Skip to content

Commit

Permalink
Update various package metadata + cleanup README
Browse files Browse the repository at this point in the history
  • Loading branch information
@brownag
brownag committed Mar 25, 2022
1 parent 81d6538 commit eb16560
Show file tree
Hide file tree
Showing 4 changed files with 81 additions and 121 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ Depends: R (>= 3.5.0)
Imports: aqp, grDevices, graphics, stats, utils, xml2, sp, raster, curl, methods, data.table, DBI
Suggests: rgdal, jsonlite, httr, sf, wk, rvest, odbc, RSQLite, testthat, scales
Repository: CRAN
URL: http://ncss-tech.github.io/AQP/
URL: http://ncss-tech.github.io/soilDB/
BugReports: https://github.com/ncss-tech/soilDB/issues
RoxygenNote: 7.1.2
Roxygen: list(markdown = TRUE)
59 changes: 21 additions & 38 deletions README.Rmd
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
---
output: md_document
---
[![CRAN Version (Stable)](http://www.r-pkg.org/badges/version/soilDB)](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)
[![CRAN Version (Stable)](http://www.r-pkg.org/badges/version-ago/soilDB)](https://cran.r-project.org/package=soilDB)
[![CRAN status](https://cranchecks.info/badges/summary/soilDB)](https://cran.r-project.org/web/checks/check_results_soilDB.html)
[![Development Version](https://ncss-tech.r-universe.dev/badges/soilDB)](https://ncss-tech.r-universe.dev/)
[![R-CMD-check Build Status](https://github.com/ncss-tech/soilDB/workflows/R-CMD-check/badge.svg)](https://github.com/ncss-tech/soilDB/actions)
[![Total CRAN Downloads](http://cranlogs.r-pkg.org/badges/grand-total/soilDB)](https://cran.r-project.org/package=soilDB)
![CRAN/METACRAN](https://img.shields.io/cran/l/soilDB)
Expand All @@ -26,49 +27,31 @@ Get the stable version (`r soilDB_CRAN_VERSION`) from CRAN:
install.packages('soilDB', dependencies = TRUE)
```

Get the development version (`r packageVersion("soilDB")`) from GitHub:
Get the development version from GitHub:

