This short document is intended to get you started with using
RavenR
to aid your analysis with the Raven Hydrologic
Modelling Framework. This tutorial will get you up and running with the
RavenR
package and comfortable running a few commands. Some
knowledge or R is presumed in this document. If you are not comfortable
with R, take a look at any number of R training and Introductory
resources, such as the tRaining repository) on
Github.
This exercise will use the Nith River modelled output available from within the RavenR package, thus the functions to read in data from csv files are not required. However, it is recommended that you download the Nith river model files, and try to both run the model and read in the output files. The Nith river model can be downloaded from the Raven Tutorial #2.
Note that the RavenR
package is focused on handling
Raven input/output files, model diagnostics, and generating plots with
the ggplot2
library. The dependencies required by the
package are kept at a relative minimum to preserve stability. An
additional package, RavenR.extras
, is available on Github and contains
additional functionality.
If you don’t have RavenR yet installed in your R library, run the following commands to install the RavenR package directly from the Comprehensive R Archive Network (CRAN), which is available on CRAN.
install.packages("RavenR")
For those interested in the latest versions of RavenR or in
contributing to the development of RavenR, the package may be found on
Github at https://github.com/rchlumsk/RavenR. Packages on Github
may also be installed from within R using the devtools
library with the code below.
# install.packages("devtools")
library(devtools)
devtools::install_github("rchlumsk/RavenR")
Load the RavenR library from the console and view its contents with the following commands:
library(RavenR)
# view first 20 functions in RavenR
ls("package:RavenR") %>%
head(., 20)
Each function in the package is documented, which includes a description of the function, its inputs and outputs, and an example. You can look at any of the function examples by typing out the name of the function beginning with a question mark, which will show the help information at the right of the RStudio environment.
?rvn_flow_scatterplot
The name of each external function in the RavenR package begins with the “rvn_” prefix, so you in practice ‘search’ for functions by beginning to type them out. Try this to see what functions are available with “rvn_rvh_”.
The RavenR package contains a number of sample data files, which are useful for training purposes and testing of functions. The package contains sample data both in R format (under RavenR/data) and as raw data files in their native formats (RavenR/inst/extdata). The sample data set from the RavenR package (in R format) can be loaded in using the data function (with either quotes or just the name of the data), e.g.,
data("rvn_forcing_data")
# ?rvn_forcing_data
plot(rvn_forcing_data$forcings$temp_daily_ave,
main="Daily Avg. Temperature")
Notice as well that the sample data set in R format also has a built in help file to describe the data.
To locate the raw data from the RavenR package, we will use a syntax to find the data by file name in the RavenR package directory, which ends up looking more similar to a raw file call. This raw data file comes from the inst/extdata folder in the RavenR package. Note that this is done so that the sample data in raw format can be used and tested with functions, and the syntax to locate the data file is more portable across various computer operating systems.
# read in hydrograph sample csv data from RavenR package
ff <- system.file("extdata","run1_Hydrographs.csv", package = "RavenR")
# ff is a simple string, which can be substituted with any file location
ff
## [1] "C:/Users/rober/AppData/Local/Temp/Rtmpay6QOW/Rinst42e82fee49af/RavenR/extdata/run1_Hydrographs.csv"
# read in sample rvi file from the RavenR package
rvi_file <- system.file("extdata", "Nith.rvi", package = "RavenR")
# show first 6 lines of the file
readLines(rvi_file) %>% head()
## [1] "# ----------------------------------------------"
## [2] "# Raven Input file"
## [3] "# HBV-EC Nith River emulation test case"
## [4] "# ----------------------------------------------"
## [5] "# --Simulation Details -------------------------"
## [6] ":StartDate 2002-10-01 00:00:00"
The system.file
command will simply build a file path
for where this data file is located on your machine with the RavenR
package installation, which can then be passed to any function as
required to provide a file location. This command will be used
throughout this tutorial in place of local files for portability,
however, your own data files may be swapped in place of the system.file
locations. For example, you may wish to pass files from other Raven
Tutorial files by changing the file paths throughout this tutorial.
