Merge pull request #26 from ldecicco-USGS/master

Adding more communication

.Rbuildignore

@@ -0,0 +1,5 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+.travis.yml
+images
+CONDUCT.md

.gitignore

@@ -1,6 +1,5 @@
 src-i386
 src-x64
-.Rbuildignore
 .Rproj.user
 .Rhistory
 .RData

.travis.yml

@@ -0,0 +1,52 @@
+# Sample .travis.yml for R projects.
+#
+# See README.md for instructions, or for more configuration options,
+# see the wiki:
+#   https://github.com/craigcitro/r-travis/wiki
+
+language: r
+cache: packages
+dist: trusty
+
+matrix:
+  include:
+    - os: linux
+      r: release
+    - os: linux
+      r: devel
+      env: R_CODECOV=true
+
+addons:
+  apt:
+    packages:
+    - libcurl4-openssl-dev
+
+env:
+   global:
+     - R_BUILD_ARGS="--no-build-vignettes --no-manual"
+     - R_CHECK_ARGS="--no-build-vignettes --no-manual --as-cran"
+     - NOT_CRAN="true"
+     - _R_CHECK_FORCE_SUGGESTS_=false
+
+repos:
+  CRAN: https://cran.rstudio.com
+  GRAN: https://owi.usgs.gov/R 
+
+warnings_are_errors: true
+
+script: 
+  - |
+    R CMD build .
+    travis_wait 20 R CMD check rloadest*tar.gz
+
+r_github_packages:
+  - jimhester/covr
+
+after_success:
+  - if [[ "${R_CODECOV}" ]]; then R -e 'covr::coveralls()'; fi
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change
+

CONDUCT.md

@@ -0,0 +1,25 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant 
+(http:contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: rloadest
 Type: Package
 Title: River Load Estimation
-Version: 0.4.4
-Date: 2017-01-10
-Authors@R: c( person("Dave", "Lorenz", email = "lorenz@usgs.gov", role = "cre"),
+Version: 0.4.5
+Date: 2017-07-26
+Authors@R: c( person("Dave", "Lorenz", role = "cre", email = "gs-w_r_admin@usgs.gov"),
               person("Rob", "Runkel", role = "aut"),
               person("Laura", "De Cicco", role = "aut"), 
-              person("David", "Watkins", role = "ctb"))
-Maintainer: Dave Lorenz <lorenz@usgs.gov>
+              person("David", "Watkins", role = "ctb"),
+              person("Joseph", "Stachelek", role = "ctb"))
 Description: Collection of functions to make constituent load estimations
     based on the LOADEST program.
 License: CC0
@@ -26,6 +26,7 @@ Suggests:
     EGRET,
     survival,
     knitr
+BugReports: https://github.com/USGS-R/rloadest/issues
 LazyLoad: yes
 LazyData: yes
 RoxygenNote: 6.0.1

R/rloadest-package.R

@@ -3,8 +3,6 @@
 #' \tabular{ll}{
 #' Package: \tab rloadest\cr
 #' Type: \tab Package\cr
-#' Version: \tab 0.4.3\cr
-#' Date: \tab 2015-12-03\cr
 #' License: \tab CC0\cr
 #' LazyLoad: \tab yes\cr
 #' }
@@ -31,9 +29,19 @@
 #'
 #' @name rloadest-package
 #' @docType package
-#' @author Dave Lorenz \email{lorenz@@usgs.gov}
 #' @keywords load estimation
 NULL
 .onAttach <- function(libname, pkgname) {
-  packageStartupMessage("Although this software program has been used by the U.S. Geological Survey (USGS), no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.")
+  packageStartupMessage("This information is preliminary or provisional and
+is subject to revision. It is being provided to meet
+the need for timely best science. The information
+has not received final approval by the U.S. Geological
+Survey (USGS) and is provided on the condition that
+neither the USGS nor the U.S. Government shall be held
+liable for any damages resulting from the authorized
+or unauthorized use of the information.
+
+****Orphaned Package****
+This package is looking for a new maintainer. For more information, 
+see: https://owi.usgs.gov/R/packages.html#orphan")
 }

README.md

@@ -3,9 +3,42 @@ rloadest
 
 USGS water science R functions for LOAD ESTimation of constituents in rivers and streams.
 
