Use the HYSPLIT model from inside R and do more with it
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README.md

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SplitR is an R package for conducting trajectory and dispersion modeling with HYSPLIT. You can determine where air (came from | is going), or, where gas-phase or particulate matter (came from | is going). It's a means to help explain how, where, and when chemicals and materials are atmospherically transported, dispersed, and deposited.

This model has many applications. Some have modeled the atmospheric transport of moisture to determine probable extreme rainfall locations leading to flood events (Gustafsson et al., 2010). Similarly, Creamean et al., 2013 have presented a direct link between long-range transported dust and biological aerosols affecting cloud ice formation and precipitation processes in western United States.

Others have successfully improved understanding of invasive species dispersal abilities to inform conservation and landscape management (Lander et al., 2014). Along similar lines, the long-distance transport of high-risk plant pathogens can be modeled with HYSPLIT to assist with plant disease management decisions, such as applications of fungicide or pesticide to potentially-affected agricultural areas (Schmale and Ross, 2015).

SplitR allows you to build and run HYSPLIT models in a fast, easy, and organized manner. A few or, perhaps, thousands of trajectory or dispersion runs can be conducted with minimal code. Because SplitR is an R interface to HYSPLIT, we can store output in memory and take advantage of the vast selection of R packages to perform statistical analyses and to generate visualizations. This package furthermore simplifies the process of running HYSPLIT models by automating the retrieval and storage of associated meteorological data files.

Some of the things you can do with SplitR are:

  • create and execute model runs with an easily readable magrittr pipeline workflow
  • run multiple trajectory and dispersion model runs (forward or backward) with multiple temporal and spatial variations
  • visualize wind trajectories and particle positions throughout trajectory and dispersion runs
  • use the returned tbl_df object with dplyr to filter(), select(), group_by(), summarize(), mutate(), and transmute() the model output data

HYSPLIT Trajectory Model Runs

To perform a series of HYSPLIT trajectory model runs, one can use the SplitR hysplit_trajectory() function:

library(SplitR)

setwd("~/Documents/SplitR_wd")

trajectory <- 
  hysplit_trajectory(
    lat = 42.83752,
    lon = -80.30364,
    height = 50,
    duration = 24,
    run_period = "2012-03-12",
    daily_hours = c(0, 6, 12, 18),
    direction = "forward",
    met_type = "gdas1",
    extended_met = TRUE) 

This use of hysplit_trajectory() sets up four trajectory runs that start at 00:00, 06:00, 12:00, and 18:00 UTC on March 12, 2012 (using run_period = "2012-03-12" and daily_hours = c(0, 6, 12, 18)). Several years of runs can be initiated using run_period = c(2012, 2014), model runs can be performed between a range of dates as well (run_period = c("2012-03-12", "2013-05-23")). These runs are 24 h in duration (duration = 24).

The receptor/origin locations are set using lat and lon for the latitude(s) and longitude(s). The starting location of 42.83752ºN and 80.30364ºW is set here using lat = 42.83752 and lon = -80.30364. Equal-length vectors of lat and lon values can be used here to create an ensemble of model runs. The starting height of 5 m above ground level is set by height = 5.

The model runs as set above are forward runs (moving forward in time, set here using direction = "forward") and not backtrajectory runs (set with direction = "backward").

The meteorological options include the type of met data to use. The 1º GDAS data is used here with met_type = "gdas1" but there is also the option to use NCEP reanalysis data with the met_type = "reanalysis" setting and NARR (North American Regional Reanalysis) data with met_type = "narr". The necessary meteorological data files relevant to the period being modeled will be downloaded from the NOAA FTP server if they are not present in the working directory.

The function will return a data frame containing trajectory information. The data frame (named here as the object trajectory) will be have the following columns when extended_met is set to FALSE:

  • receptor a numeric label for the receptor
  • year, month, day, hour integer values for date/time components
  • hour.inc the integer hour difference compared to the run starting time
  • lat, lon, height the latitude, longitude, and height (meters above ground level) of the air mass along the trajectory
  • pressure the air pressure along the trajectory (in hPa)
  • date2 a POSIXct date-time value (in UTC) for the air mass along the trajectory
  • date a POSIXct date-time value (in UTC) for the time of release or time of incidence at the receptor site

If the model is run with extended_met set to TRUE then the following columns will also be available in the output data frame:

  • theta the potential temperature (in K) along the trajectory
  • air_temp the ambient air temperature (in K) along the trajectory
  • rainfall the rate of rainfall (in mm/h) along the trajectory
  • mixdepth the mixing depth (or mixing height, in meters) along the trajectory
  • rh the relative humidity along the trajectory
  • sp_humidity the specific humidity (in g/kg) along the trajectory
  • h2o_mixrate the mixed layer depth (in meters) along the trajectory
  • terr_msl the terrain height at the location defined by lat and long
  • sun_flux the downward solar radiation flux (in watts) along the trajectory