Now you are ready to start using RavenR to directly visualize and manipulate model output. This section of the exercise will make use of raw sample data in the RavenR package to illustrate some of the diagnostics and plotting capabilities of RavenR.
Start by finding the raw run1_ForcingFunctions.csv
file with the system.file
command. Note that this can be
replaced with your own forcing functions file location if preferred. We
will store the forcing functions data into an object called ff (and
obtain just the subobject using the ‘$’ operator), and then view the
first few rows using the head function. We will show
only the first six columns of the data for brevity.
ff <- system.file("extdata","run1_ForcingFunctions.csv", package = "RavenR")
# ff <- "C:/TEMP/Nith/output/ForcingFunctions.csv" # replace with your own file
ff_data <- RavenR::rvn_forcings_read(ff)
head(ff_data$forcings[,1:6])
## Warning: object timezone (UTC) is different from system timezone ()
## NOTE: set 'options(xts_check_TZ = FALSE)'to disable this warning
## This note is displayed once per session
## day_angle rain snow temp temp_daily_min temp_daily_max
## 2002-10-01 4.70809 3.468690 0 22.5956 17.92510 27.2662
## 2002-10-02 4.70809 3.468690 0 22.5956 17.92510 27.2662
## 2002-10-03 4.72530 1.189180 0 19.2076 15.40780 23.0075
## 2002-10-04 4.74251 2.083260 0 13.3714 11.49870 15.2440
## 2002-10-05 4.75973 6.474310 0 19.0304 12.50970 25.5510
## 2002-10-06 4.77694 0.125591 0 11.0186 7.43466 14.6024
Now we can plot the forcing data using the rvn_forcings_plot function. This creates an output of the five main forcings from the data set, from which we can plot one or more forcings, including a plot of the whole set of plots. This is typically a reasonable reality check on the model forcings.
Here, we plot the PET from the set of created plots.
myplots <- rvn_forcings_plot(ff_data$forcings)
# myplots$Temperature
# myplots$Radiation
# myplots$AllForcings
myplots$PET
The legend for the forcing plot functions is turned off by default,
but can be added back in using the theme
function from
ggplot2
to add the legend to the plot.
library(ggplot2)
myplots <- rvn_forcings_plot(ff_data$forcings)
myplots$Radiation +
theme(legend.position = "bottom")
We can similarly access the hydrograph fit. Here the hydrograph
sample data is located with the usual system.file
command,
then read into R with the rvn_hyd_read
function intended
for reading Hydrographs file. The flows from a specific subbasin can be
extracted using the rvn_hyd_extract
function, which is done
here for subbasin 36. The precipitation can be extracted similarly.
ff <- system.file("extdata","run1_Hydrographs.csv", package = "RavenR")
# ff <- "mydirectory/Hydrographs.csv" # replace with your own file
hy <- rvn_hyd_read(ff)
head(hy$hyd)
## Warning: object timezone (UTC) is different from system timezone ()
## precip Sub36 Sub36_obs Sub43 Sub43_obs
## 2002-10-01 NA 5.96354 NA 11.25050 NA
## 2002-10-02 3.468690 11.96430 0.801 18.59070 3.07
## 2002-10-03 1.189180 15.43700 0.828 25.74430 2.99
## 2002-10-04 2.083260 8.76948 0.860 18.68610 3.06
## 2002-10-05 6.474310 4.66501 0.903 9.82648 2.93
## 2002-10-06 0.125591 4.20829 1.040 7.90952 3.15
flow36 <- rvn_hyd_extract("Sub36",hy)
precip <- hy$hyd$precip
The hydrograph object flow36 now stores the simulated hydrograph
(flow36$sim
) and the observed hydrograph
(flow36$obs
), and the null subobject
(flow36$inflow
). The precip object stores the entire time
series of watershed-averaged precip (precip$sim
). We can
plot the simulated and observed hydrograph with the following commands
in base R, extracting the date:
plot(lubridate::date(flow36$sim), flow36$sim,col='red',
type='l', panel.first=grid())
lines(lubridate::date(flow36$obs), flow36$obs,col='black')
A ggplot format plot can also be created using the
rvn_hyd_plot
function in the RavenR library. This function
can save some of the trouble of plotting the precipitation on the
secondary axis.
