Skip to content

Commit 0cfe91f

Browse files
itsrainingdataitsrainingdata
committed
Merge branch 'release_v0_0_2' into dev
2 parents 15833c6 + 2bad06b commit 0cfe91f

File tree

9 files changed

+139
-41
lines changed

9 files changed

+139
-41
lines changed

‎.Rbuildignore‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -4,3 +4,8 @@
44
^ccdrAlgorithm\.Rproj$
55
^\.Rproj\.user$
66
^\.travis\.yml$
7+
inst/db
8+
man-roxygen
9+
^\.httr-oauth$
10+
^revdep$
11+
^codecov\.yml$

‎DESCRIPTION‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
Package: ccdrAlgorithm
22
Title: CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks
3-
Version: 0.0.1
4-
Date: 2016-08-08
3+
Version: 0.0.2
4+
Date: 2016-11-19
55
Authors@R: c(
66
person("Bryon", "Aragam", email = "sparsebn@gmail.com", role = c("aut", "cre")),
77
person("Dacheng", "Zhang", role = c("aut"))
@@ -17,7 +17,6 @@ LinkingTo: Rcpp
1717
Suggests:
1818
testthat,
1919
graph
20-
Remotes: itsrainingdata/sparsebnUtils@dev
2120
URL: https://github.com/itsrainingdata/ccdrAlgorithm
2221
BugReports: https://github.com/itsrainingdata/ccdrAlgorithm/issues
2322
License: GPL (>= 2)

‎NEWS.md‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,10 @@
1+
# ccdrAlgorithm 0.0.2
2+
3+
## Features
4+
5+
* `ccdr.run()` is now compatible with interventional data
6+
7+
# ccdrAlgorithm 0.0.1
8+
9+
* Initial stable release
10+

‎R/s3-SparseBlockMatrixR.R‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -329,7 +329,7 @@ to_graphNEL.SparseBlockMatrixR <- function(x){
329329
} # END TO_GRAPHNEL.SPARSEBLOCKMATRIXR
330330

331331
get.adjacency.matrix.SparseBlockMatrixR <- function(x){
332-
sparsebnUtils::get.adjacency.matrix(as.edgeList(x))
332+
sparsebnUtils::get.adjacency.matrix(sparsebnUtils::as.edgeList(x))
333333
} # END GET.ADJACENCY.MATRIX.SPARSEBLOCKMATRIXR
334334

335335
num.nodes.SparseBlockMatrixR <- function(x){
@@ -339,7 +339,7 @@ num.nodes.SparseBlockMatrixR <- function(x){
339339

340340
num.edges.SparseBlockMatrixR <- function(x){
341341
### The number of nodes should be exactly the same as the length of the rows list
342-
sparsebnUtils::num.edges(as.edgeList(x))
342+
sparsebnUtils::num.edges(sparsebnUtils::as.edgeList(x))
343343
} # END NUM.EDGES.SPARSEBLOCKMATRIXR
344344

345345
# This function is (so far) only used in unit tests

‎cran-comments.md‎

Lines changed: 5 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -1,43 +1,15 @@
11
## Test environments
2-
* local OS X install, R 3.3.1
3-
* ubuntu 12.04 (travis-ci), R 3.2.4
2+
* local OS X install, R 3.3.2
3+
* ubuntu 12.04.5 (travis-ci), R 3.3.2 (oldrel, devel, and release)
44
* win-builder (devel and release)
55

66
## R CMD check results
7-
There were no ERRORs or WARNINGs.
8-
9-
There was 1 NOTE:
10-
11-
* checking CRAN incoming feasibility ... NOTE
12-
Maintainer: ‘Bryon Aragam <sparsebn@gmail.com>’
13-
14-
New submission
15-
16-
This is the first version of this package that has been submitted to CRAN.
7+
There were no ERRORs, WARNINGs, or NOTEs.
178

