() - 365)

## End(Not run)
## Not run: 
phenocam_info()

## End(Not run)
## Not run: 
phenocam_download()
df <- read_phenocam(file.path(tempdir(),"macleish_DB_1000_3day.csv"))
print(str(df))

## End(Not run)

MacLeish Data Plot 1

Description

Data on change in tree diameter (in centimeters) for parasitic Hemlock Woolly Adelgid dominated areas on the Western side of MacLeish. Tree diameter was measured at 1.4 meters high above the ground.

Usage

tree_diameter1

Format

Module

Module number that represents one of the 10 subplot modules that are 110 m and 20 x 50 m. There are five 10 x 10 modules along central 50 m axis.

Tag

Tag numbers used to identify each tree.

Species

Tree species include Red Maple (Acer rubrum), Sweet Birch (Betula lenta), Paper Birch (Betula papyrifera), American Beech (Fagus grandifolia), American witch-hazel (Hamamelis virginiana), Eastern White Pine (Pinus strobus), Northern Red Oak (Quercus rubra), and Eastern Hemlock (Tsuga canadensis).

Position

Stage of growth for each individual tree. The emergent position are the tallest trees, followed by canopy, subcanopy, and finally, sapling trees, which are the smallest trees.

Year

Data collected from 2010-2015 in the fall semesters.

Notes

Notes collected on the wellbeing of tree species, including notes on death or poor health.

Diameter

Tree diameter measured in centimeters and at 1.4 meters high above the ground.

People

Data obtained from Jesse Bellemare and Smith College students from BIO364-365 courses.

See Also

tree_diameter2

MacLeish Data Plot 2

Description

Data on change in tree diameter (in centimeters) for parasitic Hemlock Woolly Adelgid dominated areas on the Western side of MacLeish. Tree diameter was measured at 1.4 meters high above the ground.

Usage

tree_diameter2

Format

Module

Module number that represents one of the 10 subplot modules that are 110 m and 20 x 50 m. There are five 10 x 10 modules along central 50 m axis.

Tag

Tag numbers used to identify each tree.

Species

Tree species include Red Maple (Acer rubrum), Sweet Birch (Betula lenta), American Beech (Fagus grandifolia), Eastern White Pine (Pinus strobus), Northern Red Oak (Quercus rubra), and Eastern Hemlock (Tsuga canadensis).

Year

Data collected from 2009-2012 in the fall semesters.

Notes

Notes collected on the wellbeing of tree species, including notes on death or poor health.

Diameter

Tree diameter measured in centimeters and at 1.4 meters high above the ground.

People

Data obtained from Jesse Bellemare and Smith College students from BIO364-365 courses.

See Also

tree_diameter1

Weather data from Macleish Field Stations

Description

Weather data collected at the Macleish Field Station in Whately, MA during 2015.

Usage

whately_2015

orchard_2015

Format

For both, a data frame (dplyr::tbl_df()) with roughly 52,560 rows and 8 or 9 variables.

The following variables are values that are found in either the whately_2015 or orchard_2015 data tables.

All variables are averaged over the 10 minute interval unless otherwise noted.

when

Timestamp for each measurement set in Eastern Standard Time.

temperature

average temperature, in Celsius

wind_speed

Wind speed, in meters per second

wind_dir

Wind direction, in degrees

rel_humidity

How much water there is in the air, in millimeters

pressure

Atmospheric pressure, in millibars

rainfall

Total rainfall, in millimeters

solar_radiation

Amount of radiation coming from the sun, in Watts/meters^2. Solar measurement for Whately

par_density

Photosynthetically Active Radiation (sunlight between 400 and 700 nm), in average density of Watts/meters^2. One of two solar measurements for Orchard

par_total

Photosynthetically Active Radiation (sunlight between 400 and 700 nm), in average total over measurement period of Watts/meters^2. One of two solar measurements for Orchard

An object of class tbl_df (inherits from tbl, data.frame) with 52547 rows and 9 columns.

Details

The Macleish Field Station is a remote outpost owned by Smith College and used for field research. There are two weather stations on the premises. One is called WhatelyMet and the other is OrchardMet.

The WhatelyMet station is located at (42.448470, -72.680553) and the OrchardMet station is at (42.449653, -72.680315).

WhatelyMet is located at the end of Poplar Hill Road in Whately, Massachusetts, USA. The meteorological instruments of WhatelyMet (except the rain gauge) are mounted at the top of a tower 25.3 m tall, well above the surrounding forest canopy. The tower is located on a local ridge at an elevation 250.75m above sea level.

OrchardMet is located about 250 m north of the first tower in an open field next to an apple orchard. Full canopy trees (~20 m tall) are within 30 m of this station. This station has a standard instrument configuration with temperature, relative humidity, solar radiation, and barometric pressure measured between 1.5 and 2.0 m above the ground. Wind speed and direction are measured on a 10 m tall tower and precipitation is measured on the ground. Ground temperature is measured at 15 and 30 cm below the ground surface 2 m south of the tower. The tower is located 258.1 m above sea level. Data collection at OrchardMet began on June 27th, 2014.

The variables shown above are weather data collected at WhatelyMet and OrchardMet during 2015. Solar radiation is measured in two different ways: see SlrW_Avgor the PAR variables for Photosynthetic Active Radiation.

Note that a loose wire resulted in erroneous temperature reading at OrchardMet in late November, 2015.

Source

These data are recorded at https://www.smith.edu/about-smith/sustainable-smith/ceeds

Examples

## Not run: 
#' # loose wire anomalies
if (require(dplyr) & require(ggplot2) & require(lubridate)) {
 orchard_2015 %>%
 filter(month(when) == 11) %>%
   ggplot(aes(x = when, y = temperature)) +
   geom_line() + geom_smooth()
}

## End(Not run)