Merge pull request #71 from aappling-usgs/master

follow-ups to PC meeting
DOI-USGS · Aug 14, 2015 · ec45141 · ec45141
2 parents ee1b432 + 045f791
commit ec45141
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diff --git a/.travis.yml b/.travis.yml
@@ -24,8 +24,9 @@ r_github_packages:
   - appling/unitted
   - USGS-R/streamMetabolizer
   - USGS-R/sbtools
-  - USGS-R/mda.streams
+  - USGS-R/gsplot
   - USGS-R/geoknife
+  - USGS-R/mda.streams
 
 after_success:
   - Rscript -e 'covr::coveralls()'

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: powstreams
 Type: Package
 Title: powstreams
-Version: 0.7.11
-Date: 2015-07-31
+Version: 0.7.12
+Date: 2015-08-13
 Author: Jordan S Read, Luke A Winslow, Alison Appling
 Maintainer: Jordan S Read <jread@usgs.gov>
 Description: tools for working Powell Center working group on stream metabolism.

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,6 +11,9 @@ export(get_metab_model)
 export(get_site_info)
 export(get_ts)
 export(get_ts_metadata)
+export(list_metab_models)
+export(list_metab_run_files)
+export(list_metab_runs)
 export(list_sites)
 export(list_tses)
 export(locate_folder)
@@ -35,6 +38,9 @@ importFrom(mda.streams,get_meta)
 importFrom(mda.streams,get_metab_model)
 importFrom(mda.streams,get_ts)
 importFrom(mda.streams,get_var_src_codes)
+importFrom(mda.streams,list_metab_models)
+importFrom(mda.streams,list_metab_run_files)
+importFrom(mda.streams,list_metab_runs)
 importFrom(mda.streams,list_sites)
 importFrom(mda.streams,list_tses)
 importFrom(mda.streams,locate_folder)

diff --git a/R/export_data.R b/R/export_data.R
@@ -17,7 +17,7 @@
 #' @seealso \code{\link[unitted]{write_unitted}}, \code{\link{write.table}}
 #' @export
 export_data <- function(data, file="", keep.units=is.unitted(data), comment.char = "#", sep = "\t", row.names = FALSE, quote = FALSE, ...) {
-  if(is.unitted(data) & isTRUE(with.units)) {
+  if(is.unitted(data) & isTRUE(keep.units)) {
     write_unitted(data, file=file, comment.char=comment.char, sep=sep, row.names=row.names, quote=quote, ...)
   } else {
     write.table(v(data), file=file, sep=sep, row.names=row.names, quote=quote, ...)

diff --git a/R/list_metab_models.R b/R/list_metab_models.R
@@ -0,0 +1,9 @@
+#' List the available metab_model objects
+#' 
+#' @return a character vector of titles of the metab_model .RData files posted on SB
+#' 
+#' @importFrom mda.streams list_metab_models
+#' @name list_metab_models
+#' @rdname list_metab_models
+#' @export
+NULL
diff --git a/R/list_metab_run_files.R b/R/list_metab_run_files.R
@@ -0,0 +1,11 @@
+#' List the files stored in a metabolism runs
+#' 
+#' @param title a metab_run title
+#' @param out the columns to return
+#' @return dataframe of file names and sizes within a metab_run
+#' 
+#' @importFrom mda.streams list_metab_run_files
+#' @name list_metab_run_files
+#' @rdname list_metab_run_files
+#' @export
+NULL
diff --git a/R/list_metab_runs.R b/R/list_metab_runs.R
@@ -0,0 +1,9 @@
+#' List the available metabolism runs
+#' 
+#' @return a character vector of titles of the metab_runs posted on SB
+#' 
+#' @importFrom mda.streams list_metab_runs
+#' @name list_metab_runs
+#' @rdname list_metab_runs
+#' @export
+NULL
diff --git a/R/locate_metab_model.R b/R/locate_metab_model.R
@@ -10,7 +10,8 @@
 #' @param browser logical. Should the URL be opened in a browser?
 #' @examples 
 #' \dontrun{
-#' locate_metab_model("nwis_01473900-16-150730 0.0.7 MLE_for_PRK_wHarvey_and_sw", format="url", browser=FALSE)
+#' locate_metab_model("nwis_01473900-16-150730 0.0.7 MLE_for_PRK_wHarvey_and_sw", 
+#'   format="url", browser=FALSE)
 #' }
 #' @importFrom mda.streams locate_metab_model
 #' @name locate_metab_model

