From 0d2552efb70d5a13a0d51e1d73c5a99af01121fe Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Tue, 29 Nov 2022 22:53:42 +0000
Subject: [PATCH] spell checks

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 R/download_dataset.R               | 2 +-
 R/get_data_path.R                  | 2 +-
 R/get_downloaded_datasets.R        | 4 ++--
 R/get_ice_mask.R                   | 2 +-
 R/get_land_mask.R                  | 2 +-
 R/is_region_series.R               | 4 ++--
 R/location_series.R                | 4 ++--
 R/location_slice.R                 | 2 +-
 R/sample_region_slice.R            | 2 +-
 man/climate_for_locations.Rd       | 2 +-
 man/download_dataset.Rd            | 2 +-
 man/get_data_path.Rd               | 2 +-
 man/get_downloaded_datasets.Rd     | 2 +-
 man/get_ice_mask.Rd                | 2 +-
 man/get_land_mask.Rd               | 2 +-
 man/is_region_series.Rd            | 4 ++--
 man/location_series.Rd             | 2 +-
 man/sample_region_slice.Rd         | 2 +-
 man/time_series_for_locations.Rd   | 2 +-
 vignettes/a0_pastclim_overview.Rmd | 2 +-
 vignettes/a2_custom_datasets.Rmd   | 8 ++++----
 22 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index bd74f87c..76b77e5c 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, terra_41]
+    branches: [main, master, cran_changes]
   pull_request:
     branches: [main, master]
 
diff --git a/R/download_dataset.R b/R/download_dataset.R
index c19b2cda..f01b8216 100644
--- a/R/download_dataset.R
+++ b/R/download_dataset.R
@@ -1,4 +1,4 @@
-#' Download palaeoclimatereconstructions.
+#' Download palaeoclimate reconstructions.
 #'
 #' This function downloads palaeoclimate reconstructions. Files will be stored
 #' in the data path of `pastclim`, which can be inspected with
diff --git a/R/get_data_path.R b/R/get_data_path.R
index fb249268..b4ad2cd6 100644
--- a/R/get_data_path.R
+++ b/R/get_data_path.R
@@ -4,7 +4,7 @@
 #' 
 #' The path is stored in an option for `pastclim` named `data_path`. If
 #' a configuration file was saved when using \code{set_data_path}, the path
-#' is retrived from a file named "pastclim_data.txt", which
+#' is retrieved from a file named "pastclim_data.txt", which
 #' is found in the directory returned by 
 #' `tools::R_user_dir("pastclim","config")` (i.e.
 #' the default configuration directory for the package as set in R >= 4.0).
diff --git a/R/get_downloaded_datasets.R b/R/get_downloaded_datasets.R
index c01c9912..aa788bda 100644
--- a/R/get_downloaded_datasets.R
+++ b/R/get_downloaded_datasets.R
@@ -2,7 +2,7 @@
 #'
 #' List the downloaded variable for each dataset.
 #'
-#' @param data_path leave it to NULL to use the default datapath
+#' @param data_path leave it to NULL to use the default data_path
 #' @returns a list of variable names per dataset.
 #'
 #' @export
@@ -22,4 +22,4 @@ get_downloaded_datasets <- function(data_path = NULL) {
     ]
   }
   downloaded_vars
-}
\ No newline at end of file
+}
diff --git a/R/get_ice_mask.R b/R/get_ice_mask.R
index 2c7cba3c..9a82b07a 100644
--- a/R/get_ice_mask.R
+++ b/R/get_ice_mask.R
@@ -1,6 +1,6 @@
 #' Get the ice mask for a dataset.
 #'
-#' Get the ice mask for a dataset at a given timepoint.
+#' Get the ice mask for a dataset at a given time point.
 #'
 #' @param time_bp time slice in years before present (negative)
 #' @param dataset string defining dataset to be downloaded (a list of possible
diff --git a/R/get_land_mask.R b/R/get_land_mask.R
index e29b0e0f..440856b2 100644
--- a/R/get_land_mask.R
+++ b/R/get_land_mask.R
@@ -1,6 +1,6 @@
 #' Get the land mask for a dataset.
 #'
-#' Get the land mask for a dataset at a given timepoint.
+#' Get the land mask for a dataset at a given time point.
 #'
 #' @param time_bp time slice in years before present (negative)
 #' @param dataset string defining dataset to be downloaded (a list of possible
diff --git a/R/is_region_series.R b/R/is_region_series.R
index aab4ad81..b8dca74a 100644
--- a/R/is_region_series.R
+++ b/R/is_region_series.R
@@ -1,11 +1,11 @@
 #' Check the object is a valid region series
 #'
 #' A region series is a \code{terra::SpatRasterDataset} for which each
-#' subdataset is a variable, and all variables have the same number of 
+#' sub-dataset is a variable, and all variables have the same number of 
 #' time steps.
 #' 
 #' The standard test only checks that each SpatRaster has the same number of
-#' layers. The more thorough test (obtainedwith strict=TRUE) actually checks
+#' layers. The more thorough test (obtained with strict=TRUE) actually checks
 #' that all time steps are identical by comparing the result of 
 #' \code{terra::time} applied to each variable
 #'
diff --git a/R/location_series.R b/R/location_series.R
index a20fc540..cb43879e 100644
--- a/R/location_series.R
+++ b/R/location_series.R
@@ -22,7 +22,7 @@
 #' @param path_to_nc the path to the custom nc file containing the palaeoclimate
 #' reconstructions. All the variables of interest need to be included in
 #' this file.
-#' @returns a data.frame with teh climatic variables of interest
+#' @returns a data.frame with the climatic variables of interest
 #' @export
 