rvn_hyd_plot(sim=flow36$sim, obs=flow36$obs, precip = precip)
There are some other helpful functions in RavenR for understanding our hydrographs. For example, the ‘spaghetti’ plot overlays the hydrographs from the supplied series and plots them against day of year on the x-axis, facilitating a comparison across multiple years.
rvn_flow_spaghetti(flow36$sim)
The annual quantiles function compute the flow quantiles for a given time series for each day of the year, and plot those quantiles with the corresponding plot function. This provides a similar look to the spaghetti plot, but with smooth quantiles instead of overlaying time series.
rvn_annual_quantiles(flow36$sim) %>%
rvn_annual_quantiles_plot(., ribboncolor = 'magenta')
Other plots indicate the agreement between peak flows in the modelled and observed.
rvn_annual_peak(flow36$sim, obs = flow36$obs)
## $df_peak
## date.end sim.peak obs.peak
## 1 2003-09-30 98.1327 74.4
## 2 2004-09-30 155.3560 168.0
##
## $p1
rvn_annual_peak_event(flow36$sim, obs = flow36$obs)
## $df_peak_event
## obs.dates sim.peak.event obs.peak.event
## 1 2003-03-23 35.7503 74.4
## 2 2004-03-07 98.9858 168.0
##
## $p1
We can also use some of the Raven plots to get some diagnostics and comparisons on the simulated and observed hydrographs. For example, the plots below compare the annual cumulative flow and the monthly volume bias, respectively.
rvn_cum_plot_flow(flow36$sim, obs = flow36$obs)
rvn_monthly_vbias(flow36$sim, obs = flow36$obs)
## $df.mvbias
## mvbias
## Jan 14.218038
## Feb -31.634886
## Mar 15.934117
## Apr -36.526804
## May -61.526206
## Jun -55.782838
## Jul -69.457872
## Aug -70.455088
## Sep 35.169824
## Oct 1.325446
## Nov 83.761819
## Dec 29.171061
##
## $plot
A fun feature in the RavenR package is the addition of dygraphs,
which produces a dynamic hydrograph plot with a slider on the time
scale. This is particularly helpful for viewing subsections of a
hydrograph dynamically, and comparing the simulated and observed
hydrographs in an interactive environment. Only the output object from
the rvn_hyd_read
function and the name of headings to
extract is required. Note that this interactive plot does not work well
in a PDF file, so try this out in R/RStudio.
library(htmltools)
rvn_hyd_dygraph(hy, basins="Sub36") %>%
htmltools::tagList()
While this tutorial focuses on the forcing functions and hydrograph data, similar routines exist for reading in the reservoir stages output, the watershed mass energy balance files, and other Raven outputs.
One utility that does not exist in the xts
package, but
is nonetheless useful in hydrology, is the application of functions to
the water year period rather than the calendar year. In the RavenR
package, the rvn_apply_wyearly
function accomplishes this.
The water year is by default set to index by the October 1st water year
(specifying the period ending September 30th), but this may be provided
as an argument to the function for different water years. Here, we apply
the mean function to the water year using sample hydrograph data in
RavenR.
myhyd <- system.file("extdata","run1_Hydrographs.csv", package = "RavenR") %>%
rvn_hyd_read()
library(xts)
# apply mean to calendar year in hydrograph data
xts::apply.yearly(myhyd$hyd$Sub36, colMeans, na.rm = TRUE)
## Sub36
## 2002-12-31 3.886438
## 2003-12-31 4.962424
## 2004-09-30 5.549967
# apply mean as FUN to daily average temperature
RavenR::rvn_apply_wyearly(myhyd$hyd$Sub36, colMeans, na.rm = TRUE)
## Sub36
## 2003-09-30 3.994746
## 2004-09-30 6.096847
The RavenR package can read the rvi file and generate a network plot
of the model connections, which is helpful in understanding the model
configuration. This can be done as follows, again using the Nith rvi
file as an example. The network plot may be directly written to file by
supplying a file name to the pdfout
argument, which is NULL
by default. Similar functionality is also available with the
rvn_rvi_process_diagrammer
function, which uses the
DiagrammeR
library.
rvi <- rvn_rvi_read(system.file("extdata","Nith.rvi", package = "RavenR"))
rvn_rvi_connections(rvi) %>%
rvn_rvi_process_ggplot()
The Raven User’s Manual (Appendix D) provides a number of model
templates that can be used to emulate existing model structures or act
as starting points for modellers to then adapt to their applications.
