Merge pull request #87 from ropensci/doc-updates

Updated docs + examples + vignette

Author: mbjoseph

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: smapr
 Type: Package
 Title: Acquisition and Processing of NASA Soil Moisture Active-Passive (SMAP) Data
-Version: 0.2.1
+Version: 0.3.0
 Authors@R: c(
-    person("Maxwell", "Joseph", email = "[email protected]",
-            role = c("aut", "cre")),
+    person("Maxwell", "Joseph", email = "[email protected]",
+            role = c("aut", "cre", "cph")),
     person("Matthew", "Oakley", email = "[email protected]",
             role = "aut"),
     person("Zachary", "Schira", email = "[email protected]",
@@ -18,13 +18,12 @@ Imports:
     methods,
     rappdirs (>= 0.3.1),
     terra
-Maintainer: Maxwell Joseph <[email protected]>
+Maintainer: Maxwell Joseph <[email protected]>
 Description:
     Facilitates programmatic access to NASA Soil Moisture Active
     Passive (SMAP) data with R. It includes functions to search for, acquire,
     and extract SMAP data.
 License: GPL-3
-LazyData: TRUE
 RoxygenNote: 7.3.3
 Suggests:
     knitr,
@@ -34,6 +33,6 @@ Suggests:
     utils,
     covr
 VignetteBuilder: knitr
-URL: https://docs.ropensci.org/smapr, https://github.com/ropensci/smapr
+URL: https://docs.ropensci.org/smapr/, https://github.com/ropensci/smapr
 BugReports: https://github.com/ropensci/smapr/issues
 Encoding: UTF-8

R/download_smap.R

@@ -23,7 +23,7 @@
 #' vector specifying the local directory containing the downloaded files.
 #' @examples
 #' \dontrun{
-#' files <- find_smap(id = "SPL4SMGP", dates = "2015-03-31", version = 4)
+#' files <- find_smap(id = "SPL4SMGP", dates = "2015-03-31", version = 8)
 #' # files[1, ] refers to the first available data file
 #' downloads <- download_smap(files[1, ])
 #' }

R/extract_smap.R

@@ -13,7 +13,7 @@
 #' @return Returns a SpatRaster object.
 #' @examples
 #' \dontrun{
-#' files <- find_smap(id = "SPL4SMGP", dates = "2015-03-31", version = 4)
+#' files <- find_smap(id = "SPL4SMGP", dates = "2015-03-31", version = 8)
 #' downloads <- download_smap(files[1, ])
 #' sm_raster <- extract_smap(downloads, name = '/Geophysical_Data/sm_surface')
 #' }

R/find_smap.R

@@ -6,7 +6,7 @@
 #' There are many SMAP data products that can be accessed with this function.
 #' Currently, smapr supports level 3 and level 4 data products, each of which
 #' has an associated Data Set ID which is specified by the \code{id} argument,
-#' described at \url{https://nsidc.org/data/smap/smap-data.html} and summarized
+#' described at \url{https://nsidc.org/data/smap/data} and summarized
 #' below:
 #'
 #' \describe{
@@ -40,20 +40,20 @@
 #' such as produced by \code{seq.Date}.
 #' @param version Which data version would you like to search for? Version
 #'   information for each data product can be found at
-#'   \url{https://nsidc.org/data/smap/data_versions}
+#'   \url{https://nsidc.org/data/smap/version-history}
 #' @return A data.frame with the names of the data files, the remote directory,
 #'   and the date.
 #'
 #' @examples
 #' \dontrun{
 #' # looking for data on one day:
-#' find_smap(id = "SPL4SMGP", dates = "2015-03-31", version = 4)
+#' find_smap(id = "SPL4SMGP", dates = "2015-03-31", version = 8)
 #'
 #' # searching across a date range
 #' start_date <- as.Date("2015-03-31")
 #' end_date <- as.Date("2015-04-02")
 #' date_sequence <- seq(start_date, end_date, by = 1)
-#' find_smap(id = "SPL4SMGP", dates = date_sequence, version = 4)
+#' find_smap(id = "SPL4SMGP", dates = date_sequence, version = 8)
 #' }
 #'
 #' @importFrom httr GET

