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R/flywire_googledrive.R

@@ -528,14 +528,14 @@ flywire_ids <-function(local = FALSE, folder = "flywire_neurons/", sql = FALSE,
 
 #' Update the flywire.id column in a set of google sheets based on flywire xyz positions
 #'
-#' @description This function retreives flywire IDs based on xyz positions in flywire voxel space, from a set of google sheets.
+#' @description This function retrieves flywire IDs based on xyz positions in flywire voxel space, from a set of google sheets.
 #' It also writes the updated flywire IDs to the same google sheets. This is often helpful because flywire IDs are inherently unstable, they change every time
 #' a neuron is modified even slightly. Users can record 'stable' points in a neuron that identify it, e.g. a single xyz position in the cell body fibre, or at the soma, and
 #' then use this function to update and get the correct flywire ID whenever they wish.
 #'
 #' @param selected_sheets character vector. the google sheet(s) to update. Each entry is a unique google sheet ID. You can find these in a sheet's URL.
 #' If \code{NULL} then defaults to \code{option('hemibrainr_gsheets')}.
-#' @param chosen.columns as well as writing column updates to the specified google sheets, this function returns a \code{data.frame} built fromm all given sheets and their
+#' @param chosen.columns as well as writing column updates to the specified google sheets, this function returns a \code{data.frame} built from all given sheets and their
 #' individual tabs, that have been updated. This argument specifies which column you want returned. Filled with NAs if it does not exist.
 #' @param numCores if run in parallel, the number of cores to use. This is not necessary unless you have >10k points and want to see if you can get a speed up.
 #' @param max.tries maximum number of attempts to write to/read from the google sheets before aborting. Sometimes attempts fail due to sporadic connections or API issues.
@@ -713,7 +713,7 @@ flywire_ids_update <- function(selected_sheets = NULL,
 
 #' Update neuron match information on a google sheet
 #'
-#' @description This function retreives neuron matches (\code{\link{hemibrain_matches}}) from a master-matching google sheet. If then
+#' @description This function retrieves neuron matches (\code{\link{hemibrain_matches}}) from a master-matching google sheet. If then
 #' can update other google sheets, specified by the user to update neuron-match information.
 #' Just columns giving the match, match quality and cell type are updated.
 #'
@@ -728,7 +728,7 @@ flywire_ids_update <- function(selected_sheets = NULL,
 #' @param match.field which match to record. E.g. if \code{id} is \code{"flywire.id"} you may want to add the hemibrain match from the master matching sheets. To do this
 #' set \code{match.field} to \code{"hemibrain"}. Then, if there is a \code{"hemibrain.match"} and/or \code{"hemibrain.match.quality"} column, it will be updated. You
 #' may also want to know the hemispheric match within FAFB, in which case \code{"FAFB.hemisphere"} could be used.
-#' @param chosen.columns as well as writing column updates to the specified google sheets, this function returns a \code{data.frame} built fromm all given sheets and their
+#' @param chosen.columns as well as writing column updates to the specified google sheets, this function returns a \code{data.frame} built from all given sheets and their
 #' individual tabs, that have been updated. This argument specifies which column you want returned. Filled with NAs if it does not exist.
 #'
 #' @details For this function to work, the specified google sheet(s) must have either the column specified with the argument \code{id},