189
## Dependencies
1910

2011
CHECK has been run on all dependencies and passed.
2112

22-
## Re-submission note
23-
24-
- Pls explain CCDr, and provide a DOI for the reference.
25-
26-
Pls write these as
27-
28-
Authors (year) <DOI:.....>
29-
30-
(with no space after 'DOI:').
31-
32-
The description has been updated with a more detailed description of the CCDr algorithm, and the citation has been removed entirely.
33-
34-
- Again, we would prefer if you explained the acronym, and ideally
35-
provided a reference with a DOI. I see that this is
36-
37-
Concave penalized Coordinate Descent with reparametrization (CCDr)
38-
39-
and the reference has URL
40-
<http://www.jmlr.org/papers/v16/aragam15a.html>: if you cannot find a
41-
DOI, then pls use the URL.
13+
## Reverse dependencies
4214

43-
URL has been added (no DOI available) and acronym is now explained.
15+
* sparsebn: You will receive updates to this package that fixes these issues very soon from myself. This package depends on the current submission for basic functionality.

‎revdep/README.md‎

Lines changed: 56 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,56 @@
1+
# Setup
2+
3+
## Platform
4+
5+
|setting |value |
6+
|:--------|:----------------------------|
7+
|version |R version 3.3.2 (2016-10-31) |
8+
|system |x86_64, darwin13.4.0 |
9+
|ui |RStudio (1.0.44) |
10+
|language |(EN) |
11+
|collate |en_US.UTF-8 |
12+
|tz |America/New_York |
13+
|date |2016-11-19 |
14+
15+
## Packages
16+
17+
|package |* |version |date |source |
18+
|:-------------|:--|:-------|:----------|:---------------------------------------------|
19+
|ccdrAlgorithm |* |0.0.2 |2016-11-19 |local (itsrainingdata/ccdrAlgorithm@NA) |
20+
|Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) |
21+
|sparsebnUtils |* |0.0.2 |2016-11-19 |Github (itsrainingdata/sparsebnUtils@db676a0) |
22+
23+
# Check results
24+
1 packages
25+
26+
## sparsebn (0.0.1)
27+
Maintainer: Bryon Aragam <sparsebn@gmail.com>
28+
Bug reports: https://github.com/itsrainingdata/sparsebn/issues
29+
30+
0 errors | 1 warning | 0 notes
31+
32+
```
33+
checking re-building of vignette outputs ... WARNING
34+
Error in re-building vignettes:
35+
...
36+
Loading required package: sparsebnUtils
37+
Loading required package: ccdrAlgorithm
38+
Loading required package: discretecdAlgorithm
39+
40+
sparsebn v0.0.1, Copyright (c) 2016
41+
Bryon Aragam, University of California, Los Angeles
42+
Jiaying Gu, University of California, Los Angeles
43+
... 6 lines ...
44+
---> Bugs? Please report any bugs at https://github.com/itsrainingdata/sparsebn/issues.
45+
46+
A list of interventions was not specified: Assuming data is purely observational.
47+
Note: method with signature 'ddiMatrix#dMatrix' chosen for function '-',
48+
target signature 'ddiMatrix#dtCMatrix'.
49+
"diagonalMatrix#triangularMatrix" would also be valid
50+
A list of interventions was not specified: Assuming data is purely observational.
51+
Quitting from lines 144-153 (sparsebn-vignette.Rmd)
52+
Error: processing vignette 'sparsebn-vignette.Rmd' failed with diagnostics:
53+
could not find function "get.solution"
54+
Execution halted
55+
```
56+