 location_series <-
@@ -111,7 +111,7 @@ location_series <-
 #' Deprecated version of \code{location_series}
 #'
 #' @param ... arguments to be passed to \code{series}
-#' @returns a data.frame with teh climatic variables of interest
+#' @returns a data.frame with the climatic variables of interest
 #'
 #' @export
 
diff --git a/R/location_slice.R b/R/location_slice.R
index 3b97d38a..0fdf1346 100644
--- a/R/location_slice.R
+++ b/R/location_slice.R
@@ -152,7 +152,7 @@ location_slice <-
 #' Deprecated version of \code{location_slice}
 #'
 #' @param ... arguments to be passed to \code{location_slice}
-#' @returns a data.frame with teh climatic variables of interest
+#' @returns a data.frame with the climatic variables of interest
 #'
 #' @export
 
diff --git a/R/sample_region_slice.R b/R/sample_region_slice.R
index 6f106155..6b0a36ae 100644
--- a/R/sample_region_slice.R
+++ b/R/sample_region_slice.R
@@ -1,6 +1,6 @@
 #' Sample points from a region time slice
 #'
-#' This function samples points from a region time slice (i.e. a timepoint).
+#' This function samples points from a region time slice (i.e. a time point).
 #' 
 #' This function wraps \code{terra::spatSample} to appropriate sample the
 #' \code{terra::SpatRaster} returned
diff --git a/man/climate_for_locations.Rd b/man/climate_for_locations.Rd
index 7fba68f6..e3648205 100644
--- a/man/climate_for_locations.Rd
+++ b/man/climate_for_locations.Rd
@@ -10,7 +10,7 @@ climate_for_locations(...)
 \item{...}{arguments to be passed to \code{location_slice}}
 }
 \value{
-a data.frame with teh climatic variables of interest
+a data.frame with the climatic variables of interest
 }
 \description{
 Deprecated version of \code{location_slice}
diff --git a/man/download_dataset.Rd b/man/download_dataset.Rd
index f78e6d5d..1c785ca9 100644
--- a/man/download_dataset.Rd
+++ b/man/download_dataset.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/download_dataset.R
 \name{download_dataset}
 \alias{download_dataset}
-\title{Download palaeoclimatereconstructions.}
+\title{Download palaeoclimate reconstructions.}
 \usage{
 download_dataset(dataset, bio_variables = NULL)
 }
diff --git a/man/get_data_path.Rd b/man/get_data_path.Rd
index 535ec4ae..b11e480e 100644
--- a/man/get_data_path.Rd
+++ b/man/get_data_path.Rd
@@ -19,7 +19,7 @@ This function returns the path where climate reconstructions are stored.
 \details{
 The path is stored in an option for `pastclim` named `data_path`. If
 a configuration file was saved when using \code{set_data_path}, the path
-is retrived from a file named "pastclim_data.txt", which
+is retrieved from a file named "pastclim_data.txt", which
 is found in the directory returned by 
 `tools::R_user_dir("pastclim","config")` (i.e.
 the default configuration directory for the package as set in R >= 4.0).
diff --git a/man/get_downloaded_datasets.Rd b/man/get_downloaded_datasets.Rd
index 560ae291..16b07540 100644
--- a/man/get_downloaded_datasets.Rd
+++ b/man/get_downloaded_datasets.Rd
@@ -7,7 +7,7 @@
 get_downloaded_datasets(data_path = NULL)
 }
 \arguments{
-\item{data_path}{leave it to NULL to use the default datapath}
+\item{data_path}{leave it to NULL to use the default data_path}
 }
 \value{
 a list of variable names per dataset.
diff --git a/man/get_ice_mask.Rd b/man/get_ice_mask.Rd