R/hemibrain_data.R

@@ -117,15 +117,15 @@
 #'  axis aligned with the Y axis (rather than the Z axis, which is more commonly
 #'  observed).
 #'
-#'  These meshes were generated by Sri Jagannathan and Tomke Stuermer based on
+#'  These meshes were generated by Sri Jagannathan and Tomke Stuerner based on
 #'  the location of PN dendritic synapses.
 #'
 #'@return \code{hemibrain_glomeruli_summary} is a \code{data.frame} with the
 #'  columns:
 #'
 #'  \itemize{
 #'
-#'  \item{"excpected_cit"}{a citation that describes this glomerulus},
+#'  \item{"expected_cit"}{a citation that describes this glomerulus},
 #'
 #'  \item{"expected_RN_female_1h"}{.}
 #'
@@ -326,7 +326,7 @@
 #' if they have an authenticated email.
 #'
 #' @return a \code{data.frame} where each row is a neuron, either from the hemibrain or FAFB data sets. Each row gives you its matching neuron in the other data set. These matches have been
-#' manually assigned using \code{\link{fafb_matching}}, \code{\link{hemibrain_matching}} and \code{\link{LR_matching}}. If you use this information make sure you credit it appriopriately.
+#' manually assigned using \code{\link{fafb_matching}}, \code{\link{hemibrain_matching}} and \code{\link{LR_matching}}. If you use this information make sure you credit it appropriately.
 #' Contact us if unsure:
 #' \itemize{
 #'
@@ -340,7 +340,7 @@
 #'
 #'   \item{"match"}{ - the ID of the manual match from the other data set. If \code{dataset=="hemibrain"} then this is a \code{flywire.id} that can be found in \code{flywire_neurons}.If \code{"CATMAID"} or \code{"flywire"} then it is a hemibrain body ID.}
 #'
-#'   \item{"quality"}{ - the matcher makers qualitative assement of how good this match is.}
+#'   \item{"quality"}{ - the matcher makers qualitative assessment of how good this match is.}
 #'
 #'   \item{"FAFB.hemisphere.match"}{ - the flywire coordinates of a neuron on the opposite hemisphere, which a match maker has designated as this \code{id}'s cognate.}
 #'
@@ -406,7 +406,7 @@
 #'
 #'   \item{"FAFB.match"}{ - the ID of the manual match from the FAFB data set. ID indicates a neuron reconstructed in FAFBv14 CATMAID. Many of these neurons will be available through Virtual Fly Brain.}
 #'
-#'   \item{"FAFB.match.quality"}{ - the matcher makers qualitative assement of how good this match is: a poor match could be a neuron from a very similar same cell type or a highly untraced neuron that may be the correct cell type. An okay match should be a neuron that looks to be from the same morphological cell type but there may be some discrepancies in its arbour. A good match is a
+#'   \item{"FAFB.match.quality"}{ - the matcher makers qualitative assessment of how good this match is: a poor match could be a neuron from a very similar same cell type or a highly untraced neuron that may be the correct cell type. An okay match should be a neuron that looks to be from the same morphological cell type but there may be some discrepancies in its arbour. A good match is a
 #'   neuron that corresponds well between FAFB and the hemibrain data.}
 #'
 #'   \item{"layer"}{ - probabilistic mean path length from neuron from ALRNs, depends on connection strengths.}
@@ -434,7 +434,7 @@
 #'
 #'   \item{"notes"}{- other notes from annotators.}
 #'
-#'   \item{"excpected_cit"}{a citation that describes this glomerulus},
+#'   \item{"expected_cit"}{a citation that describes this glomerulus},
 #'
 #'   \item{"expected_RN_female_1h"}{.}
 #'

R/hemibrain_matching.R

@@ -724,7 +724,7 @@ fafb_matching <- function(ids = NULL,
 #'   to neurons of your choosing on the rightmost column 'Users'.
 #'
 #' @return a \code{data.frame} where each row is a neuron, either from the hemibrain or FAFB data sets. Each row gives you its matching neuron in the other data set. These matches have been
-#' manually assigned using \code{\link{fafb_matching}}, \code{\link{hemibrain_matching}} and \code{\link{LR_matching}}. If you use this information make sure you credit it appriopriately.
+#' manually assigned using \code{\link{fafb_matching}}, \code{\link{hemibrain_matching}} and \code{\link{LR_matching}}. If you use this information make sure you credit it appropriately.
 #' Contact us if unsure:
 #' \itemize{
 #'
@@ -738,7 +738,7 @@ fafb_matching <- function(ids = NULL,
 #'
 #'   \item{"match"}{ - the ID of the manual match from the other data set. If \code{dataset=="hemibrain"} then this is a \code{flywire.id} that can be found in \code{flywire_neurons}.If \code{"CATMAID"} or \code{"flywire"} then it is a hemibrain body ID.}
 #'
-#'   \item{"quality"}{ - the matcher makers qualitative assement of how good this match is.}
+#'   \item{"quality"}{ - the matcher makers qualitative assessment of how good this match is.}
 #'
 #'   \item{"FAFB.hemisphere.match"}{ - the flywire coordinates of a neuron on the opposite hemisphere, which a match maker has designated as this \code{id}'s cognate.}
 #'