-##Package Installation
+## Package Status
+[![status](https://img.shields.io/badge/USGS-Orphan-red.svg)](https://owi.usgs.gov/R/packages.html#orphan)
+
+This package is currently in an 'orphaned' state, and
+looking for a new maintainer. For more information, see:
+[https://owi.usgs.gov/R/packages.html#orphan](https://owi.usgs.gov/R/packages.html#orphan)
+
+If you are interested in becoming the official maintainer of `rloadest`, please email gs-w_r_admin@usgs.gov.
+
+In the meantime, we rely on community involvement to report and fix bugs.
+
+### Current build tests:
+
+|Linux|Test Coverage|
+|----------|------------|
+| [![travis](https://travis-ci.org/USGS-R/rloadest.svg?branch=master)](https://travis-ci.org/USGS-R/rloadest)|[![Coverage Status](https://coveralls.io/repos/github/USGS-R/rloadest/badge.svg?branch=master)](https://coveralls.io/github/USGS-R/rloadest?branch=master)|
+
+### Reporting bugs
+
+Please consider reporting bugs and asking questions on the Issues page:
+[https://github.com/USGS-R/rloadest/issues](https://github.com/USGS-R/rloadest/issues)
+
+Follow `@USGS_R` on Twitter for updates on USGS R packages:
+
+[![Twitter Follow](https://img.shields.io/twitter/follow/USGS_R.svg?style=social&label=Follow%20USGS_R)](https://twitter.com/USGS_R)
+
+
+## Code of Conduct
+
+We want to encourage a warm, welcoming, and safe environment for contributing to this project. See the [code of conduct](https://github.com/USGS-R/rloadest/blob/master/CONDUCT.md) for more information.
+
+## Package Installation
 To install the `rloadest` package:
 
+USGS R Installation Instructions: [https://owi.usgs.gov/R/training-curriculum/installr/](https://owi.usgs.gov/R/training-curriculum/installr/)
+
 1. Install R (version 3.0 or greater) from: [https://cran.r-project.org/](https://cran.r-project.org/)
 
 2. Install RStudio from: [https://www.rstudio.com/products/rstudio/download/](https://www.rstudio.com/products/rstudio/download/)
@@ -39,9 +72,108 @@ To install the `rloadest` package:
 
 7. Make sure to keep your version of R up-to-date. CRAN and the USGS repository will only update packages for the most recent version of R, and one version behind that.
 
