Merge pull request #4 from ldecicco-USGS/master

minor updates
USGS-R · Jun 9, 2017 · 4fc5b8f · 4fc5b8f
2 parents b20145c + b455be2
commit 4fc5b8f
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Showing 54 changed files with 68 additions and 82 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,4 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+travis.yml
+
diff --git a/.travis.yml b/.travis.yml
@@ -1,38 +1,46 @@
-# Sample .travis.yml for R projects from https://github.com/craigcitro/r-travis
+# 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: c
+language: r
+cache: packages
+dist: trusty
 
-os:
-  - osx
-  - linux
+matrix:
+  include:
+    - os: linux
+      r: release
+      env: R_CODECOV=true
+
+addons:
+  apt:
+    packages:
+    - libcurl4-openssl-dev
 
 env:
    global:
-     - CRAN: http://cran.rstudio.com
      - R_BUILD_ARGS="--no-build-vignettes --no-manual"
      - R_CHECK_ARGS="--no-build-vignettes --no-manual --as-cran"
-     - BOOTSTRAP_LATEX=""
-     - NOT_CRAN="true" 
+     - NOT_CRAN="true"
+     - _R_CHECK_FORCE_SUGGESTS_=false
+
+warnings_are_errors: true
 
-script: "./travis-tool.sh run_tests"
+r_github_packages:
+  - jimhester/covr
+  - USGS-R/smwrData
+  - USGS-R/smwrBase
+  - USGS-R/smwrGraphs
+  - USGS-R/smwrStats
+  - USGS-R/smwrQW
 
-before_script:
-  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
-  - chmod 755 ./travis-tool.sh
-  - "./travis-tool.sh bootstrap"
-  - "./travis-tool.sh aptget_install r-cran-rodbc"
-  - "./travis-tool.sh install_deps - ./travis-tool.sh install_r methods stats digest memoise testthat KernSmooth akima lubridate dataRetrieval car leaps boot coin XML evd stats4 robust randtests
-  survival XML zCompositions NADA psych"
-  - "./travis-tool.sh install_github USGS-R/smwrData"
-  - "./travis-tool.sh install_github USGS-R/smwrBase"
-  - "./travis-tool.sh install_github USGS-R/smwrGraphs"
-  - "./travis-tool.sh install_github USGS-R/smwrStats"
-  - "./travis-tool.sh install_github USGS-R/smwrQW"
+after_success:
+  - if [[ "${R_CODECOV}" ]]; then R -e 'covr::coveralls()'; fi
 
-after_script:
-  - "./travis-tool.sh dump_logs"
-
 notifications:
   email:
     on_success: change
     on_failure: change
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: DVstats
-Version: 0.3.3
+Version: 0.3.3.9000
 Date: 2016-01-25
 Title: Functions to manipulate daily-values data
 Author: Dave Lorenz <lorenz@usgs.gov>
@@ -71,4 +71,4 @@ Collate:
     'setSeasons.R'
     'subset.fall.R'
     'wtf.R'
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -56,6 +56,13 @@ import(smwrGraphs)
 import(smwrQW)
 import(smwrStats)
 import(stats)
+importFrom(grDevices,dev.off)
+importFrom(graphics,par)
+importFrom(graphics,plot)
+importFrom(graphics,plot.new)
+importFrom(graphics,text)
 importFrom(robust,lmRob)
 importFrom(stats4,mle)
+importFrom(utils,capture.output)
+importFrom(utils,menu)
 useDynLib(DVstats,roraf)
diff --git a/R/plot.baseflow.R b/R/plot.baseflow.R
@@ -15,6 +15,9 @@
 #' @seealso \code{\link{bfi}}, \code{\link{hysep}}, \code{\link{part}}, 
 #' @keywords hplot
 #' @method plot baseflow
+#' @importFrom grDevices dev.off
+#' @importFrom graphics par plot plot.new text
+#' @importFrom utils capture.output menu
 #' @export
 plot.baseflow <- function(x, which = "All", set.up = TRUE, ...) {
   STAID <- attr(x, "STAID")

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@ USGS water science R functions for the analysis of daily-values data.
 