The rvn_rvi_write_template
function allows these templates
to be written directly to an rvi file, which reduces the effort in
creating these initial template files.
We can call this command to create a template rvi file for one of these models as per below.
td <- tempdir() # temporary directory to write model files to
tf <- file.path(td,"mymodel.rvi")
rvn_rvi_write_template(template_name="HMETS",
filename=tf,
author="Your Name")
## [1] TRUE
This file can also be used in the rvp file tools to quickly develop parameter files based on the model structure, discussed in the RVP section.
The discretization file, rvh, may be read in and modified using the
RavenR package. The rvn_rvh_read
function also computes the
upstream area of each subbasin. The corresponding
rvn_rvh_write
function also writes the rvh object back to
file.
# read in rvh file
rvh <- rvn_rvh_read(system.file("extdata","Nith.rvh", package = "RavenR"))
rvh$SBtable[, c("SBID","Downstream_ID","Area","TotalUpstreamArea")]
## SBID Downstream_ID Area TotalUpstreamArea
## 30 30 36 318.5 318.5
## 36 36 39 219.2 537.7
## 39 39 43 271.7 809.4
## 43 43 -1 205.0 1014.4
Similar to the rvi functionality, the subbasin connections from the
rvh file may be plotted using one of two ways. The
rvn_rvh_read
function has built-in functionality to build a
network plot, which may be plotted directly. The
rvn_rvh_subbasin_network_plot
function uses the subbasin
table to plot the network from the lat/long coordinates, generating a
more spatially accurate plot.
Compare these two plots to the map of the Nith basin from Tutorial #2.
# plot network from rvh file directly
plot(rvh$SBnetwork)
# create network plot of watershed structure from rvh file
rvn_rvh_subbasin_network_plot(rvh$SBtable, labeled = TRUE)
Another useful rvh functionality is the simplification of an HRU
file. Often in the initial HRU discretization, many HRUs with similar
properties and/or very small areas exist that are worthwhile
consolidating for the purpose of modelling. The
rvn_rvh_cleanrhus
function accomplishes this. Try the
example in the help file - ?rvn_rvh_cleanhrus
.
Finally, rvh files can be created with the rvn_rvh_write
function, and the basic subbasin table and hru table can be created with
the rvn_rvh_blankSBdf
and rvn_rvh_blankHRUdf
functions, respectively. More complex discretizations would require some
manual editing or other discretization tools to first create this
network.
A number of useful rvp utilities may be found in the RavenR package
by searching for ?rvn_rvp_
. A useful workflow to create
initial rvp files based on the Raven templates is available, and
demonstrated below in a few steps.
An rvp template file could be generated by running Raven with the
:CreateRVPTemplate
option in Raven.
rvn_run(fileprefix = "mymodel",
indir=td, # temporary directory created earlier
outdir=td, # write to same temporary directory
rvi_options=":CreateRVPTemplate",
showoutput = TRUE)
From the rvp template file, the file can be infilled to a usable rvp file using default values for parameter values and the various classes and other information from the rvh file. Additional rvp options can be added as well, such as average annual runoff and redirect file commands.
# temporary file path
tf <- tempfile()
# infill template file with default parameter values
rvn_rvp_fill_template(
rvi_file = system.file("extdata","Nith.rvi", package = "RavenR"),
rvh_file = system.file("extdata","Nith.rvh", package = "RavenR"),
rvp_template_file = system.file("extdata","nithmodel.rvp_temp.rvp", package = "RavenR"),
avg_annual_runoff = 123,
extra_commands=":RedirectToFile channel_properties.rvp",
rvp_out = tf)
## [1] TRUE
A table of default values and ranges for parameters required in a
model may be obtained by use of the rvn_rvi_getparams
function, which reads the rvi file and uses the database files stored
with the RavenR installation to query any required parameters and their
information. This is demonstrated for the Nith model file below.