diff --git a/R/powstreams.R b/R/powstreams.R
@@ -20,48 +20,56 @@
 #'   
 #'   }
 #'   
-#' @section Logging in:
+#' @section Logging into ScienceBase:
 #'   
 #'   \itemize{
 #'   
-#'   \item \code{\link{login_sb}}
+#'   \item \code{\link{login_sb}} - log into SB with your myUSGS credentials
 #'   
 #'   }
 #'   
 #' @section Querying ScienceBase:
 #'   
 #'   \itemize{
 #'   
-#'   \item \code{\link{list_sites}}
+#'   \item \code{\link{list_sites}} - list the sites stored on SB
 #'   
-#'   \item \code{\link{list_tses}}
+#'   \item \code{\link{list_tses}} - list the timeseries data on SB for a site
 #'   
-#'   \item \code{\link{summarize_ts}}
+#'   \item \code{\link{summarize_ts}} - get date ranges, num rows, etc. for a ts
 #'   
-#'   \item \code{\link[mda.streams]{list_metab_runs}}
+#'   \item \code{\link{list_metab_runs}} - list the metabolism modeling runs on 
+#'   SB
 #'   
-#'   \item \code{\link[mda.streams]{list_metab_run_files}}
+#'   \item \code{\link{list_metab_run_files}} - list the raw files from one 
+#'   modeling run
+#'   
+#'   \item \code{\link{list_metab_models}} - list the metab_model objects on SB
 #'   
 #'   }
 #'   
 #' @section Navigating ScienceBase:
 #'   
 #'   \itemize{
 #'   
-#'   \item \code{\link{locate_folder}}
+#'   \item \code{\link{locate_folder}} - find a high-level folder on the SB 
+#'   website
 #'   
-#'   \item \code{\link{locate_meta}}
+#'   \item \code{\link{locate_meta}} - find a site data table on the SB website
 #'   
-#'   \item \code{\link{locate_metab_model}}
+#'   \item \code{\link{locate_metab_model}} - find a metab_model object on the 
+#'   SB website
 #'   
-#'   \item \code{\link{locate_metab_run}}
+#'   \item \code{\link{locate_metab_run}} - find a metabolism modeling run 
+#'   folder on the SB website
 #'   
-#'   \item \code{\link{locate_site}}
+#'   \item \code{\link{locate_site}} - find a site folder on the SB website
 #'   
-#'   \item \code{\link{locate_ts}}
+#'   \item \code{\link{locate_ts}} - find a timeseries data item on the SB 
+#'   website
 #'   
 #'   }
-#'
+#'   
 #' @section Reading data from ScienceBase:
 #'   
 #'   \itemize{
@@ -81,39 +89,39 @@
 #'   \item \code{\link{get_ts}} - loads data from SB into R
 #'   
 #'   \item \code{\link{get_ts_metadata}} - get info about ts data
-#'
+#'   
 #'   }
 #'   
 #' @section Exporting data from R to text:
 #'   
 #'   \itemize{
 #'   
-#'   \item \code{\link{export_data}} - exports data from R into a text file
+#'   \item \code{\link{export_data}} - export data from R into a text file
 #'   
-#'   \item \code{\link{view_file}}
+#'   \item \code{\link{view_file}} - open a file in your system's default app
 #'   
-#'   \item \code{\link{view_folder}}
+#'   \item \code{\link{view_folder}} - open a folder in your file explorer
 #'   
 #'   }
 #'   
 #' @section Reading models from ScienceBase:
 #'   
 #'   \itemize{
 #'   
-#'   \item \code{\link{get_config}} - gets a config file from SB
+#'   \item \code{\link{get_config}} - get a config file from SB
+#'   
+#'   \item \code{\link{get_metab_model}} - get a metab_model object from SB
 #'   
-#'   \item \code{\link{get_metab_model}} - gets a metab_model object from SB
-#'
 #'   }
 #'   
 #' @section Other actions for ScienceBase:
 #'   
 #'   \itemize{
 #'   
-#'   \item \code{\link{upload_presentation}} - uploads a presentation to the 
+#'   \item \code{\link{upload_presentation}} - upload a presentation to the 
 #'   Presentations folder on SB
 #'   
-#'   \item \code{\link{upload_publication}} - uploads a presentation to the 
+#'   \item \code{\link{upload_publication}} - upload a presentation to the 
 #'   Publications folder on SB
 #'   
 #'   }

diff --git a/appveyor.yml b/appveyor.yml
@@ -18,6 +18,7 @@ build_script:
   - travis-tool.sh install_github appling/unitted
   - travis-tool.sh install_github USGS-R/streamMetabolizer
   - travis-tool.sh install_github USGS-R/sbtools
+  - travis-tool.sh install_github USGS-R/gsplot
   - travis-tool.sh install_github USGS-R/geoknife
   - travis-tool.sh install_github USGS-R/mda.streams
   - travis-tool.sh install_deps

