An R package that assists with the setup and operation of a collection of soil data summary, comparison, and evaluation reports. These reports are primarily used by USDA-NRCS soil scientists in both initial and update mapping.
This pull request creates a new report (shiny-pedon-summary) in the region2 directory.
Basic setup
The report has a config.R file where the following are specified:
cache_data -- toggle to auto-load SoilProfileCollection and linework from Rda file
use_regex_ghz -- toggle to regular expressions to apply generalized horizon labels (component layer ID); otherwise, assign them manually in NASIS;
poly.dsn -- polygon feature class data source name (path without trailing slash, may be an ESRI GDB)
poly.layer -- shapefile layer containing map unit delineations
poly.bounds -- shapefile layer denoting boundary of survey area / map units (currently not used)
p.low.rv.high -- quantiles to assign to "LO" "RV" and "HI"
q.type -- quantile type
ml.profile.smoothing -- smoothing parameter for density plots
rasters -- named list of rasters of environmental data; values will be extracted at point locations for pedons (NOT SAMPLED FROM MAPUNITS) and summarized in output
Walkthrough
Here is a picture of shiny-pedon-summary v0.1 in action:
In the above example, the NASIS selected set contains all pedons and DMUs from CA630. First and foremost pedons are filtered by mapunit (MUSYM '6074'), Pedon overlap with mapunits is based on linework from the CA630 GDB. Generalized horizons were assigned manually during the process of populating the 607X MUs. The profile plot shows the pedons that are currently being aggregated together. Here, two taxa that are similar soils (Sierra and Auberry) are selected via a regex pattern and then are both subjected to the same horizonation scheme to come up with the component ranges. In this particular MU, the component was named Sierra.
There are many other tabs on the main information pane in addition to the grouped profile plot shown above. These tabs include:
spatial (mapview) overview - click on pedon locations to view site-level data from SPC.
slab-wise profile plot - makes 1cm slabs of all pedons in the filtered set shown in GPP; plots the 25-75% quantiles in grey, the median in blue and the modal pedon value (user selected via drop down on left side) in red.
generalized GPP - shows grouped profile plot using generalized horizons as labels instead of field-described designations
generalized horizon probability - plots probability density functions as a function of depth for each generalized horizon. this is useful to look at to make sure there isn't anything super wacky with your generalization, but currently the "crossover" depths aren't used for anything since depth RVs come from modal not a "50% probability threshold"
geomorphology - tabular / proportional summary of 2D/3D/Geomorphon/Drainage Class/SurfaceShape for all pedon locations. based on either data entered in NASIS or extracted from rasters at pedon locations. shows proportional summary along side the selected modal pedon value.
aspect - plot of distribution of aspects at pedon locations
ecology - tabular / proportional summary of ecological site assignment by pedon
horizon - shows matrix of field-described (columns) versus generalized (rows) horizons. currently rownames (GENHZs) don't show up correctly in Shiny output due to issues with kable.
modal - shows the pedon selected as modal in the drop down box. shows field-described versus generalized horizons. this is useful to see where multiple interpretively-similar horizons from the modal are collapsed into a single general horizon.
texture - tabular / proportional summary of textural classes from NASIS across generalized horizons TODO: show along side the selected modal pedon values
color - graphical / proportional summary of soil colors from NASIS across generalized horizons. useful for refining soil series range in characteristics. TODO: show along side the selected modal pedon values
morphology - clay, sand, pH, rock fragment fractions, albedo - the bread and butter of the component, quantiles for each variable:horizon combination (min, LO, RV, HI, max). Quantiles defined in config.R. TODO: include modal pedon value in comparison with (or in lieu of) median.
surface fragments - LO-RV-HI by size fraction; TODO: show along side the selected modal pedon values
diagnostics - diagnostic horizons from NASIS; number of each occurring in filtered set, LO-RV-HI for top depth, bottom depth and thickness; TODO: show selected modal pedon values
diagnostics plot - graphical summary of above, showing individual pedon IDs and clustering; TODO: highlight the selected modal
mapunit summary - when pedons from multiple mapunits are combined in a filtered set, you will get one boxplot per variable per horizon per mapunit. for mapunits with a ton of data, this provides an excellent opportunity to test out the "components are special snowflakes" hypothesis
Trying it out for yourself...
Aside from getting config.R set up in a way that works with your system, you will also need to prepare your NASIS selected set. Many of the morphology summaries and the actual static "report" output all rely on most pedons having generalized horizon labels assigned in NASIS via the Comp. Layer ID field. Individual pedons or horizons are allowed to have blanks in this field if they are not intended to be included in the range of characteristics (RIC). The RIC for each component horizon (modal pedon horizon defines RVs) is determined by aggregating other similar horizons from the non-modal pedons. This aggregation is achieved by assigning them the same "label" in the Comp Layer ID.