R/hemibrain_meta.R

@@ -51,7 +51,7 @@
 #'
 #'   \item{"FAFB.match"}{ - the ID of the manual match from the FAFB data set. ID indicates a neuron reconstructed in FAFBv14 CATMAID. Many of these neurons will be available through Virtual Fly Brain.}
 #'
-#'   \item{"FAFB.match.quality"}{ - the matcher makers qualitative assement of how good this match is: a poor match could be a neuron from a very similar same cell type or a highly untraced neuron that may be the correct cell type. An okay match should be a neuron that looks to be from the same morphological cell type but there may be some discrepancies in its arbour. A good match is a
+#'   \item{"FAFB.match.quality"}{ - the matcher makers qualitative assessment of how good this match is: a poor match could be a neuron from a very similar same cell type or a highly untraced neuron that may be the correct cell type. An okay match should be a neuron that looks to be from the same morphological cell type but there may be some discrepancies in its arbour. A good match is a
 #'   neuron that corresponds well between FAFB and the hemibrain data.}
 #'
 #'   \item{"layer"}{ - probabilistic mean path length from neuron from ALRNs, depends on connection strengths.}

README.Rmd

@@ -144,7 +144,7 @@ hemibrainr_set_drive("hemibrainr") # No need to run this each time though, this
 hemibrainr_team_drive()
 ```
 
-Option 2, this is free. You still need authenticated access to the hemibrainr Gogle team drive. It cna then be moutned using [rclone](https://rclone.org/). 
+Option 2, this is free. You still need authenticated access to the hemibrainr Gogle team drive. It can then be mounted using [rclone](https://rclone.org/). 
 First, [download](https://rclone.org/downloads/) rclone for your operating system. You can also download from your system's command line (e.g. from terminal) and then configure it for the drive:
 
 ```{r rclone_download, engine = 'bash', eval = FALSE}

README.md

@@ -3,9 +3,9 @@
 
 <img src="man/figures/logo.svg" align="right" height="139" /> [![Travis
 build
-status](https://travis-ci.org/flyconnectome/hemibrainr.svg?branch=master)](https://travis-ci.org/flyconnectome/hemibrainr)
+status](https://travis-ci.org/natverse/hemibrainr.svg?branch=master)](https://travis-ci.org/natverse/hemibrainr)
 [![Codecov test
-coverage](https://codecov.io/gh/flyconnectome/hemibrainr/branch/master/graph/badge.svg)](https://codecov.io/gh/flyconnectome/hemibrainr?branch=master)
+coverage](https://codecov.io/gh/natverse/hemibrainr/branch/master/graph/badge.svg)](https://codecov.io/gh/natverse/hemibrainr?branch=master)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
 <!-- badges: end -->
@@ -32,7 +32,7 @@ below. It is \~21,662 \~full neurons, 9.5 million synapses and is about
 
 <center>
 
-![hemibrain](https://raw.githubusercontent.com/flyconnectome/hemibrainr/master/inst/images/hemibrain.png)
+![hemibrain](https://raw.githubusercontent.com/natverse/hemibrainr/master/inst/images/hemibrain.png)
 
 </center>
 
@@ -44,7 +44,7 @@ Get started with hemibrainr
 ``` r
 # install
 if (!require("remotes")) install.packages("remotes")
-remotes::install_github("flyconnectome/hemibrainr")
+remotes::install_github("natverse/hemibrainr")
 
 # use 
 library(hemibrainr)
@@ -166,7 +166,7 @@ application is run, you should be able to see your drives mounted like
 external hard drive, as so:
 
 <center>
-![google_filestream](https://raw.githubusercontent.com/flyconnectome/hemibrainr/master/inst/images/google_filestream.png "fig:")
+![google_filestream](https://raw.githubusercontent.com/natverse/hemibrainr/master/inst/images/google_filestream.png "fig:")
 </center>
 
 Then, this should work:
@@ -181,7 +181,7 @@ hemibrainr_team_drive()
 ```
 
 Option 2, this is free. You still need authenticated access to the
-hemibrainr Gogle team drive. It cna then be moutned using
+hemibrainr Gogle team drive. It can then be mounted using
 [rclone](https://rclone.org/). First,
 [download](https://rclone.org/downloads/) rclone for your operating
 system. You can also download from your system’s command line (e.g. from
@@ -215,7 +215,7 @@ options("Gdrive_hemibrain_data")
 ```
 
 For more detailed instructions, see [this
-article](https://flyconnectome.github.io/hemibrainr/articles/google_filestream.html).
+article](https://natverse.github.io/hemibrainr/articles/google_filestream.html).
 
 ### Example: ‘splitting’ neurons
 
@@ -284,4 +284,4 @@ citation(package = "hemibrainr")
 
 **Bates AS, Jefferis GSXE** (2020). *hemibrainr: Code for working with
 data from Janelia FlyEM’s hemibrain project.* **R package** version
-0.1.0. <https://github.com/flyconnectome/hemibrainr>
+0.1.0. <https://github.com/natverse/hemibrainr>