R/list_smap.R

@@ -10,7 +10,7 @@
 #' of each data file in \code{files}.
 #' @examples
 #' \dontrun{
-#' files <- find_smap(id = "SPL4SMGP", dates = "2015-03-31", version = 4)
+#' files <- find_smap(id = "SPL4SMGP", dates = "2015-03-31", version = 8)
 #' files <- download_smap(files[1, ])
 #' list_smap(files)
 #' list_smap(files, all = TRUE)

R/set_smap_credentials.R

@@ -18,8 +18,8 @@
 #' be overwritten unless \code{overwrite = TRUE}.
 #' @param overwrite Logical: whether to overwrite previous Earthdata credentials
 #' in your .Renviron file (only applies when \code{save = TRUE})
-#' @return A data.frame with the names of the data files, the remote directory,
-#'   and the date.
+#' @return No return value, called for side effects (sets environment variables
+#'   and optionally saves credentials to .Renviron).
 #'
 #' @examples
 #' \dontrun{

README.md

@@ -1,17 +1,17 @@
 smapr
 ================
 
-[![codecov](https://codecov.io/gh/ropensci/smapr/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/smapr)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/smapr)](https://cran.r-project.org/package=smapr)
-[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
-[![](http://cranlogs.r-pkg.org/badges/grand-total/smapr)](http://cran.rstudio.com/web/packages/smapr/index.html)
-[![](https://badges.ropensci.org/231_status.svg)](https://github.com/ropensci/onboarding/issues/231)
+[![codecov](https://app.codecov.io/gh/ropensci/smapr/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/smapr)
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/smapr)](https://cran.r-project.org/package=smapr)
+[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
+[![](https://cranlogs.r-pkg.org/badges/grand-total/smapr)](https://cran.r-project.org/package=smapr)
+[![](https://badges.ropensci.org/231_status.svg)](https://github.com/ropensci/software-review/issues/231)
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
-developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 
 An R package for acquisition and processing of [NASA (Soil Moisture
-Active-Passive) SMAP data](http://smap.jpl.nasa.gov/)
+Active-Passive) SMAP data](https://smap.jpl.nasa.gov/)
 
 ## Installation
 
@@ -91,19 +91,19 @@ including surface soil moisture, root zone soil moisture, freeze/thaw
 status, surface temperature, vegetation water content, vegetation
 opacity, net ecosystem carbon exchange, soil temperature, and
 evapotranspiration. NSIDC provides documentation for all SMAP data
-products on their [website](https://nsidc.org/data/smap/smap-data.html),
+products on their [website](https://nsidc.org/data/smap/data),
 and we provide a summary of data products supported by smapr below.
 
-| Dataset id | Description                                         | Resolution |
-|------------|-----------------------------------------------------|------------|
-| SPL2SMAP_S | SMAP/Sentinel-1 Radiometer/Radar Soil Moisture      | 3 km       |
-| SPL3FTA    | Radar Northern Hemisphere Daily Freeze/Thaw State   | 3 km       |
-| SPL3SMA    | Radar Global Daily Soil Moisture                    | 3 km       |
-| SPL3SMP    | Radiometer Global Soil Moisture                     | 36 km      |
-| SPL3SMAP   | Radar/Radiometer Global Soil Moisture               | 9 km       |
-| SPL4SMAU   | Surface/Rootzone Soil Moisture Analysis Update      | 9 km       |
-| SPL4SMGP   | Surface/Rootzone Soil Moisture Geophysical Data     | 9 km       |
-| SPL4CMDL   | Carbon Net Ecosystem Exchange                       | 9 km       |
+| Dataset id | Description                                       | Resolution |
+|------------|---------------------------------------------------|------------|
+| SPL2SMAP_S | SMAP/Sentinel-1 Radiometer/Radar Soil Moisture    | 3 km       |
+| SPL3FTA    | Radar Northern Hemisphere Daily Freeze/Thaw State | 3 km       |
+| SPL3SMA    | Radar Global Daily Soil Moisture                  | 3 km       |
+| SPL3SMP    | Radiometer Global Soil Moisture                   | 36 km      |
+| SPL3SMAP   | Radar/Radiometer Global Soil Moisture             | 9 km       |
+| SPL4SMAU   | Surface/Rootzone Soil Moisture Analysis Update    | 9 km       |
+| SPL4SMGP   | Surface/Rootzone Soil Moisture Geophysical Data   | 9 km       |
+| SPL4CMDL   | Carbon Net Ecosystem Exchange                     | 9 km       |
 