system.file("extdata","Nith.rvi", package = "RavenR") %>%
rvn_rvi_read() %>%
rvn_rvi_getparams() %>%
head() # preview of parameter data frame
## param class_type units auto default min max
## 1 FOREST_COVERAGE LULT [0..1] False 0 0 1
## 5 IMPERMEABLE_FRAC LULT [0..1] False 0.0 0 1
## 13 REFREEZE_FACTOR LULT [mm/dC/d] False 5.04 0.0 10
## 37 POROSITY SOIL [0..1] True 0.4 0.0 1
## 42 PET_CORRECTION SOIL [0..1] True 1.0 0.0 1
## 43 FIELD_CAPACITY SOIL [0..1] True 0.0 0.0 1
The types of rvt files in Raven are plentiful, as rvt files are used
in Raven for time series observations, forcing data, gauge data, etc. A
handful of highly useful rvt utilities exist in the RavenR package for
reading and building these input files (, , and ). For example, gauge
observation data can be written to rvt format from the
tidyhydat
package for scraping Water Survey of Canada
data.
Here, we use sample data from the tidyhydat
function,
and write this to an rvt file for use within a Raven model. The commands
that would be used to extract data with the tidyhydat
function is also provided below (but commented out). The sample data is
used here to help meet compliance, but you are encouraged to try using
the tidyhydat
commands to try this functionality for
yourself.
stations <- c("05CB004","05CA002")
## Gather station data/info using tidyhydat functions
# library(tidyhydat)
# hd <- tidyhydat::hy_daily_flows(station_number = stations,
# start_date = "1996-01-01", end_date = "1997-01-01")
## load RavenR package sample data
data(rvn_tidyhydat_sample)
hd <- rvn_tidyhydat_sample
tf1 <- file.path(tempdir(), "station1.rvt")
tf2 <- file.path(tempdir(), "station2.rvt")
# Create RVT files
rvn_rvt_tidyhydat(hd, subIDs=c(3,11),
filename=c(tf1,tf2))
# preview first 6 lines of rvt file 1
readLines(tf1) %>% head()
Similar support for the weathercan
package to write
gauge forcing data exists within the RavenR
package through
the rvn_rvt_write_met
function. The
rvn_rvt_write_met
function supports writing of all valid
Raven forcing information, and will write all supplied (valid) data to
rvt file. Here, we use the function to write the total precipitation,
maximum daily temperature, and minimum daily temperature from the
‘Kamloops A’ station to a Raven-compliant rvt format. The station
metadata, also required for Raven gauge forcing data, is written to a
separate file. The sample data within RavenR is used once again, this
time using the sample data obtained from the weathercan
.
However, you are encouraged to try obtaining the data from the
weathercan
package directly using the commented out
commands below.
## Obtain data using the weathercan package
# library(weathercan)
# kam <- weather_dl(station_ids = 51423,
# start = "2016-10-01", end = "2019-09-30", interval="day")
## load RavenR package sample data
data(rvn_weathercan_sample)
kam <- rvn_weathercan_sample
fpath1 <- file.path(tempdir(), "met_data.rvt")
fpath2 <- file.path(tempdir(), "met_gauges.rvt")
## basic use, provide temporary file names for writing
## filter for particular columns to write to file
result <- kam[,c("station_name","date","lat","lon","elev","max_temp","min_temp","total_precip")] %>%
rvn_rvt_write_met(metdata = .,
filenames = fpath1,
filename_stndata = fpath2)
## [1] "Imported data from 1 station"
# preview files
readLines(fpath1) %>% head() # data rvt file
## [1] ":MultiData"
## [2] " 2016-10-01 00:00:00 1 1095"
## [3] " :Parameters TEMP_MAX TEMP_MIN PRECIP"
## [4] " :Units DegC DegC mm/d"
## [5] " 16.8 5.5 0"
## [6] " 18.1 2.5 0"
readLines(fpath2) %>% head() # gauge data file
## [1] ":Gauge KAMLOOPS_A"
## [2] " :Latitude 50.700000"
## [3] " :Longitude -120.450000"
## [4] " :Elevation 345.30"
## [5] " :RedirectToFile C:\\Users\\rober\\AppData\\Local\\Temp\\Rtmpe6TSjR/met_data.rvt"
## [6] ":EndGauge"
Now we will build a simple script which will provide a number of visualizations, which we can use to look at the Nith river model each time we run it. This can be made as complex as you want. You may also choose to run this for a different Raven model as part of this exercise.