Models can also be defined and executed using a modeling object in a magrittr workflow. Here's an example:

library(SplitR)
library(magrittr)

setwd("~/Documents/SplitR_wd")

# Create the `trajectory_model` object, add
# a grid of starting locations, add run
# parameters, and execute the model runs
trajectory_model <-
  create_traj_model() %>%
  add_grid(
    lat = 49.0,
    lon = -123.0,
    range = c(0.8, 0.8),
    division = c(0.2, 0.2)) %>%
  add_params(
    height = 50,
    duration = 6,
    run_period = "2015-07-01",
    daily_hours = c(0, 12),
    direction = "backward",
    met_type = "reanalysis") %>%
  run_model()

Here, we create a trajectory_model object which serves as a container for the model definition and for the results. Read left to right, the order of operations is: create_traj_model() -> add_grid() -> add_params -> run_model().

This pipeline setup allows for more flexibility as R objects can be piped in for variation in the types of models created. The create_traj_model() function creates the trajectory model object. The add_grid() allows for the simple creation of a grid for multiple starting locations in an ensemble run. As shown, a grid centered on 49ºN and 123ºW has bounds 0.8º in each direction and grid points at every 0.2º in each direction. One or more add_params() statements can be used to write model parameters to the model object. Ending the pipeline with run_model() runs the model and creates results.

The trajectory data can be be extracted from the trajectory model object using get_output_df()...

# Get a data frame containing the model results
trajectory_df <-
  trajectory_model %>% get_output_df()

...and a tbl_df (tibble) object is now available:

trajectory_df
#> Source: local data frame [175 x 21]
#> 
#>    receptor  year month   day  hour hour.inc    lat      lon height
#>       (int) (int) (int) (int) (int)    (dbl)  (dbl)    (dbl)  (dbl)
#> 1         1    15     7     1     0        0 49.400 -123.400   50.0
#> 2         1    15     7     1     1        1 49.359 -123.203   49.9
#> 3         1    15     7     1     2        2 49.326 -123.039   49.3
#> 4         1    15     7     1     3        3 49.300 -122.905   48.2
#> 5         1    15     7     1     4        4 49.282 -122.800   46.7
#> 6         1    15     7     1     5        5 49.268 -122.723   44.8
#> 7         1    15     7     1     6        6 49.260 -122.672   42.5
#> 8         2    15     7     1     0        0 49.400 -123.200   50.0
#> 9         2    15     7     1     1        1 49.369 -123.008   49.9
#> 10        2    15     7     1     2        2 49.346 -122.848   49.4
#> ..      ...   ...   ...   ...   ...      ...    ...      ...    ...
#> Variables not shown: pressure (dbl), date2 (time), date (time), theta
#>   (dbl), air_temp (dbl), rainfall (dbl), mixdepth (dbl), rh (dbl),
#>   sp_humidity (dbl), h2o_mixrate (dbl), terr_msl (dbl), sun_flux (dbl)

Plotting Trajectory Data

Trajectories can be plotted onto an interactive map. Use the trajectory_plot() function with either the trajectory data frame (created directly by the hysplit_trajectory() function), or, even better, with a trajectory model object.

library(SplitR)
library(magrittr)

# Plot results using the trajectory data frame
trajectory_plot(trajectory)

# Plot results using the trajectory model object
trajectory_model %>% trajectory_plot()

The visualization will appear in the RStudio Viewer:

The trajectory points and paths are layers where their visibility can be toggled using the Layers icon at the top-right of the view. The following selection of basemaps is also provided:

  • CartoDB Dark Matter
  • CartoDB Positron
  • ESRI World Terrain
  • Stamen Toner

Clicking any of the points along the trajectory will provide an informative popup with time/position info and meteorological data for that location at that point in time:

HYSPLIT Dispersion Runs

Dispersion models can also be conveniently built and executed using a magrittr workflow. Instantiate the dispersion model with the create_disp_model() function. Use one or more add_params() statements to write parameters to the model object. The add_grid() function here facilitates the creation of sampling grids. Using add_emissions() function anywhere in the pipeline will define emissions properties for one or more emitted pollutants. With add_species(), the physical properties and deposition parameters of one or more emitted species can be added to the model.