 ## Typical workflow
 
@@ -124,18 +124,18 @@ returns a data frame of available data. As data mature and pass checks,
 versions advance. At any specific time, not all versions of all datasets
 for all dates may exist. For the most up to date overview of dataset
 versions, see the NSIDC SMAP data version
-[webpage](https://nsidc.org/data/smap/smap-data.html).
+[webpage](https://nsidc.org/data/smap/version-history).
 
 ``` r
 library(smapr)
 library(terra)
-#> terra 1.7.18
+#> terra 1.8.86
 available_data <- find_smap(id = "SPL3SMAP", date = "2015-05-25", version = 3)
 str(available_data)
 #> 'data.frame':    1 obs. of  3 variables:
 #>  $ name: chr "SMAP_L3_SM_AP_20150525_R13080_001"
 #>  $ date: Date, format: "2015-05-25"
-#>  $ dir : chr "SPL3SMAP.003/2015.05.25/"
+#>  $ dir : chr "SPL3SMAP/003/2015/05/25/"
 ```
 
 ### Downloading and inspecting SMAP data
@@ -146,14 +146,14 @@ an argument, the data are stored in the user’s cache.
 
 ``` r
 downloads <- download_smap(available_data)
-#> Downloading https://n5eil01u.ecs.nsidc.org/SMAP/SPL3SMAP.003/2015.05.25/SMAP_L3_SM_AP_20150525_R13080_001.h5
-#> Downloading https://n5eil01u.ecs.nsidc.org/SMAP/SPL3SMAP.003/2015.05.25/SMAP_L3_SM_AP_20150525_R13080_001.qa
-#> Downloading https://n5eil01u.ecs.nsidc.org/SMAP/SPL3SMAP.003/2015.05.25/SMAP_L3_SM_AP_20150525_R13080_001.h5.iso.xml
+#> Downloading https://data.nsidc.earthdatacloud.nasa.gov/nsidc-cumulus-prod-protected/SMAP/SPL3SMAP/003/2015/05/25/SMAP_L3_SM_AP_20150525_R13080_001.h5
+#> Downloading https://data.nsidc.earthdatacloud.nasa.gov/nsidc-cumulus-prod-protected/SMAP/SPL3SMAP/003/2015/05/25/SMAP_L3_SM_AP_20150525_R13080_001.qa
+#> Downloading https://data.nsidc.earthdatacloud.nasa.gov/nsidc-cumulus-prod-protected/SMAP/SPL3SMAP/003/2015/05/25/SMAP_L3_SM_AP_20150525_R13080_001.h5.iso.xml
 str(downloads)
 #> 'data.frame':    1 obs. of  4 variables:
 #>  $ name     : chr "SMAP_L3_SM_AP_20150525_R13080_001"
 #>  $ date     : Date, format: "2015-05-25"
-#>  $ dir      : chr "SPL3SMAP.003/2015.05.25/"
+#>  $ dir      : chr "SPL3SMAP/003/2015/05/25/"
 #>  $ local_dir: chr "~/.cache/smap"
 ```