Merge pull request #75 from aappling-usgs/master

updates for sM & mda.streams changes
DOI-USGS · Sep 18, 2015 · b7139aa · b7139aa
2 parents f6cdce1 + 4f8b580
commit b7139aa
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Showing 4 changed files with 17 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: powstreams
 Type: Package
 Title: powstreams
-Version: 0.7.13
-Date: 2015-09-08
+Version: 0.7.14
+Date: 2015-09-17
 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.
@@ -16,6 +16,7 @@ Depends:
     R (>= 3.0)
 Imports:
     mda.streams (>= 0.7.21),
+    streamMetabolizer,
     sbtools,
     shiny,
     unitted,
@@ -26,6 +27,6 @@ Imports:
     gsplot (>= 0.2.2),
     leaflet
 Suggests:
-   testthat
+    testthat
 LazyLoad: yes
 LazyData: yes
diff --git a/R/get_ts.R b/R/get_ts.R
@@ -7,7 +7,8 @@
 #' ts-getting.
 #' 
 #' @usage get_ts(var_src, site_name, method = "approx", approx_tol = 
-#'   as.difftime(3, units = "hours"), on_local_exists = "skip")
+#'   as.difftime(3, units = "hours"), on_local_exists = "skip", on_invalid =
+#'   "stop")
 #' @param var_src a valid variable name for timeseries data (see 
 #'   \code{dplyr::select(dplyr::filter(var_src_codes, data_type=='ts'), 
 #'   var_src)})
@@ -18,6 +19,8 @@
 #'   2nd:nth data argument to combine_ts (relative to the first argument)
 #' @param on_local_exists character indicating what to do if the folder already 
 #'   contains a file with the intended download name
+#' @param on_invalid character in \code{c("stop","warn")} indicating how to 
+#'   handle invalid timeseries
 #'   
 #' @importFrom mda.streams get_ts
 #' @name get_ts

diff --git a/inst/shiny/model/server.R b/inst/shiny/model/server.R
@@ -1,6 +1,7 @@
 library(dygraphs)
 library(datasets)
 library(DT)
+library(streamMetabolizer)
 library(powstreams)
 
 noneselected = "-- no variable selected --"
@@ -28,8 +29,8 @@ shinyServer(function(input, output) {
       if (is.null(names(models)) || !names(models) %in% r.chr){
         file = download_metab_model(metab_models[row, ]$model_name, on_local_exists = 'skip')
         if (file.size(file) > 0){
-          load(file) # site-specific, run-specific model object
-          models[[r.chr]] <- mm
+          varname <- load(file) # site-specific, run-specific model object
+          models[[r.chr]] <- mda.streams::modernize_metab_model(get(varname))
         } else {
           models[[r.chr]] <- list() # empty model
         }
@@ -50,8 +51,8 @@ shinyServer(function(input, output) {
     } else {
       ts.out <- null.xts
       for (nm in names(models)){
-        df <- data.frame(xts::xts(models[[nm]]@fit[[var]], order.by=models[[nm]]@fit[['date']])) %>% 
-          setNames(paste(var,models[[nm]]@info$site, models[[nm]]@info$strategy, models[[nm]]@info$tag, sep='.'))
+        df <- data.frame(xts::xts(get_fit(models[[nm]])[[var]], order.by=get_fit(models[[nm]])[['local.date']])) %>% 
+          setNames(paste(var,get_info(models[[nm]])$config$site, get_info(models[[nm]])$config$strategy, get_info(models[[nm]])$config$tag, sep='.'))
         ts.out <- merge(ts.out, df)
       }
       return(ts.out)

diff --git a/man/get_ts.Rd b/man/get_ts.Rd
@@ -21,7 +21,10 @@ over which an approximation will be used to fill in data gaps in the
 2nd:nth data argument to combine_ts (relative to the first argument)}
 
 \item{on_local_exists}{character indicating what to do if the folder already
-  contains a file with the intended download name}
+contains a file with the intended download name}
+
+\item{on_invalid}{character in \code{c("stop","warn")} indicating how to
+  handle invalid timeseries}
 }
 \description{
 Downloads the file from SB if either (1) the file has not yet been downloaded