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README.Rmd
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README.Rmd
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---
output: md_document
---
[](https://cran.r-project.org/package=soilDB)
[![GitHub Version (Development)](https://img.shields.io/badge/GitHub-`r packageVersion("soilDB")`-yellowgreen)](https://github.com/ncss-tech/soilDB)
[](https://github.com/ncss-tech/soilDB/actions)
[](https://cran.r-project.org/package=soilDB)
[](https://ncss-tech.github.io/soilDB/docs)
## Installation
Get the stable version from CRAN:
```r
install.packages('soilDB', dependencies = TRUE)
```
Get the development version from GitHub:
```r
remotes::install_github("ncss-tech/soilDB", dependencies = FALSE, upgrade = FALSE, build = FALSE)
```
## Website
- http://ncss-tech.github.io/AQP/
## Citation
Dylan Beaudette, Jay Skovlin, Stephen Roecker and Andrew Brown (2021). soilDB: Soil Database Interface. R package version `r packageVersion("soilDB")`. https://CRAN.R-project.org/package=soilDB
## soilDB `r packageVersion("soilDB")`
### Notices on Database Interfaces
#### NASIS
* all NASIS queries now use {DBI}, tested to work with {odbc} or {RSQLite} drivers; replacing {RODBC}
* Install required R packages with `install.packages(c("DBI","odbc","RSQLite"), dependencies = TRUE)`
* new methods for connecting to NASIS and querying NASIS data allow for `dsn` argument to specify a local "static" SQLite file containing NASIS tables.
* Default argument `dsn = NULL` uses `"nasis_local"` [ODBC connection](http://ncss-tech.github.io/AQP/soilDB/setup_local_nasis.html) to a local NASIS SQL Server instance
#### Soil Data Access (SDA)
* `SDA_query` returns a `try-error` for queries with invalid syntax or on network error; empty results are an empty `data.frame()`
* `fetchSDA_spatial` can return STATSGO `gsmmupolygon` or Soil Survey Area `sapolygon` data; and can join to the `legend` table
* Added several new SDA query methods based on [ssurgoOnDemand](https://github.com/ncss-tech/ssurgoOnDemand) by Jason Nemecek and Chad Ferguson:
* `get_SDA_property`, `get_SDA_interpretation`, `get_SDA_muaggatt`, `get_SDA_hydric`, `get_SDA_pmgroupname`
#### MS Access
* AKSite, Montana RangeDB, and PedonPC 6.x get and fetch methods now use {DBI}+{odbc}
#### SoilWeb API
* `ISSR800.wcs` and `mukey.wcs` now return a result that inherits from `try-error` (and a message) if the Web Coverage Service fails
## Functions by Data Source
* SDA
+ [`fetchSDA`](http://ncss-tech.github.io/soilDB/docs/reference/fetchSDA_component.html)
+ [`fetchSDA_spatial`](http://ncss-tech.github.io/soilDB/docs/reference/fetchSDA_spatial.html)
+ [`SDA_query`](http://ncss-tech.github.io/soilDB/docs/reference/SDA_query.html)
+ [`SDA_spatialQuery`](http://ncss-tech.github.io/soilDB/docs/reference/SDA_spatialQuery.html)
+ "SSURGO On Demand" Queries
- [`get_SDA_hydric`](http://ncss-tech.github.io/soilDB/docs/reference/get_SDA_hydric.html)
- [`get_SDA_interpretation`](http://ncss-tech.github.io/soilDB/docs/reference/get_SDA_interpretation.html)
- [`get_SDA_muaggatt`](http://ncss-tech.github.io/soilDB/docs/reference/get_SDA_muaggatt.html)
- [`get_SDA_pmgroupname`](http://ncss-tech.github.io/soilDB/docs/reference/get_SDA_pmgroupname.html)
- [`get_SDA_property`](http://ncss-tech.github.io/soilDB/docs/reference/get_SDA_property.html)
* SSURGO Local Geodatabases
+ [`fetchGDB`](http://ncss-tech.github.io/soilDB/docs/reference/fetchGDB.html)
* ROSETTA
+ [`ROSETTA`](http://ncss-tech.github.io/soilDB/docs/reference/ROSETTA.html)
* SSURGO/KSSL via SoilWeb
+ [`fetchKSSL`](http://ncss-tech.github.io/soilDB/docs/reference/fetchKSSL.html)
+ [`fetchOSD`](http://ncss-tech.github.io/soilDB/docs/reference/fetchOSD.html)
+ [`siblings`](http://ncss-tech.github.io/soilDB/docs/reference/siblings.html)
+ [`OSDquery`](http://ncss-tech.github.io/soilDB/docs/reference/OSDquery.html)
+ [`seriesExtent`](http://ncss-tech.github.io/soilDB/docs/reference/seriesExtent.html)
+ [`taxaExtent`](http://ncss-tech.github.io/soilDB/docs/reference/taxaExtent.html)
+ [`mukey.wcs`](http://ncss-tech.github.io/soilDB/docs/reference/mukey.wcs.html)
+ [`ISSR800.wcs`](http://ncss-tech.github.io/soilDB/docs/reference/ISSR800.wcs.html)