 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 [http://www.usgs.gov/visual-id/credit_usgs.html#copyright](http://www.usgs.gov/visual-id/credit_usgs.html#copyright)
+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.
 
@@ -16,9 +16,9 @@ Installation
 
 ```R
 install.packages("DVstats", 
-    repos=c("http://owi.usgs.gov/R",
+    repos=c("https://owi.usgs.gov/R",
     "http://cran.us.r-project.org"), 
     dependencies = TRUE)
 ```
 
-Linux: [![travis](https://travis-ci.org/USGS-R/smwrQW.svg?branch=master)](https://travis-ci.org/USGS-R/DVstats)
+Linux: [![travis](https://travis-ci.org/USGS-R/DVstats.svg?branch=master)](https://travis-ci.org/USGS-R/DVstats)
diff --git a/inst/doc/MasterRecessionCurve.pdf b/inst/doc/MasterRecessionCurve.pdf
diff --git a/inst/doc/SevenDay.pdf b/inst/doc/SevenDay.pdf
diff --git a/man/DVstats-package.Rd b/man/DVstats-package.Rd
diff --git a/man/Lognormal3.Rd b/man/Lognormal3.Rd
diff --git a/man/PredModels.Rd b/man/PredModels.Rd
diff --git a/man/QPPQ.Rd b/man/QPPQ.Rd
diff --git a/man/aggregate.baseflow.Rd b/man/aggregate.baseflow.Rd
diff --git a/man/aggregate.rise.Rd b/man/aggregate.rise.Rd
diff --git a/man/aggregate.rora.Rd b/man/aggregate.rora.Rd
diff --git a/man/antecedentRR.Rd b/man/antecedentRR.Rd
diff --git a/man/baseDur.Rd b/man/baseDur.Rd
diff --git a/man/bfi.Rd b/man/bfi.Rd
diff --git a/man/climateYear.Rd b/man/climateYear.Rd
diff --git a/man/confirm.Rd b/man/confirm.Rd
diff --git a/man/confirm.fall.Rd b/man/confirm.fall.Rd
diff --git a/man/confirm.recess.Rd b/man/confirm.recess.Rd
diff --git a/man/consistentFDC.Rd b/man/consistentFDC.Rd
diff --git a/man/dvStat.Rd b/man/dvStat.Rd
diff --git a/man/estFDC.Rd b/man/estFDC.Rd
diff --git a/man/extend.Rd b/man/extend.Rd
diff --git a/man/fall.Rd b/man/fall.Rd
diff --git a/man/flowDurClasses.Rd b/man/flowDurClasses.Rd
diff --git a/man/freqAnal.Rd b/man/freqAnal.Rd
diff --git a/man/freqReport.Rd b/man/freqReport.Rd
diff --git a/man/hmean.Rd b/man/hmean.Rd
diff --git a/man/hysep.Rd b/man/hysep.Rd
diff --git a/man/join.Rd b/man/join.Rd
diff --git a/man/part.Rd b/man/part.Rd
diff --git a/man/plot.baseflow.Rd b/man/plot.baseflow.Rd
diff --git a/man/plot.fall.Rd b/man/plot.fall.Rd
diff --git a/man/plot.freqAnal.Rd b/man/plot.freqAnal.Rd
diff --git a/man/plot.recess.Rd b/man/plot.recess.Rd
diff --git a/man/plot.rise.Rd b/man/plot.rise.Rd
diff --git a/man/plot.rora.Rd b/man/plot.rora.Rd
diff --git a/man/predict.freqAnal.Rd b/man/predict.freqAnal.Rd
diff --git a/man/print.baseflow.Rd b/man/print.baseflow.Rd
diff --git a/man/print.fall.Rd b/man/print.fall.Rd
diff --git a/man/print.freqAnal.Rd b/man/print.freqAnal.Rd
diff --git a/man/print.recess.Rd b/man/print.recess.Rd
diff --git a/man/print.rise.Rd b/man/print.rise.Rd