Introduction to RavenR
Robert Chlumsky, Dr. James R. Craig
June 8, 2021
Introduction to RavenR Tutorial
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.
Getting Acquainted with RavenR
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_scatterplotThe 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_”.
Sample Data in RavenR
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/RtmpeWaGUx/Rinst39e4327813d3/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.
Diagnostics and Plotting
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.
Forcing Functions
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: timezone of object (UTC) is different than current timezone ().## 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 14.6024Now 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$Radiation +
theme(legend.position="bottom")
Hydrograph and Diagnostics
We can similarly access the hydrograph fit. Here the hydrograph sample data is located with the usual system.file command, then read into R with the rvn_hyd_read function intended for reading Hydrographs file. The flows from a specific subbasin can be extracted using the rvn_hyd_extract function, which is done here for subbasin 36. The precipitation can be extracted similarly.
ff <- system.file("extdata","run1_Hydrographs.csv",package="RavenR")
# ff <- "mydirectory/Hydrographs.csv" # replace with your own file
hy <- rvn_hyd_read(ff)
head(hy$hyd)## Warning: timezone of object (UTC) is different than current 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 3.15flow36 <- rvn_hyd_extract("Sub36",hy)
precip <- hy$hyd$precipThe 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 14.21804
## Feb -31.63489
## Mar 15.93412
## Apr -36.52680
## May -61.52621
## Jun -55.78284
## Jul -69.45787
## Aug -70.45509
## Sep 35.16982
## Oct 281.28584
## Nov 83.76182
## Dec 29.17106
##
## $plot
Flow DyGraphs
A fun feature in the RavenR package is the addition of dygraphs, which produces a dynamic hydrograph plot with a slider on the time scale. This is particularly helpful for viewing subsections of a hydrograph dynamically, and comparing the simulated and observed hydrographs in an interactive environment. Only the output object from the rvn_hyd_read function and the name of headings to extract is required. Note that this interactive plot does not work well in a PDF file, so try this out in R/RStudio.
rvn_hyd_dygraph(hy, basins="Sub36")While this tutorial focuses on the forcing functions and hydrograph data, similar routines exist for reading in the reservoir stages output, the watershed mass energy balance files, and other Raven outputs.
RavenR Time Series Utilities
One utility that does not exist in the xts package, but is nonetheless useful in hydrology, is the application of functions to the water year period rather than the calendar year. In the RavenR package, the rvn_apply_wyearly function accomplishes this. The water year is by default set to index by the October 1st water year (specifying the period ending September 30th), but this may be provided as an argument to the function for different water years. Here, we apply the mean function to the water year using sample hydrograph data in RavenR.
myhyd <- system.file("extdata","run1_Hydrographs.csv", package="RavenR") %>%
rvn_hyd_read()
library(xts)
# apply mean to calendar year in hydrograph data
xts::apply.yearly(myhyd$hyd$Sub36, mean, na.rm=TRUE)## Sub36
## 2002-12-31 3.886438
## 2003-12-31 4.962424
## 2004-09-30 5.549967# apply mean as FUN to daily average temperature
RavenR::rvn_apply_wyearly(myhyd$hyd$Sub36, mean, na.rm=TRUE)## Sub36
## 2003-09-30 3.994746
## 2004-09-30 6.096847RVI File Utilities
The RavenR package can read the rvi file and generate a network plot of the model connections, which is helpful in understanding the model configuration. This can be done as follows, again using the Nith rvi file as an example. The network plot may be directly written to file by supplying a file name to the pdfout argument, which is NULL by default.
rvi <- rvn_rvi_read(system.file("extdata","Nith.rvi", package="RavenR"))
rvn_rvi_connections(rvi) %>%
rvn_rvi_process_plot(., pdfout = NULL)
RVH File Utilities
The discretization file, rvh, may be read in and modified using the RavenR package. The rvn_rvh_read function also computes the upstream area of each subbasin. The corresponding rvn_rvh_write function also writes the rvh object back to file.
# read in rvh file
rvh <- rvn_rvh_read(system.file("extdata","Nith.rvh", package="RavenR"))
rvh$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 1014.4Similar 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_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$SBnetwork)
# create network plot of watershed structure from rvh file
rvn_subbasin_network_plot(rvh$SBtable, labeled=TRUE)
One more 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.
RVT File Utilities
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 building these input files. 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))Similar support for the weathercan package to write gauge forcing data exists within the RavenR package through the rvn_rvt_ECmet function. The rvn_rvt_ECmet function currently has two options for writing sets of forcing data. Here, we use the first option 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 file when write_stndata is TRUE. The sample data obtained from the weathercan package is used here once again, but 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
## basic use, override filename to temporary file
## default forcing_set (PRECIP, MAX TEMP, MIN TEMP)
result <- rvn_rvt_ECmet(metdata = kam, forcing_set = 1,
write_stndata = TRUE)## [1] "Imported 1 data set"
## [1] "Overview of generated timeseries"
Exercise 1 - Build a model workflow
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.
Building a model workflow script
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 promptOnce 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 fileModify the script
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.
Exercise 2 - Build Raven Input rvt Files
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.
- build an rvt file of daily observed hydrograph flows from the Raven River WSC gauge; and
- build rvt file(s) for at least one daily meteorological gauge located close to the WSC gauge (within 10km).
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?
Conclusion
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.