index 9a1acc29..e8806ebb 100644
--- a/man/get_ice_mask.Rd
+++ b/man/get_ice_mask.Rd
@@ -14,5 +14,5 @@ values can be obtained with \code{get_available_datasets}). This function
 will not work on custom datasets.}
 }
 \description{
-Get the ice mask for a dataset at a given timepoint.
+Get the ice mask for a dataset at a given time point.
 }
diff --git a/man/get_land_mask.Rd b/man/get_land_mask.Rd
index c12f2af1..01383f30 100644
--- a/man/get_land_mask.Rd
+++ b/man/get_land_mask.Rd
@@ -14,5 +14,5 @@ values can be obtained with \code{get_available_datasets}). This function
 will not work on custom datasets.}
 }
 \description{
-Get the land mask for a dataset at a given timepoint.
+Get the land mask for a dataset at a given time point.
 }
diff --git a/man/is_region_series.Rd b/man/is_region_series.Rd
index 0192b1c2..74a22a45 100644
--- a/man/is_region_series.Rd
+++ b/man/is_region_series.Rd
@@ -18,12 +18,12 @@ TRUE if the object is a region series
 }
 \description{
 A region series is a \code{terra::SpatRasterDataset} for which each
-subdataset is a variable, and all variables have the same number of 
+sub-dataset is a variable, and all variables have the same number of 
 time steps.
 }
 \details{
 The standard test only checks that each SpatRaster has the same number of
-layers. The more thorough test (obtainedwith strict=TRUE) actually checks
+layers. The more thorough test (obtained with strict=TRUE) actually checks
 that all time steps are identical by comparing the result of 
 \code{terra::time} applied to each variable
 }
diff --git a/man/location_series.Rd b/man/location_series.Rd
index 5921d947..bd7355a0 100644
--- a/man/location_series.Rd
+++ b/man/location_series.Rd
@@ -29,7 +29,7 @@ reconstructions. All the variables of interest need to be included in
 this file.}
 }
 \value{
-a data.frame with teh climatic variables of interest
+a data.frame with the climatic variables of interest
 }
 \description{
 This function extract a time series of local climate for
diff --git a/man/sample_region_slice.Rd b/man/sample_region_slice.Rd
index 657af855..c1f7715f 100644
--- a/man/sample_region_slice.Rd
+++ b/man/sample_region_slice.Rd
@@ -24,7 +24,7 @@ a data.frame with the sampled cells and their respective values for
 the climate variables.
 }
 \description{
-This function samples points from a region time slice (i.e. a timepoint).
+This function samples points from a region time slice (i.e. a time point).
 }
 \details{
 This function wraps \code{terra::spatSample} to appropriate sample the
diff --git a/man/time_series_for_locations.Rd b/man/time_series_for_locations.Rd
index 720b21e0..a612925d 100644
--- a/man/time_series_for_locations.Rd
+++ b/man/time_series_for_locations.Rd
@@ -10,7 +10,7 @@ time_series_for_locations(...)
 \item{...}{arguments to be passed to \code{series}}
 }
 \value{
-a data.frame with teh climatic variables of interest
+a data.frame with the climatic variables of interest
 }
 \description{
 Deprecated version of \code{location_series}
diff --git a/vignettes/a0_pastclim_overview.Rmd b/vignettes/a0_pastclim_overview.Rmd
index e322b807..9c265d94 100644
--- a/vignettes/a0_pastclim_overview.Rmd
+++ b/vignettes/a0_pastclim_overview.Rmd
@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 
 # Install the library
 
