Updated load_data.R #1592

docker/depends/pecan.depends.R

@@ -23,6 +23,7 @@ wanted <- c(
 'binaryLogic',
 'BioCro',
 'bit64',
+'BrownDog',
 'coda',
 'corrplot',
 'data.table',

modules/benchmark/DESCRIPTION

@@ -15,26 +15,28 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation.
 Imports:
+    dbplyr,
+    dplyr,
+    ggplot2,
+    gridExtra,
+    lubridate (>= 1.6.0),
+    magrittr,
+    ncdf4 (>= 1.15),
     PEcAn.DB,
     PEcAn.logger,
     PEcAn.remote,
     PEcAn.settings,
     PEcAn.utils,
-    lubridate (>= 1.6.0),
-    ncdf4 (>= 1.15),
-    udunits2 (>= 0.11),
-    XML (>= 3.98-1.4),
-    dplyr,
-    ggplot2,
-    gridExtra,
     reshape2,
-    dbplyr,
     SimilarityMeasures,
-    zoo,
-    stringr
+    stringr,
+    udunits2 (>= 0.11),
+    XML (>= 3.98-1.4),
+    zoo 
 Suggests:
     PEcAn.data.land,
-    testthat (>= 2.0.0)
+    testthat (>= 2.0.0),
+    BrownDog
 License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyLoad: yes

modules/benchmark/NAMESPACE

@@ -44,3 +44,4 @@ importFrom(ggplot2,geom_path)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,labs)
+importFrom(magrittr,"%>%")

modules/benchmark/R/load_data.R

@@ -9,6 +9,7 @@
 ##' @author Betsy Cowdery, Istem Fer, Joshua Mantooth
 ##' Generic function to convert input files containing observational data to 
 ##' a common PEcAn format. 
+#' @importFrom magrittr %>%
 
 load_data <- function(data.path, format, start_year = NA, end_year = NA, site = NA, 
                       vars.used.index=NULL, ...) {
@@ -30,12 +31,6 @@ load_data <- function(data.path, format, start_year = NA, end_year = NA, site =
     vars.used.index <- setdiff(seq_along(format$vars$variable_id), format$time.row)
   }
 
-  library(PEcAn.utils)
-  library(PEcAn.benchmark)
-  library(lubridate)
-  library(udunits2)
-  library(dplyr)
-
   # Determine the function that should be used to load the data
   mimetype <- gsub("-", "_", format$mimetype)
   fcn1 <- paste0("load_", format$file_name)
@@ -44,13 +39,13 @@ load_data <- function(data.path, format, start_year = NA, end_year = NA, site =
     fcn <- match.fun(fcn1)
   } else if (exists(fcn2)) {
     fcn <- match.fun(fcn2)
-  } else if (!exists(fcn1) & !exists(fcn2) & require(bd)) { 
+  } else if (!exists(fcn1) & !exists(fcn2) & requireNamespace(bd, quietly = TRUE)) { 
     #To Do: call to DAP to see if conversion to csv is possible
     #Brown Dog API call through BDFiddle, requires username and password
-    key   <- get_key("https://bd-api.ncsa.illinois.edu",username,password)
-    token <- get_token("https://bd-api.ncsa.illinois.edu",key)
+    key   <- BrownDog::get_key("https://bd-api.ncsa.illinois.edu",username,password)
+    token <- BrownDog::get_token("https://bd-api.ncsa.illinois.edu",key)
     #output_path = where are we putting converted file?
-    converted.data.path <- convert_file(url = "https://bd-api.ncsa.illinois.edu", input_filename = data.path, 
+    converted.data.path <- BrownDog::convert_file(url = "https://bd-api.ncsa.illinois.edu", input_filename = data.path, 
                                         output = "csv", output_path = output_path, token = token)
     if (is.na(converted.data.path)){
       PEcAn.logger::logger.error("Converted file was not returned from Brown Dog")
@@ -94,11 +89,11 @@ load_data <- function(data.path, format, start_year = NA, end_year = NA, site =
                       vars_used$pecan_name[i], vars_used$pecan_units[i]))
         out[col] <- udunits2::ud.convert(as.numeric(x), u1, u2)
         colnames(out)[col] <- vars_used$pecan_name[i]
-      } else if (misc.are.convertible(u1, u2)) {
+      } else if (PEcAn.utils::misc.are.convertible(u1, u2)) {
         print(sprintf("convert %s %s to %s %s", 
                       vars_used$input_name[i], u1, 
                       vars_used$pecan_name[i], u2))
-        out[col] <- as.vector(misc.convert(x, u1, u2)) # Betsy: Adding this because misc.convert returns vector with attributes original agrument x, which causes problems later
+        out[col] <- as.vector(PEcAn.utils::misc.convert(x, u1, u2)) # Betsy: Adding this because misc.convert returns vector with attributes original agrument x, which causes problems later
         colnames(out)[col] <- vars_used$pecan_name[i]
       } else {
         PEcAn.logger::logger.warn(paste("Units cannot be converted. Removing variable. please check the units of",vars_used$input_name[i]))
@@ -115,7 +110,7 @@ load_data <- function(data.path, format, start_year = NA, end_year = NA, site =
     names(out)[col] <- format$vars$pecan_name[time.row]
 
     # Need a much more spohisticated approach to converting into time format. 
-    y <- dplyr::select(out, one_of(format$vars$pecan_name[time.row]))
+    y <- dplyr::select(out, tidyselect::one_of(format$vars$pecan_name[time.row]))
 
     if(!is.null(site$time_zone)){
       tz = site$time_zone
@@ -145,4 +140,3 @@ load_data <- function(data.path, format, start_year = NA, end_year = NA, site =
 
   return(out)
 } # load_data
-