For my personal use, I have manually entered component layer IDs after selecting my modal pedon (and therefor my "modal horizon scheme"). This becomes increasingly less practical as the number of pedons involved in the analysis increases.
An alternate way of doing the horizon aggregation if you can't stomach doing it in NASIS manually is to use the old generalized horizon script. Various vintages of this kick around in the 2-SON office but it is currently not publically available. These scripts use regular expressions (1 expression per generalized horizon; matches many horizon designations and aggregates to a single label) and taxonname (each taxon can have its own set of generalized horizons). Then the script spits out a horizonagg.txt file that can be imported into NASIS component layer ID fields via a calculation. This script is long overdue for an overhaul and will be one of the near-future projects to bring in as a new soilReport.
Future plans
Tying in with re-vamping the horizon generalization script, I would like to have a really slick way to interactively generate regex patterns/manually assign horizonation. This could likely be a separate shiny interface report (e.g. shiny-pedon-aggregation) or a "prequel" to running the pedon-summary stage (say, if generalized horizons don't already exist in the SPC or if the user asks to override NASIS). It also would be fun to drive the "horizon similarity" metrics off of the numerical data we have and try to programmatically assign GHZ that way. Though most components/series/etc. in our region are probably not well documented enough to actually rely on this, we probably do have a handful that would be really great demonstration datasets.
The shiny interface would show a plot and graphs of properties from the selected modal pedon in a side pane. The modal pedon defines the actual "label" and number of labels for a particular component's generalized horizons. In a larger pane would be the "unaggregated" pedons. The user would be able to rapidly visualize the original description, generalized description, numerical effects on ranges of including/excluding different horizons from a particular generalized horizon group, and so on.
This pull request creates a new report (shiny-pedon-summary) in the region2 directory.
Basic setup
The report has a
config.Rfile where the following are specified:Walkthrough
Here is a picture of shiny-pedon-summary v0.1 in action:
In the above example, the NASIS selected set contains all pedons and DMUs from CA630. First and foremost pedons are filtered by mapunit (MUSYM '6074'), Pedon overlap with mapunits is based on linework from the CA630 GDB. Generalized horizons were assigned manually during the process of populating the 607X MUs. The profile plot shows the pedons that are currently being aggregated together. Here, two taxa that are similar soils (Sierra and Auberry) are selected via a regex pattern and then are both subjected to the same horizonation scheme to come up with the component ranges. In this particular MU, the component was named Sierra.
There are many other tabs on the main information pane in addition to the grouped profile plot shown above. These tabs include:
kable.config.R. TODO: include modal pedon value in comparison with (or in lieu of) median.Trying it out for yourself...
Aside from getting
config.Rset up in a way that works with your system, you will also need to prepare your NASIS selected set. Many of the morphology summaries and the actual static "report" output all rely on most pedons having generalized horizon labels assigned in NASIS via the Comp. Layer ID field. Individual pedons or horizons are allowed to have blanks in this field if they are not intended to be included in the range of characteristics (RIC). The RIC for each component horizon (modal pedon horizon defines RVs) is determined by aggregating other similar horizons from the non-modal pedons. This aggregation is achieved by assigning them the same "label" in the Comp Layer ID.For my personal use, I have manually entered component layer IDs after selecting my modal pedon (and therefor my "modal horizon scheme"). This becomes increasingly less practical as the number of pedons involved in the analysis increases.
An alternate way of doing the horizon aggregation if you can't stomach doing it in NASIS manually is to use the old generalized horizon script. Various vintages of this kick around in the 2-SON office but it is currently not publically available. These scripts use regular expressions (1 expression per generalized horizon; matches many horizon designations and aggregates to a single label) and taxonname (each taxon can have its own set of generalized horizons). Then the script spits out a
horizonagg.txtfile that can be imported into NASIS component layer ID fields via a calculation. This script is long overdue for an overhaul and will be one of the near-future projects to bring in as a new soilReport.Future plans
Tying in with re-vamping the horizon generalization script, I would like to have a really slick way to interactively generate regex patterns/manually assign horizonation. This could likely be a separate shiny interface report (e.g. shiny-pedon-aggregation) or a "prequel" to running the pedon-summary stage (say, if generalized horizons don't already exist in the SPC or if the user asks to override NASIS). It also would be fun to drive the "horizon similarity" metrics off of the numerical data we have and try to programmatically assign GHZ that way. Though most components/series/etc. in our region are probably not well documented enough to actually rely on this, we probably do have a handful that would be really great demonstration datasets.
The shiny interface would show a plot and graphs of properties from the selected modal pedon in a side pane. The modal pedon defines the actual "label" and number of labels for a particular component's generalized horizons. In a larger pane would be the "unaggregated" pedons. The user would be able to rapidly visualize the original description, generalized description, numerical effects on ranges of including/excluding different horizons from a particular generalized horizon group, and so on.