+## Model Archive
+
+When using the `rloadest` model, it is important to be able to reproduce the results in the future. The following version of R and package dependencies were used most recently to pass the embedded tests within this package. There is no guarantee of reproducible results using future versions of R or updated versions of package dependencies.
+
+```
+devtools::session_info()
+Session info -----------------------------------------------------------------------------
+ setting  value                       
+ version  R version 3.4.1 (2017-06-30)
+ system   x86_64, mingw32             
+ ui       RStudio (1.0.143)           
+ language (EN)                        
+ collate  English_United States.1252  
+ tz       America/Chicago             
+ date     2017-07-27                  
+
+Packages ---------------------------------------------------------------------------------
+ package       * version  date       source                          
+ akima           0.6-2    2016-12-20 CRAN (R 3.4.0)                  
+ assertthat      0.2.0    2017-04-11 CRAN (R 3.4.0)                  
+ base          * 3.4.1    2017-06-30 local                           
+ bindr           0.1      2016-11-13 CRAN (R 3.4.0)                  
+ bindrcpp        0.2      2017-06-17 CRAN (R 3.4.0)                  
+ boot            1.3-19   2017-02-11 CRAN (R 3.4.1)                  
+ car             2.1-5    2017-07-04 CRAN (R 3.4.1)                  
+ codetools       0.2-15   2016-10-05 CRAN (R 3.4.1)                  
+ coin            1.2-1    2017-07-17 CRAN (R 3.4.1)                  
+ compiler        3.4.1    2017-06-30 local                           
+ curl            2.8.1    2017-07-21 CRAN (R 3.4.1)                  
+ dataRetrieval * 2.7.2    2017-05-23 CRAN (R 3.4.1)                  
+ datasets      * 3.4.1    2017-06-30 local                           
+ devtools        1.13.2   2017-06-02 CRAN (R 3.4.1)                  
+ digest          0.6.12   2017-01-27 CRAN (R 3.4.0)                  
+ dplyr           0.7.2    2017-07-20 CRAN (R 3.4.1)                  
+ glue            1.1.1    2017-06-21 CRAN (R 3.4.0)                  
+ graphics      * 3.4.1    2017-06-30 local                           
+ grDevices     * 3.4.1    2017-06-30 local                           
+ grid            3.4.1    2017-06-30 local                           
+ hms             0.3      2016-11-22 CRAN (R 3.4.0)                  
+ httr            1.2.1    2016-07-03 CRAN (R 3.3.1)                  
+ jsonlite        1.5      2017-06-01 CRAN (R 3.4.0)                  
+ KernSmooth      2.23-15  2015-06-29 CRAN (R 3.4.1)                  
+ lattice         0.20-35  2017-03-25 CRAN (R 3.4.1)                  
+ leaps           3.0      2017-01-10 CRAN (R 3.4.0)                  
+ lme4            1.1-13   2017-04-19 CRAN (R 3.4.0)                  
+ lubridate     * 1.6.0    2016-09-13 CRAN (R 3.4.0)                  
+ magrittr        1.5      2014-11-22 CRAN (R 3.4.0)                  
+ MASS            7.3-47   2017-02-26 CRAN (R 3.4.1)                  
+ Matrix          1.2-10   2017-05-03 CRAN (R 3.4.1)                  
+ MatrixModels    0.4-1    2015-08-22 CRAN (R 3.4.0)                  
+ memoise         1.1.0    2017-04-21 CRAN (R 3.4.0)                  
+ methods       * 3.4.1    2017-06-30 local                           
+ mgcv            1.8-17   2017-02-08 CRAN (R 3.4.0)                  
+ minqa           1.2.4    2014-10-09 CRAN (R 3.4.0)                  
+ modeltools      0.2-21   2013-09-02 CRAN (R 3.4.0)                  
+ multcomp        1.4-6    2016-07-14 CRAN (R 3.4.0)                  
+ mvtnorm         1.0-6    2017-03-02 CRAN (R 3.4.0)                  
+ NADA            1.6-1    2017-03-31 CRAN (R 3.4.0)                  
+ nlme            3.1-131  2017-02-06 CRAN (R 3.4.1)                  
+ nloptr          1.0.4    2014-08-04 CRAN (R 3.4.0)                  
+ nnet            7.3-12   2016-02-02 CRAN (R 3.4.1)                  
+ parallel        3.4.1    2017-06-30 local                           
+ pbkrtest        0.4-7    2017-03-15 CRAN (R 3.4.0)                  
+ pkgconfig       2.0.1    2017-03-21 CRAN (R 3.4.0)                  
+ plyr            1.8.4    2016-06-08 CRAN (R 3.3.1)                  
+ quantreg        5.33     2017-04-18 CRAN (R 3.4.0)                  
+ R6              2.2.2    2017-06-17 CRAN (R 3.4.0)                  
+ randtests       1.0      2014-11-17 CRAN (R 3.4.0)                  
+ Rcpp            0.12.12  2017-07-15 CRAN (R 3.4.1)                  
+ readr           1.1.1    2017-05-16 CRAN (R 3.4.0)                  
+ reshape2        1.4.2    2016-10-22 CRAN (R 3.4.0)                  
+ rlang           0.1.1    2017-05-18 CRAN (R 3.4.1)                  
+ rloadest      * 0.4.5    2017-07-26 local                           
+ rstudioapi      0.6      2016-06-27 CRAN (R 3.3.1)                  
+ sandwich        2.3-4    2015-09-24 CRAN (R 3.4.0)                  
+ segmented       0.5-2.1  2017-06-14 CRAN (R 3.4.0)                  
+ smwrBase      * 1.1.3    2017-05-02 Github (USGS-R/smwrBase@f7bef98)
+ smwrGraphs    * 1.1.3    2017-07-27 local                           
+ smwrQW        * 0.7.13   2017-07-26 local                           
+ smwrStats     * 0.7.6    2017-07-26 local                           
+ sp              1.2-5    2017-06-29 CRAN (R 3.4.1)                  
+ SparseM         1.77     2017-04-23 CRAN (R 3.4.0)                  
+ splines         3.4.1    2017-06-30 local                           
+ stats         * 3.4.1    2017-06-30 local                           
+ stats4          3.4.1    2017-06-30 local                           
+ stringi         1.1.5    2017-04-07 CRAN (R 3.4.0)                  
+ stringr         1.2.0    2017-02-18 CRAN (R 3.4.0)                  
+ survival        2.41-3   2017-04-04 CRAN (R 3.4.0)                  
+ TH.data         1.0-8    2017-01-23 CRAN (R 3.4.0)                  
+ tibble          1.3.3    2017-05-28 CRAN (R 3.4.0)                  
+ tools           3.4.1    2017-06-30 local                           
+ truncnorm       1.0-7    2014-01-21 CRAN (R 3.3.0)                  
+ utils         * 3.4.1    2017-06-30 local                           
+ withr           1.0.2    2016-06-20 CRAN (R 3.3.1)                  
+ XML             3.98-1.9 2017-06-19 CRAN (R 3.4.0)                  
+ xml2            1.1.1    2017-01-24 CRAN (R 3.4.0)                  
+ zCompositions   1.0.3-1  2016-04-14 CRAN (R 3.4.0)                  
+ zoo             1.8-0    2017-04-12 CRAN (R 3.4.0)
+```
+
+## Disclaimer
 
-Disclaimer
-----------
 This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at [https://www.usgs.gov/visual-id/credit_usgs.html#copyright](https://www.usgs.gov/visual-id/credit_usgs.html#copyright)
 
 Although this software program has been used by the U.S. Geological Survey (USGS), no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.