typos small fixes

.Rbuildignore

@@ -1,6 +1,6 @@
 ^renv$
 ^renv\.lock$
-^rirods2\.Rproj$
+^rirods\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^data-raw$
@@ -10,3 +10,4 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^\.covrignore$

README.Rmd

@@ -60,7 +60,7 @@ rirods:::iadmin(action = "add", target = "user", arg2 = "bobby", arg3 = "rodsuse
 rirods:::iadmin(action = "modify", target = "user", arg2 = "bobby", arg3 = "password", arg4  = "passWORD")
 ```
 
-Then to connect a project from R with the iRODS server you have to provide the host name of the server, like so:
+Provide the host name of the server to connect an R project with an iRODS server, like so:
 
 ```{r start, eval=FALSE}
 library(rirods)
@@ -82,7 +82,7 @@ iauth()
 iauth("bobby", "passWORD")
 ```
 
-Suppose Bobby would like to upload an R object from his current R session to an iRODS collection. For this, use the iput command:
+Suppose Bobby would like to upload an R object from his current R session to an iRODS collection. For this, use the `iput()` command:
 
 ```{r put}
 # some data
@@ -93,7 +93,11 @@ ipwd()
 
 # store
 iput(foo)
+```
+
+To truly appreciate the strength of iRODS, we can add some metadata that describes the data object "foo". 
 
+```{r meta}
 # add some metadata
 imeta(
   "foo", 
@@ -106,8 +110,7 @@ imeta(
 ils(metadata = TRUE)
 ```
 
-If Bobby wanted to copy the foo R object from an iRODS collection to his local directory, he would use
-iget:
+If Bobby wanted to copy the foo R object from an iRODS collection to his local directory, he would use `iget()`:
 
 ```{r get}
 # retrieve in native R format
@@ -141,7 +144,7 @@ iget("foo.csv")
 read_csv("foo.csv")
 ```
 
-Objects can also be discovered by using General Queries and `iquery()`:
+By adding metadata you and others can more easily discover data in future projects. Objects can be searched with General Queries and `iquery()`:
 
 ```{r query, options}
 # look for objects in the home directory with a wildcard `%`
@@ -186,8 +189,3 @@ ils()
 file.remove("rirods.irods")
 ```
 
-## Stop your local iRODS server
-
-```{bash, eval=FALSE}
-docker-compose down
-```

README.md

@@ -38,8 +38,8 @@ cd ../irods_demo
 docker-compose up
 ```
 
-Then to connect a project from R with the iRODS server you have to
-provide the host name of the server, like so:
+Provide the host name of the server to connect an R project with an
+iRODS server, like so:
 
 ``` r
 library(rirods)
@@ -58,7 +58,7 @@ iauth()
 ```
 
 Suppose Bobby would like to upload an R object from his current R
-session to an iRODS collection. For this, use the iput command:
+session to an iRODS collection. For this, use the `iput()` command:
 
 ``` r
 # some data
@@ -70,7 +70,12 @@ ipwd()
 
 # store
 iput(foo)
+```
+
+To truly appreciate the strength of iRODS, we can add some metadata that
+describes the data object “foo”.
 
+``` r
 # add some metadata
 imeta(
   "foo", 
@@ -81,12 +86,13 @@ imeta(
 
 # check if file is stored with associated metadata
 ils(metadata = TRUE)
-#>               logical_path      metadata        type
-#> 1 /tempZone/home/bobby/foo foo, bar, baz data_object
+#>                logical_path      metadata        type
+#> 1  /tempZone/home/bobby/foo foo, baz, bar data_object
+#> 2 /tempZone/home/bobby/test          NULL data_object
 ```
 
 If Bobby wanted to copy the foo R object from an iRODS collection to his
-local directory, he would use iget:
+local directory, he would use `iget()`:
 
 ``` r
 # retrieve in native R format
@@ -114,6 +120,7 @@ ils()
 #>                   logical_path        type
 #> 1     /tempZone/home/bobby/foo data_object
 #> 2 /tempZone/home/bobby/foo.csv data_object
+#> 3    /tempZone/home/bobby/test data_object
 ```
 
 Later on somebody else might want to download this file again and store
@@ -139,28 +146,33 @@ read_csv("foo.csv")
 #> 3     9 z
 ```
 
-Objects can also be discovered by using General Queries and `iquery()`:
+By adding metadata you and others can more easily discover data in
+future projects. Objects can be searched with General Queries and
+`iquery()`:
 
 ``` r
 # look for objects in the home directory with a wildcard `%`
 iquery("SELECT COLL_NAME, DATA_NAME WHERE COLL_NAME LIKE '/tempZone/home/%'")
 #>             collection data_object
 #> 1 /tempZone/home/bobby         foo
 #> 2 /tempZone/home/bobby     foo.csv
+#> 3 /tempZone/home/bobby        test
 ```
 
 ``` r
 # or where data objects named "foo" can be found
 iquery("SELECT COLL_NAME, DATA_NAME WHERE DATA_NAME LIKE 'foo%'")
-#>                   collection        data_object
-#> 1       /tempZone/home/bobby                foo
-#> 2       /tempZone/home/bobby            foo.csv
-#> 3 /tempZone/trash/home/bobby                foo
-#> 4 /tempZone/trash/home/bobby     foo.1682976494
-#> 5 /tempZone/trash/home/bobby       foo.35790442
-#> 6 /tempZone/trash/home/bobby            foo.csv
-#> 7 /tempZone/trash/home/bobby foo.csv.1247785700
-#> 8 /tempZone/trash/home/bobby   foo.csv.66409892
+#>                    collection        data_object
+#> 1        /tempZone/home/bobby                foo
+#> 2        /tempZone/home/bobby            foo.csv
+#> 3  /tempZone/trash/home/bobby                foo
+#> 4  /tempZone/trash/home/bobby     foo.1576729182
+#> 5  /tempZone/trash/home/bobby     foo.2405108537
+#> 6  /tempZone/trash/home/bobby     foo.2435297455
+#> 7  /tempZone/trash/home/bobby            foo.csv
+#> 8  /tempZone/trash/home/bobby foo.csv.1036575935
+#> 9  /tempZone/trash/home/bobby foo.csv.2236717404
+#> 10 /tempZone/trash/home/bobby foo.csv.4082161960
 ```
 
 Finally, we can clean up Bobby’s home directory:
@@ -172,13 +184,8 @@ irm("foo.csv", trash = FALSE)
 
 # check if object is removed
 ils()
-#> This collection does not contain any objects or collections.
+#>                logical_path        type
+#> 1 /tempZone/home/bobby/test data_object
 ```
 
 <!-- The user Bobby can also be removed again. -->
-
-## Stop your local iRODS server
-
-``` bash
-docker-compose down
-```

inst/WORDLIST

@@ -1,3 +1,4 @@
+CMD
 Codecov
 GeneralQuery
 IRODS
@@ -11,11 +12,8 @@ http
 https
 iCAT
 iRODS
-iget
-iput
 irods
 rebalance
-rirods
 specificQuery
 tibble
 unusedAVUs