Browse code

docs rebuild

Türei Dénes authored on 11/04/2021 00:02:55
Showing1 changed files
... ...
@@ -35,7 +35,7 @@ Filters the versions based on multiple conditions: their age and status
35 35
 # creating an example cache record
36 36
 bioc_url <- 'https://bioconductor.org/'
37 37
 version <- omnipath_cache_latest_or_new(url = bioc_url)
38
-download.file(bioc_url, destfile = version$path)
38
+httr::GET(bioc_url, httr::write_disk(version$path, overwrite = TRUE))
39 39
 omnipath_cache_download_ready(version)
40 40
 record <- dplyr::first(omnipath_cache_search('biocond'))
41 41
 
Browse code

`post_translational_interactions`: possible to provide `datasets`, not only `exclude`

Türei Dénes authored on 02/04/2021 22:00:20
Showing1 changed files
... ...
@@ -26,7 +26,7 @@ versions with `ready` (completed download) status are selected}
26 26
 }
27 27
 \value{
28 28
 Character vector with version IDs, NA if no version satisfies the
29
-    conditions
29
+    conditions.
30 30
 }
31 31
 \description{
32 32
 Filters the versions based on multiple conditions: their age and status
Browse code

avoid name collisions between col names and imported package functions

Türei Dénes authored on 11/03/2021 02:06:48
Showing1 changed files
... ...
@@ -40,7 +40,7 @@ omnipath_cache_download_ready(version)
40 40
 record <- dplyr::first(omnipath_cache_search('biocond'))
41 41
 
42 42
 # only the versions with status "ready"
43
-version_numbers <- omnipath_cache_filter_versions(status = 'ready')
43
+version_numbers <- omnipath_cache_filter_versions(record, status = 'ready')
44 44
 omnipath_cache_remove(url = bioc_url) # cleaning up
45 45
 
46 46
 }
Browse code

runnable examples whereever it's possible

Türei Dénes authored on 10/03/2021 23:06:36
Showing1 changed files
... ...
@@ -32,10 +32,15 @@ Character vector with version IDs, NA if no version satisfies the
32 32
 Filters the versions based on multiple conditions: their age and status
33 33
 }
34 34
 \examples{
35
-\donttest{
35
+# creating an example cache record
36
+bioc_url <- 'https://bioconductor.org/'
37
+version <- omnipath_cache_latest_or_new(url = bioc_url)
38
+download.file(bioc_url, destfile = version$path)
39
+omnipath_cache_download_ready(version)
36 40
 record <- dplyr::first(omnipath_cache_search('biocond'))
41
+
37 42
 # only the versions with status "ready"
38 43
 version_numbers <- omnipath_cache_filter_versions(status = 'ready')
39
-}
44
+omnipath_cache_remove(url = bioc_url) # cleaning up
40 45
 
41 46
 }
Browse code

docs: added all missing return values

Türei Dénes authored on 10/03/2021 18:45:04
Showing1 changed files
... ...
@@ -26,7 +26,7 @@ versions with `ready` (completed download) status are selected}
26 26
 }
27 27
 \value{
28 28
 Character vector with version IDs, NA if no version satisfies the
29
-conditions
29
+    conditions
30 30
 }
31 31
 \description{
32 32
 Filters the versions based on multiple conditions: their age and status
Browse code

regenerated website (not sure if successful)

Türei Dénes authored on 10/03/2021 17:50:07
Showing1 changed files
... ...
@@ -33,7 +33,7 @@ Filters the versions based on multiple conditions: their age and status
33 33
 }
34 34
 \examples{
35 35
 \donttest{
36
-record <- omnipath_cache_search('biocond') \%>\% dplyr::first
36
+record <- dplyr::first(omnipath_cache_search('biocond'))
37 37
 # only the versions with status "ready"
38 38
 version_numbers <- omnipath_cache_filter_versions(status = 'ready')
39 39
 }
Browse code

added new man pages

Türei Dénes authored on 10/03/2021 14:32:26
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,41 @@
1
+% Generated by roxygen2: do not edit by hand
2
+% Please edit documentation in R/cache.R
3
+\name{omnipath_cache_filter_versions}
4
+\alias{omnipath_cache_filter_versions}
5
+\title{Filters the versions from one cache record}
6
+\usage{
7
+omnipath_cache_filter_versions(
8
+  record,
9
+  latest = FALSE,
10
+  max_age = NULL,
11
+  min_age = NULL,
12
+  status = CACHE_STATUS$READY
13
+)
14
+}
15
+\arguments{
16
+\item{record}{A cache record}
17
+
18
+\item{latest}{Return the most recent version}
19
+
20
+\item{max_age}{The maximum age in days (e.g. 5: 5 days old or more recent)}
21
+
22
+\item{min_age}{The minimum age in days (e.g. 5: 5 days old or older)}
23
+
24
+\item{status}{Character vector with status codes. By default only the
25
+versions with `ready` (completed download) status are selected}
26
+}
27
+\value{
28
+Character vector with version IDs, NA if no version satisfies the
29
+conditions
30
+}
31
+\description{
32
+Filters the versions based on multiple conditions: their age and status
33
+}
34
+\examples{
35
+\donttest{
36
+record <- omnipath_cache_search('biocond') \%>\% dplyr::first
37
+# only the versions with status "ready"
38
+version_numbers <- omnipath_cache_filter_versions(status = 'ready')
39
+}
40
+
41
+}