check issues

DESCRIPTION

@@ -17,4 +17,4 @@ License: CC0
 LazyData: TRUE
 Encoding: UTF-8
 VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1

R/read_timeseries_dsg.R

 #'@title Read NetCDF-CF timeSeries featuretype
 #'
 #'@param nc_file character file path to the nc file to be read.
+#'@param read_data logical whether to read metadata only or not.
 #'
 #'@return list containing the contents of the NetCDF file.
 #'
@@ -67,12 +68,12 @@ check_timeseries_atts <- function(nc_atts) {
   }
   
   # Check important global atts
-  check <- filter(nc_atts, variable == "NC_GLOBAL" & name == 'Conventions')$value
+  check <- filter(nc_atts, .data$variable == "NC_GLOBAL" & .data$name == 'Conventions')$value
   if(length(check) == 0 || !grepl('CF', check)) {
     warning('File does not advertise CF conventions, unexpected behavior may result.') 
   }
   
-  check <- filter(nc_atts, variable == "NC_GLOBAL" & name == "featureType")$value
+  check <- filter(nc_atts, .data$variable == "NC_GLOBAL" & .data$name == "featureType")$value
   if(length(check) == 0 || !grepl('timeSeries', check)) {
     warning('File does not advertise use of the CF timeseries featureType, unexpected behavior may result.') 
   }
@@ -210,10 +211,10 @@ get_nc_list <- function(nc, dsg, nc_meta, read_data) {
 
 get_timeseries_id <- function(nc_atts) {
   # Look for variable with the timeseries_id in it.
-  timeseries_id <- filter(nc_atts, name == "standard_name" &
-                            value == "station_id")$variable
-  timeseries_id <- filter(nc_atts, name == "cf_role" &
-                            value == pkg.env$timeseries_id_cf_role)$variable
+  timeseries_id <- filter(nc_atts, .data$name == "standard_name" &
+                            .data$value == "station_id")$variable
+  timeseries_id <- filter(nc_atts, .data$name == "cf_role" &
+                            .data$value == pkg.env$timeseries_id_cf_role)$variable
   
   if(length(timeseries_id) == 0) { 
     stop('A timeseries id variable was not found in the file.') 
@@ -236,6 +237,8 @@ get_coord_vars <- function(nc) {
   coord_vars[!is.na(coord_vars)]
 }
 
+.data <- NULL
+
 add_globals <- function(nc_list, nc_meta) {
   nc_list$global_attributes$nc_summary <- filter(nc_meta$attribute, .data$variable == "NC_GLOBAL" &
                                                    .data$name == "summary")$value

man/read_timeseries_dsg.Rd

@@ -4,10 +4,12 @@
 \alias{read_timeseries_dsg}
 \title{Read NetCDF-CF timeSeries featuretype}
 \usage{
-read_timeseries_dsg(nc_file)
+read_timeseries_dsg(nc_file, read_data = TRUE)
 }
 \arguments{
 \item{nc_file}{character file path to the nc file to be read.}
+
+\item{read_data}{logical whether to read metadata only or not.}
 }
 \value{
 list containing the contents of the NetCDF file.

man/write_attribute_data.Rd

@@ -4,8 +4,13 @@
 \alias{write_attribute_data}
 \title{Write attribute data to NetCDF-CF}
 \usage{
-write_attribute_data(nc_file, att_data, instance_dim_name = "instance",
-  units = rep("unknown", ncol(att_data)), overwrite = FALSE)
+write_attribute_data(
+  nc_file,
+  att_data,
+  instance_dim_name = "instance",
+  units = rep("unknown", ncol(att_data)),
+  overwrite = FALSE
+)
 }
 \arguments{
 \item{nc_file}{\code{character} file path to the nc file to be created. 
@@ -35,7 +40,7 @@ example_file <-write_attribute_data(tempfile(), sample_data,
 
 try({
   ncdump <- system(paste("ncdump -h", example_file), intern = TRUE)
-  cat(ncdump ,sep = "\\n")
+  cat(ncdump ,sep = "\n")
 }, silent = TRUE)
 
 }

man/write_geometry.Rd

@@ -4,8 +4,12 @@
 \alias{write_geometry}
 \title{Write geometries and attributes to NetCDF-CF}
 \usage{
-write_geometry(nc_file, geom_data, instance_dim_name = NULL,
-  variables = list())
+write_geometry(
+  nc_file,
+  geom_data,
+  instance_dim_name = NULL,
+  variables = list()
+)
 }
 \arguments{
 \item{nc_file}{\code{character} file path to the nc file to be created.}
@@ -35,7 +39,7 @@ hucPolygons_nc <- ncdfgeom::write_geometry(nc_file=tempfile(),
                                            geom_data = hucPolygons)
 try({
   ncdump <- system(paste("ncdump -h", hucPolygons_nc), intern = TRUE)
-  cat(ncdump ,sep = "\\n")
+  cat(ncdump ,sep = "\n")
 }, silent = TRUE)
 
 }

man/write_timeseries_dsg.Rd

@@ -4,11 +4,22 @@
 \alias{write_timeseries_dsg}
 \title{Write time series to NetCDF-CF}
 \usage{
-write_timeseries_dsg(nc_file, instance_names, lats, lons, times, data,
-  alts = NA, data_unit = "", data_prec = "double",
+write_timeseries_dsg(
+  nc_file,
+  instance_names,
+  lats,
+  lons,
+  times,
+  data,
+  alts = NA,
+  data_unit = "",
+  data_prec = "double",
   data_metadata = list(name = "data", long_name = "unnamed data"),
-  time_units = "days since 1970-01-01 00:00:00", attributes = list(),
-  add_to_existing = FALSE, overwrite = FALSE)
+  time_units = "days since 1970-01-01 00:00:00",
+  attributes = list(),
+  add_to_existing = FALSE,
+  overwrite = FALSE
+)
 }
 \arguments{
 \item{nc_file}{\code{character} file path to the nc file to be created.}