As with the trajectory model, the pipeline can ended with run_model(). To extract a data frame containing the modeled output data, use the get_output_df() function. An example is in order:

library(SplitR)
library(magrittr)

setwd("~/Documents/SplitR_wd")

# Create the `dispersion_model` object, add
# a grid of starting locations, add run
# parameters, and then execute the model run
dispersion_model <-
  create_disp_model() %>%
  add_emissions(
    rate = 5,
    duration = 6,
    start_day = "2015-07-01",
    start_hour = 0) %>%
  add_species(
    pdiam = 1,
    density = 1,
    shape_factor = 1) %>%
  add_grid(
    range = c(0.5, 0.5),
    division = c(0.1, 0.1)) %>%
  add_params(
    lat = 49.0,
    lon = -123.0,
    height = 50,
    duration = 24,
    start_day = "2015-07-01",
    start_hour = 0,
    direction = "forward",
    met_type = "reanalysis") %>%
  run_model()

This dispersion model formally begins at 00:00 UTC on July 1, 2015 (using start_day = "2015-07-01" and start_hour = 0). The model run is a forward run (i.e., moving forward in time, with direction = "forward") and not backwards (would be set as direction = "backward"). Essentially, running in forward mode means the starting location is a source of emissions; running backward means that the starting location is a receptor.

This run has been set to be modeled for 24 h (duration = 24). The starting location of 49.0ºN and 123.0ºW is set using lat = 49.0 and lon = -123.0; the starting height of 50 m above ground level is set by height = 50. The meteorological options include the type of met data to use (global NCEP Reanalysis data is used here with met_type = "reanalysis).

A single emissions species is set to be emitted (using add_emissions()) for 6 hours (duration = 6) at an emission rate of 5 mass units per hour (rate = 5). Emissions begin at the same time as the start of the model (start_day = "2015-07-01" and start_hour = 0). The properties of the emitted pollutant are defined using add_species(). Here, the physical properties of particle diameter (in micrometers), density (in grams per cubic centimeter), and shape factor (value from 0 to 1), respectively, are defined with pdiam = 1, density = 1, and shape_factor = 1.

It should be noted that the order of add_emissions(), add_species(), add_grid(), and add_params() does not matter. There can even be several instances of each of these functions throughout the pipeline.

All meteorological data files needed to execute the model during the defined period will be downloaded from the NOAA FTP server if such files are not already present in the working directory.

The output data can be extracted from the dispersion model object...

# Get a data frame containing the model results
dispersion_df <-
  dispersion_model %>% get_output_df()

...and the data is conveniently supplied as a tibble object:

dispersion_df
#> Source: local data frame [54,063 x 5]
#> 
#>    particle_no       lon     lat height  hour
#>          (int)     (dbl)   (dbl)  (dbl) (int)
#> 1            1 -122.8368 48.9499    711     1
#> 2            2 -122.8419 48.9311    780     1
#> 3            3 -122.8531 48.9108    848     1
#> 4            4 -122.8401 48.9365    647     1
#> 5            5 -122.8472 48.9389    124     1
#> 6            6 -122.8124 48.9449     10     1
#> 7            7 -122.8263 48.9316    935     1
#> 8            8 -122.8144 48.9631    265     1
#> 9            9 -122.8313 48.9465    278     1
#> 10          10 -122.8105 48.9326    250     1
#> ..         ...       ...     ...    ...   ...

Plotting Dispersion Data

Dispersion data can also be plotted onto a map. Use the dispersion_plot() function with the dispersion model object.

library(SplitR)
library(magrittr)

# Plot particle data onto a map
dispersion_model %>% dispersion_plot()

The visualization will appear in the RStudio Viewer:

The dispersed particles at every hour are present as map layers, where their visibility can be toggled using the Layers icon at the top-right of the view.

Installation

SplitR is used in an R environment. If you don't have an R installation, it can be obtained from the Comprehensive R Archive Network (CRAN). It is recommended that RStudio be used as the R IDE to take advantage of its ability to visualize output in its Viewer pane.

You can install the development version of SplitR from GitHub using the devtools package.

devtools::install_github("rich-iannone/SplitR")

HYSPLIT Citations

Stein, A.F., Draxler, R.R, Rolph, G.D., Stunder, B.J.B., Cohen, M.D., and Ngan, F., (2015). NOAA's HYSPLIT atmospheric transport and dispersion modeling system, Bull. Amer. Meteor. Soc., 96, 2059-2077, http://dx.doi.org/10.1175/BAMS-D-14-00110.1

Draxler, R.R., 1999: HYSPLIT4 user's guide. NOAA Tech. Memo. ERL ARL-230, NOAA Air Resources Laboratory, Silver Spring, MD.

Draxler, R.R., and G.D. Hess, 1998: An overview of the HYSPLIT_4 modeling system of trajectories, dispersion, and deposition. Aust. Meteor. Mag., 47, 295-308.