```r
remotes::install_github("ncss-tech/soilDB", dependencies = FALSE, upgrade = FALSE, build = FALSE)
remotes::install_github("ncss-tech/soilDB", dependencies = FALSE)
```

## Website
- http://ncss-tech.github.io/AQP/
- CRAN Package: https://cran.r-project.org/package=soilDB
- Package Manual: http://ncss-tech.github.io/soilDB/
- Algorithms for Quantitative Pedology (AQP) Project: 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 soilDB_CRAN_VERSION`. [https://CRAN.R-project.org/package=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)
```{r, echo=FALSE}
citation("soilDB")
```

* `SDA_query()` returns a `try-error` for queries with invalid syntax or on network error; empty results are an empty `data.frame()`
## soilDB `r packageVersion("soilDB")`

* `SDA_spatialQuery()` can return Soil Survey Area `sapolygon` data

* `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()`, `get_SDA_coecoclass()`

#### MS Access
<!-- ### Notices on Database Interfaces -->
<!-- #### NASIS -->
<!-- #### Soil Data Access (SDA) -->
<!-- #### SoilWeb API -->
<!-- #### 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
Expand Down Expand Up @@ -113,10 +96,9 @@ Dylan Beaudette, Jay Skovlin, Stephen Roecker and Andrew Brown (2021). soilDB: S

* NASIS local database
+ [`fetchNASIS`](http://ncss-tech.github.io/soilDB/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/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/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/reference/createStaticNASIS.html) - create list of NASIS tables or write to SQLite
+ [`dbConnectNASIS`](http://ncss-tech.github.io/soilDB/reference/dbConnectNASIS.html) (alias `NASIS()`)
+ [`dbQueryNASIS`](http://ncss-tech.github.io/soilDB/reference/dbQueryNASIS.html)
+ [`createStaticNASIS`](http://ncss-tech.github.io/soilDB/reference/createStaticNASIS.html)

* SoilGrids
+ [`fetchSoilGrids`](http://ncss-tech.github.io/soilDB/reference/fetchSoilGrids.html)
Expand All @@ -143,6 +125,7 @@ Dylan Beaudette, Jay Skovlin, Stephen Roecker and Andrew Brown (2021). soilDB: S

* [aqp](https://github.com/ncss-tech/aqp)
* [sharpshootR](https://github.com/ncss-tech/sharpshootR)
* [SoilTaxonomy](https://github.com/ncss-tech/SoilTaxonomy)

## Dependency Graph

Expand Down
127 changes: 45 additions & 82 deletions README.md
View file
Original file line number Diff line number Diff line change
@@ -1,85 +1,61 @@
[![CRAN Version
(Stable)](http://www.r-pkg.org/badges/version/soilDB)](https://cran.r-project.org/package=soilDB)
[![GitHub Version
(Development)](https://img.shields.io/badge/GitHub-2.6.14-yellowgreen)](https://github.com/ncss-tech/soilDB)
(Stable)](http://www.r-pkg.org/badges/version-ago/soilDB)](https://cran.r-project.org/package=soilDB)
[![CRAN
status](https://cranchecks.info/badges/summary/soilDB)](https://cran.r-project.org/web/checks/check_results_soilDB.html)
[![Development
Version](https://ncss-tech.r-universe.dev/badges/soilDB)](https://ncss-tech.r-universe.dev/)
[![R-CMD-check Build
Status](https://github.com/ncss-tech/soilDB/workflows/R-CMD-check/badge.svg)](https://github.com/ncss-tech/soilDB/actions)
[![Total CRAN
Downloads](http://cranlogs.r-pkg.org/badges/grand-total/soilDB)](https://cran.r-project.org/package=soilDB)
![CRAN/METACRAN](https://img.shields.io/cran/l/soilDB) [![soilDB
Manual](https://img.shields.io/badge/docs-HTML-informational)](https://ncss-tech.github.io/soilDB/)

Installation
------------
## Installation

Get the stable version (2.6.14) from CRAN:

install.packages('soilDB', dependencies = TRUE)

Get the development version (2.6.14) from GitHub:

remotes::install_github("ncss-tech/soilDB", dependencies = FALSE, upgrade = FALSE, build = FALSE)
remotes::install_github("ncss-tech/soilDB", dependencies = FALSE)

Website
-------
## Website

- <a href="http://ncss-tech.github.io/AQP/" class="uri">http://ncss-tech.github.io/AQP/</a>
- CRAN Package: <https://cran.r-project.org/package=soilDB>
- Package Manual: <http://ncss-tech.github.io/soilDB/>
- Algorithms for Quantitative Pedology (AQP) Project:
<http://ncss-tech.github.io/AQP/>

Citation
--------
## Citation

Dylan Beaudette, Jay Skovlin, Stephen Roecker and Andrew Brown (2021).
soilDB: Soil Database Interface. R package version 2.6.14.
<https://CRAN.R-project.org/package=soilDB>
##
## To cite soilDB in publications use:
##
## Dylan Beaudette, Jay Skovlin, Stephen Roecker and Andrew Brown
## (2022). soilDB: Soil Database Interface. R package version 2.6.14.
## https://CRAN.R-project.org/package=soilDB
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {soilDB: Soil Database Interface},
## author = {Dylan Beaudette and Jay Skovlin and Stephen Roecker and Andrew Brown},
## note = {R package version 2.6.14},
## url = {https://CRAN.R-project.org/package=soilDB},
## year = {2022},
## }

soilDB 2.6.14
-------------
## soilDB 2.6.14

### Notices on Database Interfaces
<!-- ### Notices on Database Interfaces -->
<!-- #### NASIS -->
<!-- #### Soil Data Access (SDA) -->
<!-- #### SoilWeb API -->
<!-- #### MS Access -->

#### 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()`

- `SDA_spatialQuery()` can return Soil Survey Area `sapolygon` data

- `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()`, `get_SDA_coecoclass()`

#### 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
------------------------
## Functions by Data Source

- SDA
- [`fetchSDA`](http://ncss-tech.github.io/soilDB/reference/fetchSDA_component.html)
Expand Down Expand Up @@ -116,25 +92,14 @@ Functions by Data Source
- [`fetchHenry`](http://ncss-tech.github.io/soilDB/reference/fetchHenry.html)
- NASIS local database
- [`fetchNASIS`](http://ncss-tech.github.io/soilDB/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/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/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/reference/createStaticNASIS.html) -
create list of NASIS tables or write to SQLite
- [`dbConnectNASIS`](http://ncss-tech.github.io/soilDB/reference/dbConnectNASIS.html)
(alias `NASIS()`)
- [`dbQueryNASIS`](http://ncss-tech.github.io/soilDB/reference/dbQueryNASIS.html)
- [`createStaticNASIS`](http://ncss-tech.github.io/soilDB/reference/createStaticNASIS.html)
- SoilGrids
- [`fetchSoilGrids`](http://ncss-tech.github.io/soilDB/reference/fetchSoilGrids.html)

Miscellaneous Functions
-----------------------
## Miscellaneous Functions

- [`estimateSTR`](http://ncss-tech.github.io/soilDB/reference/estimateSTR.html)
- [`STRplot`](http://ncss-tech.github.io/soilDB/reference/STRplot.html)
Expand All @@ -145,22 +110,20 @@ Miscellaneous Functions
- [`code`](http://ncss-tech.github.io/soilDB/reference/code.html)
- [`get_NOAA_GHCND`](http://ncss-tech.github.io/soilDB/reference/get_NOAA_GHCND.html)

Tutorials and Demonstrations
----------------------------
## 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
----------------
## Related Packages

- [aqp](https://github.com/ncss-tech/aqp)
- [sharpshootR](https://github.com/ncss-tech/sharpshootR)
- [SoilTaxonomy](https://github.com/ncss-tech/SoilTaxonomy)

Dependency Graph
----------------
## Dependency Graph

![](https://cran.microsoft.com/packagedata/graphs/soilDB.png)
14 changes: 14 additions & 0 deletions inst/CITATION
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
citHeader("To cite soilDB in publications use:")

citEntry(
entry = "Manual",
title = "soilDB: Soil Database Interface",
author = "Dylan Beaudette, Jay Skovlin, Stephen Roecker and Andrew Brown",
note = paste0("R package version ", packageVersion('soilDB')),
url = "https://CRAN.R-project.org/package=soilDB",
year = format(Sys.time(), "%Y"),
textVersion = paste0("Dylan Beaudette, Jay Skovlin, Stephen Roecker and Andrew Brown (",
format(Sys.time(), "%Y"),
"). soilDB: Soil Database Interface. R package version ",
packageVersion('soilDB'), ". https://CRAN.R-project.org/package=soilDB")
)

0 comments on commit eb16560

Please sign in to comment.