diff --git a/man/list_metab_models.Rd b/man/list_metab_models.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/list_metab_models.R
+\name{list_metab_models}
+\alias{list_metab_models}
+\title{List the available metab_model objects}
+\value{
+a character vector of titles of the metab_model .RData files posted on SB
+}
+\description{
+List the available metab_model objects
+}
+
diff --git a/man/list_metab_run_files.Rd b/man/list_metab_run_files.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/list_metab_run_files.R
+\name{list_metab_run_files}
+\alias{list_metab_run_files}
+\title{List the files stored in a metabolism runs}
+\arguments{
+\item{title}{a metab_run title}
+
+\item{out}{the columns to return}
+}
+\value{
+dataframe of file names and sizes within a metab_run
+}
+\description{
+List the files stored in a metabolism runs
+}
+
diff --git a/man/list_metab_runs.Rd b/man/list_metab_runs.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/list_metab_runs.R
+\name{list_metab_runs}
+\alias{list_metab_runs}
+\title{List the available metabolism runs}
+\value{
+a character vector of titles of the metab_runs posted on SB
+}
+\description{
+List the available metabolism runs
+}
+
diff --git a/man/locate_metab_model.Rd b/man/locate_metab_model.Rd
@@ -21,7 +21,8 @@ Find a metab_model item on ScienceBase
 }
 \examples{
 \dontrun{
-locate_metab_model("nwis_01473900-16-150730 0.0.7 MLE_for_PRK_wHarvey_and_sw", format="url", browser=FALSE)
+locate_metab_model("nwis_01473900-16-150730 0.0.7 MLE_for_PRK_wHarvey_and_sw",
+  format="url", browser=FALSE)
 }
 }
 
diff --git a/man/powstreams.Rd b/man/powstreams.Rd
@@ -28,12 +28,12 @@ lower-level functions generic to all ScienceBase tasks, see \pkg{sbtools}.
   }
 }
 
-\section{Logging in}{
+\section{Logging into ScienceBase}{
 
 
   \itemize{
 
-  \item \code{\link{login_sb}}
+  \item \code{\link{login_sb}} - log into SB with your myUSGS credentials
 
   }
 }
@@ -43,15 +43,19 @@ lower-level functions generic to all ScienceBase tasks, see \pkg{sbtools}.
 
   \itemize{
 
-  \item \code{\link{list_sites}}
+  \item \code{\link{list_sites}} - list the sites stored on SB
 
-  \item \code{\link{list_tses}}
+  \item \code{\link{list_tses}} - list the timeseries data on SB for a site
 
-  \item \code{\link{summarize_ts}}
+  \item \code{\link{summarize_ts}} - get date ranges, num rows, etc. for a ts
 
-  \item \code{\link[mda.streams]{list_metab_runs}}
+  \item \code{\link{list_metab_runs}} - list the metabolism modeling runs on
+  SB
 
-  \item \code{\link[mda.streams]{list_metab_run_files}}
+  \item \code{\link{list_metab_run_files}} - list the raw files from one
+  modeling run
+
+  \item \code{\link{list_metab_models}} - list the metab_model objects on SB
 
   }
 }
@@ -61,17 +65,21 @@ lower-level functions generic to all ScienceBase tasks, see \pkg{sbtools}.
 
   \itemize{
 
-  \item \code{\link{locate_folder}}
+  \item \code{\link{locate_folder}} - find a high-level folder on the SB
+  website
 
-  \item \code{\link{locate_meta}}
+  \item \code{\link{locate_meta}} - find a site data table on the SB website
 
-  \item \code{\link{locate_metab_model}}
+  \item \code{\link{locate_metab_model}} - find a metab_model object on the
+  SB website
 
-  \item \code{\link{locate_metab_run}}
+  \item \code{\link{locate_metab_run}} - find a metabolism modeling run
+  folder on the SB website
 
-  \item \code{\link{locate_site}}
+  \item \code{\link{locate_site}} - find a site folder on the SB website
 
-  \item \code{\link{locate_ts}}
+  \item \code{\link{locate_ts}} - find a timeseries data item on the SB
+  website
 
   }
 }
@@ -105,11 +113,11 @@ lower-level functions generic to all ScienceBase tasks, see \pkg{sbtools}.
 
   \itemize{
 
-  \item \code{\link{export_data}} - exports data from R into a text file
+  \item \code{\link{export_data}} - export data from R into a text file
 
-  \item \code{\link{view_file}}
+  \item \code{\link{view_file}} - open a file in your system's default app
 
-  \item \code{\link{view_folder}}
+  \item \code{\link{view_folder}} - open a folder in your file explorer
 
   }
 }
@@ -119,9 +127,9 @@ lower-level functions generic to all ScienceBase tasks, see \pkg{sbtools}.
 
   \itemize{
 
-  \item \code{\link{get_config}} - gets a config file from SB
+  \item \code{\link{get_config}} - get a config file from SB
 
-  \item \code{\link{get_metab_model}} - gets a metab_model object from SB
+  \item \code{\link{get_metab_model}} - get a metab_model object from SB
 
   }
 }
@@ -131,10 +139,10 @@ lower-level functions generic to all ScienceBase tasks, see \pkg{sbtools}.
 
   \itemize{
 
-  \item \code{\link{upload_presentation}} - uploads a presentation to the
+  \item \code{\link{upload_presentation}} - upload a presentation to the
   Presentations folder on SB
 
-  \item \code{\link{upload_publication}} - uploads a presentation to the
+  \item \code{\link{upload_publication}} - upload a presentation to the
   Publications folder on SB
 
   }