‎revdep/checks.rds‎

1.13 KB
Binary file not shown.

‎revdep/problems.md‎

Lines changed: 56 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,56 @@
1+
# Setup
2+
3+
## Platform
4+
5+
|setting |value |
6+
|:--------|:----------------------------|
7+
|version |R version 3.3.2 (2016-10-31) |
8+
|system |x86_64, darwin13.4.0 |
9+
|ui |RStudio (1.0.44) |
10+
|language |(EN) |
11+
|collate |en_US.UTF-8 |
12+
|tz |America/New_York |
13+
|date |2016-11-19 |
14+
15+
## Packages
16+
17+
|package |* |version |date |source |
18+
|:-------------|:--|:-------|:----------|:---------------------------------------------|
19+
|ccdrAlgorithm |* |0.0.2 |2016-11-19 |local (itsrainingdata/ccdrAlgorithm@NA) |
20+
|Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) |
21+
|sparsebnUtils |* |0.0.2 |2016-11-19 |Github (itsrainingdata/sparsebnUtils@db676a0) |
22+
23+
# Check results
24+
1 packages with problems
25+
26+
## sparsebn (0.0.1)
27+
Maintainer: Bryon Aragam <sparsebn@gmail.com>
28+
Bug reports: https://github.com/itsrainingdata/sparsebn/issues
29+
30+
0 errors | 1 warning | 0 notes
31+
32+
```
33+
checking re-building of vignette outputs ... WARNING
34+
Error in re-building vignettes:
35+
...
36+
Loading required package: sparsebnUtils
37+
Loading required package: ccdrAlgorithm
38+
Loading required package: discretecdAlgorithm
39+
40+
sparsebn v0.0.1, Copyright (c) 2016
41+
Bryon Aragam, University of California, Los Angeles
42+
Jiaying Gu, University of California, Los Angeles
43+
... 6 lines ...
44+
---> Bugs? Please report any bugs at https://github.com/itsrainingdata/sparsebn/issues.
45+
46+
A list of interventions was not specified: Assuming data is purely observational.
47+
Note: method with signature 'ddiMatrix#dMatrix' chosen for function '-',
48+
target signature 'ddiMatrix#dtCMatrix'.
49+
"diagonalMatrix#triangularMatrix" would also be valid
50+
A list of interventions was not specified: Assuming data is purely observational.
51+
Quitting from lines 144-153 (sparsebn-vignette.Rmd)
52+
Error: processing vignette 'sparsebn-vignette.Rmd' failed with diagnostics:
53+
could not find function "get.solution"
54+
Execution halted
55+
```
56+

‎tests/testthat/test-s3_as.R‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -101,13 +101,13 @@ test_that("as.SparseBlockMatrixR -> as.edgeList -> as.matrix makes no changes",
101101
m <- matrix(rep(0, 1), ncol = 1)
102102
sbm <- suppressWarnings(as.SparseBlockMatrixR(m))
103103
m.sbm <- as.matrix(sbm)
104-
m.edgeL <- as.matrix(as.edgeList(sbm))
104+
m.edgeL <- as.matrix(sparsebnUtils::as.edgeList(sbm))
105105
expect_that(m.edgeL, is_equivalent_to(m.sbm))
106106

107107
m <- matrix(rep(0, 4), ncol = 2)
108108
sbm <- suppressWarnings(as.SparseBlockMatrixR(m))
109109
m.sbm <- as.matrix(sbm)
110-
m.edgeL <- as.matrix(as.edgeList(sbm))
110+
m.edgeL <- as.matrix(sparsebnUtils::as.edgeList(sbm))
111111
expect_that(m.edgeL, is_equivalent_to(m.sbm))
112112

113113
### NOTE: Cannot test on random sparse matrix since SBM class ASSUMES a block structure,
@@ -117,7 +117,7 @@ test_that("as.SparseBlockMatrixR -> as.edgeList -> as.matrix makes no changes",
117117
m <- random.dag.matrix(10, 10)
118118
sbm <- suppressWarnings(as.SparseBlockMatrixR(m))
119119
m.sbm <- as.matrix(sbm)
120-
m.edgeL <- as.matrix(as.edgeList(sbm))
120+
m.edgeL <- as.matrix(sparsebnUtils::as.edgeList(sbm))
121121

122122
m.sbm[m.sbm != 0] <- 1 # coerce to unweighted adjacencies
123123
expect_that(m.edgeL, is_equivalent_to(m.sbm))

0 commit comments

Comments
 (0)