-You will need to install the library from Github. For this step, you will need to
+You will need to install the library from GitHub. For this step, you will need to
 use `devtools` (if you haven't done so already, install it from CRAN with `install.packages("devtools")`.
 Once you have `devtools`, simply use:
 ```{r install, eval=FALSE}
diff --git a/vignettes/a2_custom_datasets.Rmd b/vignettes/a2_custom_datasets.Rmd
index 7d8feee1..1a0afcdd 100644
--- a/vignettes/a2_custom_datasets.Rmd
+++ b/vignettes/a2_custom_datasets.Rmd
@@ -21,7 +21,7 @@ This guide is aimed at formatting data in such a way that they can be used with
 
 ## An example: the Trace21k-CHELSEA
 
-Here we provide a simple example of how to format such a dataset in R. We will use a version of the Trace21k dataset, downscaled to 30 arcsecs using the CHELSEA algorithm(available from [this website](https://chelsa-climate.org/chelsa-trace21k/)). The data are stored as geoTIFF files, one file per timestep per variable. First, we need to collate all the files for a given variable (we will use *bio01* as an example) within a single `netcdf` file. As the original files are large, we will illustrate here how do to that for only a few timesteps which were aggregated to 3x3 degrees to keep files sizes small.
+Here we provide a simple example of how to format such a dataset in R. We will use a version of the Trace21k dataset, downscaled to 30 arcsecs using the CHELSEA algorithm(available from [this website](https://chelsa-climate.org/chelsa-trace21k/)). The data are stored as geoTIFF files, one file per time step per variable. First, we need to collate all the files for a given variable (we will use *bio01* as an example) within a single `netcdf` file. As the original files are large, we will illustrate here how do to that for only a few time steps which were aggregated to 3x3 degrees to keep files sizes small.
 
 We start by translating each geoTIFF into a `netcdf` file. The files have the prefix *CHELSA_TraCE21k_bio01_-**xxx**_V1.0.small.tif*, where **xxx** is the number of the time step.
 We will only use 3 time step for illustrative purposes.
@@ -35,7 +35,7 @@ list_of_tiffs <- file.path(tiffs_path,dir(tiffs_path))
 bio01 <- terra::rast(list_of_tiffs)
 ```
 
-Now we need to set the time axis of the raster (in this case, reconstructions are every 100 years), and generate some userfriendly names to layers in the raster:
+Now we need to set the time axis of the raster (in this case, reconstructions are every 100 years), and generate some user friendly names to layers in the raster:
 
 ```{r}
 terra::time(bio01)<-c(0,-100,-200)
@@ -100,8 +100,8 @@ climate_100<-slice_region_series(custom_series, time_bp = -100)
 terra::plot(climate_100)
 ```
 
-Note that these reconstructions include the ocean and the icesheets, and it would
-be much better to remove them as they are not needed for most ecological/archaological studies (and
+Note that these reconstructions include the ocean and the ice sheets, and it would
+be much better to remove them as they are not needed for most ecological/archaeological studies (and
 it allows for smaller files).
 
 # Making the data available to others