Start with a new script. From RStudio, go to the main menu.
Choose File -> New File -> R Script
. Populate the
script with the following.
You can find the Nith model files in the Raven Tutorials. Please place a Raven.exe executable (or symbolic link called Raven.exe) inside this Nith folder, and update the modelfolder variable below to the appropriate folder location on your system.
modelfolder <- "C:/TEMP/Nith/" # model folder with Raven.exe and Nith model files
fileprefix <- "Nith" # prefix for model files (i.e. Nith.rvi should be in the modelfolder)
outdir <- "./output/"
## if this generates an error for you, the Nith folder cannot be found.
# Please update the modelfolder variable accordingly
if (!dir.exists(modelfolder)) {
stop(sprintf("The folder %s does not exist, please verify!", modelfolder))
}
setwd(modelfolder)
# RUN RAVEN
# =====================================================
# writes complete command prompt command (Windows)
# > Raven.exe [filename] -o [outputdir]
RavenCMD <- sprintf("Raven.exe %s -o %s", fileprefix, outdir)
# or adjust string if in a macos/ linux environemnt
# RavenCMD <- sprintf("./Raven.exe %s -o %s", fileprefix, outdir)
system(RavenCMD) # this runs raven from the command prompt
Once the model is run, we can read in the output and save some of the plots to file. Here, we examine the forcing data and the snowpack.
# GENERATE OUTPUT PLOTS
# =====================================================
# read in the model output files
## use ggsave from ggplot2 to save plot pdf
ff_data <- rvn_forcings_read(paste0(outdir,"run1_ForcingFunctions.csv"))
myplots <- rvn_forcings_plot(ff_data$forcings)
myplots$AllForcings %>%
ggsave("Forcings.pdf", ., width = 8.5, height=11, units='in')
# plot snowpack from xts format, save using base R commands
mywshd <- rvn_watershed_read(paste0(outdir, "run1_WatershedStorage.csv"))
png("snowpack.png") # create a png file to direct plot to
plot(mywshd$watershed_storage$Snow,
main='Snowpack (mm SWE)', col='blue')
dev.off() #finishes writing plot to .png file
Modify the above script to generate png image plots of monthly
subbasin-averaged PET in Subbasin 43 using the :CustomOutput option (you
will have to add a :CustomOutput command to the Raven input rvi file).
You will also want to use the RavenR rvn_custom_read()
and
rvn_custom_output_plot()
commands.
Then, add a set of diagnostic plots related to the Hydrographs.csv file. For example, you may wish to compare annual peaks in the data or flow volumes.
If you have completed the workflow exercise above, you may build on the Introduction to R exercise from the earlier session to build Raven-compliant input files for the Raven River in Alberta. Using your knowledge of R and RavenR, undertake the following tasks using only R and a text file editor.
Based on the meteorological information in the station(s), would there be sufficient meteorological information to run a model of the Raven River? What else would be required?
Following up from Exercise 2, let’s say that we want to continue
building model files for Raven River, continuing with an rvi, rvh and
rvp file. We can use the rvn_rvi_write_template
file and
the other utilities for rvi/rvp files to create these two files directly
with the RavenR package. We can also create a basic rvh file with
assigned properties in R with the RavenR package.
For this exercise, you should do the following. Create any new model files with the prefix “ravenriver”, for example, “ravenriver.rvi”.
rvn_rvi_write_template
function, and create the file
ravenriver.rvi with this template.This tutorial is meant to serve as a brief introduction to the RavenR package. If you have any comments, suggestions or bug reports, please leave a note on the issues page of the Github project (RavenR Github page), email the authors of the package, or feel free to let us know on the Raven forum.
Additional Raven materials can be found on the Raven downloads page, and additional RavenR vignettes can be found on Github in the vignettes folder.