Merge pull request #45 from Ecosystem-Assessments/kcreview

minor changes

DESCRIPTION

@@ -20,48 +20,51 @@ BugReports: https://github.com/david-beauchesne/pipedat/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
+Depends: 
+    R (>= 3.3.0)
 Imports: 
+    archive,
+    bookdown,
     cli,
     crayon,
     curl,
     dplyr,
     glue,
+    grDevices,
     here,
+    ids,
     RefManageR,
+    rgovcan,
     rlang,
+    rmarkdown,
     sf,
     stars,
+    stringr,
+    terra,
+    tools,
     utils,
+    vroom,
     yaml
-Depends: 
-    R (>= 2.10)
 Suggests:
-    archive,
     eaMethods,
     fasterize,
     fs, 
     geojsonsf,
     graphics,
-    graphicsutils,
-    grDevices,
-    ids,
     knitr,
     latex2exp,
     purrr,
     raster,
     readr,
-    rgovcan,
     R.utils,
     sdmpredictors,
     stats,
-    stringr,
     testthat (>= 3.0.0),
     tidyr,
     usethis,
     uuid,
     viridis,
-    vroom,
     whisker,
     XML

NAMESPACE

@@ -49,7 +49,6 @@ export(write_pipeline)
 importFrom(RefManageR,BibEntry)
 importFrom(RefManageR,WriteBib)
 importFrom(cli,symbol)
-importFrom(crayon,blue)
 importFrom(glue,glue)
 importFrom(glue,glue_sql)
 importFrom(grDevices,colorRampPalette)

R/helpers.R

@@ -212,8 +212,8 @@ get_pipeline_url <- function(uid) {
 #' @export
 get_grid_info <- function(grd = here::here("project-data", "grid", "grid.tif")) {
   # Get grid
-  if (class(grd) == "character") grd <- stars::read_stars(grd)
-  if (!"stars" %in% class(grd)) grd <- stars::st_as_stars(grd)
+  if (inherits(grd, "character")) grd <- stars::read_stars(grd)
+  if (!inherits(grd, "stars")) grd <- stars::st_as_stars(grd)
 
   # Info
   list(

R/importdat.R

@@ -4,8 +4,8 @@
 #' in the global R environment for use in other pipelines or
 #' user processes.
 #'
-#' @param uid unique identifier of queried data. The full list of available data pipelines can be consulted using `pipelines()`
-#' @param type type of data to import, one of "format" or "integrated"
+#' @param uid unique identifier of queried data. The full list of available data pipelines can be consulted using `pipelist()`.
+#' @param type type of data to import, one of "format" or "integrated".
 #'
 #' @return This function returns objects in the global R environment
 #'

R/masteringrid.R

@@ -18,11 +18,11 @@
 #' @export
 masteringrid <- function(dat, grd = here::here("project-data", "grid", "grid.tif")) {
   # Get grid
-  if (class(grd) == "character") grd <- stars::read_stars(grd)
-  if (!"stars" %in% class(grd)) grd <- stars::st_as_stars(grd)
+  if (inherits(grd, "character")) grd <- stars::read_stars(grd)
+  if (!inherits(grd, "stars")) grd <- stars::st_as_stars(grd)
 
   # stars objects
-  if ("stars" %in% class(dat)) {
+  if (inherits(dat, "stars")) {
     stars::st_warp(dat, grd)
   }
 

R/pipedat.R

@@ -5,7 +5,7 @@
 #' built to access data programmatically and reproducibly, which
 #' we refer to as *data pipelines*.
 #'
-#' @param uid unique identifier of queried data. The full list of available data pipelines can be consulted using `pipelines()`
+#' @param uid unique identifier of queried data. The full list of available data pipelines can be consulted using `pipelist()`
 #' @eval dp_params()
 #' @param ... further arguments used in functions, if applicable.
 #'

R/pipelist.R

@@ -1,4 +1,4 @@
-#' List of available data pipalines
+#' List of available data pipelines
 #'
 #' This function provides the list of individual scripts
 #' built to access data programmatically and reproducibly, which

R/pipeload.R

@@ -5,10 +5,10 @@
 #' built to access data programmatically and reproducibly, which
 #' we refer to as *data pipelines*.
 #'
-#' @param urls urls for data download
-#' @param govcan unique identifier of resource on the open government federal data portal to download
+#' @param urls urls for data download.
+#' @param govcan unique identifier of resource on the open government federal data portal to download.
 #' @param output output folder for queried data.
-#' @param large logical, whether file to download is large and thus R options should be modified for longer timeout options. Default set to false
+#' @param large logical, whether file to download is large and thus R options should be modified for longer timeout options. Default set to `FALSE`.
 #'
 #' @return This function returns the queried raw data, formatted data, metadata and bibtex associated with the raw data.
 #'

R/pipereport.R

@@ -1,6 +1,6 @@
 #' Create a report from the pipedat data in a project
 #'
-#' This function create a generic report that provides a summary of the data that was loaded and formatted throught the pipedat package in a specific location. The purpose of this report is to accompany a project report by providing the relevant information concerning the data that was accessed and formated through pipedat.
+#' This function creates a generic report that provides a summary of the data that was loaded and formatted throught the pipedat package in a specific location. The purpose of this report is to accompany a project report by providing the relevant information concerning the data that was accessed and formated through pipedat.
 #'
 #' @return This function creates a new report in `pubs/pipedat/` using the template `inst/templates/report.Rmd` and all the data available in `project-data/pipedat/` and `project-data/grid/`.
 #'

R/zzz.R

@@ -1,12 +1,10 @@
 #' pipedat: pipelines to access, load, and format data from various sources
 #'
-#' @docType package
 #' @name pipedat
 #'
 #' @importFrom glue glue glue_sql
 #' @importFrom grDevices dev.off png colorRampPalette
-#' @importFrom graphics par box layout lines mtext
-#' @importFrom graphics polygon text
+#' @importFrom graphics par box layout lines mtext polygon text
 #' @importFrom RefManageR BibEntry WriteBib
 #' @importFrom rlang sym
 #' @importFrom sf st_bbox st_write st_read st_transform
@@ -22,7 +20,6 @@
 #' @importFrom yaml yaml.load_file write_yaml read_yaml
 #' @importFrom rlang abort warn
 #' @importFrom cli symbol
-#' @importFrom crayon blue
 NULL
 
 

README.Rmd

@@ -16,8 +16,6 @@ knitr::opts_chunk$set(
 # pipedat <a href='https://github.com/Ecosystem-Assessments/pipedat'><img src='man/figures/logo.png' align="right" height="175" /></a>
 
 <!-- badges: start -->
-<!-- [![Check package](https://github.com/inSileco/graphicsutils/actions/workflows/check-moreorless-standard.yaml/badge.svg)](https://github.com/inSileco/graphicsutils/actions/workflows/check-moreorless-standard.yaml) -->
-<!-- [![codecov](https://codecov.io/gh/inSileco/graphicsutils/branch/master/graph/badge.svg)](https://codecov.io/gh/inSileco/graphicsutils) -->
 [![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#preliminary)
 ![](https://img.shields.io/badge/status-preliminary-blue.svg)
 [![R-CMD-check](https://github.com/Ecosystem-Assessments/pipedat/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Ecosystem-Assessments/pipedat/actions/workflows/R-CMD-check.yaml)

inst/templates/pipeflow.yml

@@ -17,7 +17,7 @@ pipedat:
       - 2021
       - 2022
   # ==========================================================================
-  # UID of pipelines to eexecute
+  # UID of pipelines to execute
   pipelines:
     - "pipeline_id1"
     - "pipeline_id2"