* NASIS WWW interface
+ [`parseWebReport`](http://ncss-tech.github.io/soilDB/docs/reference/parseWebReport.html)
+ [`fetchNASISWebReport`](http://ncss-tech.github.io/soilDB/docs/reference/fetchNASISWebReport.html)
* SCAN/SNOTEL
+ [`fetchSCAN`](http://ncss-tech.github.io/soilDB/docs/reference/fetchSCAN.html)
+ [`SCAN_SNOTEL_metadata`](http://ncss-tech.github.io/soilDB/docs/reference/SCAN_SNOTEL_metadata.html)
* Henry Mount Soil and Water Database
+ [`fetchHenry`](http://ncss-tech.github.io/soilDB/docs/reference/fetchHenry.html)
* NASIS local database
+ [`fetchNASIS`](http://ncss-tech.github.io/soilDB/docs/reference/fetchNASIS.html)
+ <span style="color:red">**NEW:**</span> Argument `dsn` to specify path to connect to alternate (SQLite) data sources with NASIS schema
+ <span style="color:red">**NEW:**</span>[`dbConnectNASIS`](http://ncss-tech.github.io/soilDB/docs/reference/dbConnectNASIS.html) (alias `NASIS`) - create a _DBIConnection_ to local NASIS database
+ <span style="color:red">**NEW:**</span>[`dbQueryNASIS`](http://ncss-tech.github.io/soilDB/docs/reference/dbQueryNASIS.html) - query NASIS local database (and close connection with `close=TRUE`)
+ <span style="color:red">**NEW:**</span>[`createStaticNASIS`](http://ncss-tech.github.io/soilDB/docs/reference/createStaticNASIS.html) - create list of NASIS tables or write to SQLite
* SoilGrids
+ [`fetchSoilGrids`](http://ncss-tech.github.io/soilDB/docs/reference/fetchSoilGrids.html)
## Miscellaneous Functions
* [`estimateSTR`](http://ncss-tech.github.io/soilDB/docs/reference/estimateSTR.html)
* [`STRplot`](http://ncss-tech.github.io/soilDB/docs/reference/STRplot.html)
* [`KSSL_VG_model`](http://ncss-tech.github.io/soilDB/docs/reference/KSSL_VG_model.html)
* [`simplfyFragmentData`](http://ncss-tech.github.io/soilDB/docs/reference/simplfyFragmentData.html)
* [`simplifyColorData`](http://ncss-tech.github.io/soilDB/docs/reference/simplifyColorData.html)
* [`uncode`](http://ncss-tech.github.io/soilDB/docs/reference/uncode.html)
* [`code`](http://ncss-tech.github.io/soilDB/docs/reference/code.html)
* [`get_NOAA_GHCND`](http://ncss-tech.github.io/soilDB/docs/reference/get_NOAA_GHCND.html)
## Tutorials and Demonstrations
* [fetchKSSL](http://ncss-tech.github.io/AQP/soilDB/KSSL-demo.html)
* [SDA_query](http://ncss-tech.github.io/AQP/soilDB/SDA-tutorial.html)
* [fetchOSD](http://ncss-tech.github.io/AQP/sharpshootR/OSD-dendrogram.html)
* [SCAN/SNOTEL Data](http://ncss-tech.github.io/AQP/soilDB/fetchSCAN-demo.html)
## Related Packages
* [aqp](https://github.com/ncss-tech/aqp)
* [sharpshootR](https://github.com/ncss-tech/sharpshootR)
## Examples
```{r setup, warning = FALSE, message = FALSE, include = FALSE}
knitr::opts_knit$set(upload.fun = knitr::imgur_upload, base.url = NULL)
knitr::opts_chunk$set(warning = FALSE, message = FALSE,
fig.width = 14, fig.height = 8,
fig.retina = 3)
```
### Load Soil Packages
```{r packages}
library(aqp)
library(soilDB)
library(sharpshootR)
```
### Get Official Series Description Data
```{r osd}
# get morphology + extended summaries
soils <- c('cecil', 'altavista', 'lloyd', 'wickham', 'woodbridge', 'chewacla', 'congaree')
s <- fetchOSD(soils, extended = TRUE)
```
### Visualize Soil-Landscape Relationships
```{r hillslope, fig.width=11, fig.height=5}
# viz of hillslope position, from SSURGO component records
res <- vizHillslopePosition(s$hillpos, annotation.cex = 0.9)
print(res$fig)
```
### Make Profile Sketches
```{r sketches}
par(mar = c(0, 1, 0, 4), xpd = NA)
plotSPC(
s$SPC,
plot.order = res$order,
cex.names = 1,
axis.line.offset = -0.1,
width = 0.2
)
```
### Identify Tabular "Siblings"
```{r siblings}
s <- 'Amador'
amador <- siblings(s, only.major = FALSE, component.data = TRUE)
# limit to named soil series
sib.data <- subset(amador$sib.data, !compkind %in% c('Miscellaneous area', 'Family', 'Taxon above family'))
# get parsed OSD records
sibs <- fetchOSD(c(s, unique(amador$sib$sibling)), extended = TRUE)
```
### Plot Dendrograms with Taxonomic Relationships
```{r dendrogram}
# invert colors
par(mar = c(0, 0, 0, 0),
fg = 'white',
bg = 'black')
SoilTaxonomyDendrogram(
sibs$SPC,
dend.width = 1.5,
y.offset = 0.4,
scaling.factor = 0.02,
width = 0.2,
cex.taxon.labels = 1,
cex.names = 1
)
```
## Dependency Graph
