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Merge branch 'release-v0_0_3' into dev
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‎R/ccdrAlgorithm-main.R‎

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#'
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#' @examples
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#'
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#' \dontrun{
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#'
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#' ### Generate some random data
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#' dat <- matrix(rnorm(1000), nrow = 20)
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#' dat <- sparsebnData(dat, type = "continuous")
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#' dat <- sparsebnUtils::sparsebnData(dat, type = "continuous")
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#'
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#' # Run with default settings
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#' ccdr.run(data = dat)
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#' ccdr.run(data = dat, lambdas.length = 20)
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#'
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#' ### Optional: Adjust settings
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#' pp <- ncol(dat)
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#' pp <- ncol(dat$data)
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#'
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#' # Initialize algorithm with a random initial value
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#' init.betas <- matrix(0, nrow = pp, ncol = pp)
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#' init.betas[1,2] <- init.betas[1,3] <- init.betas[4,2] <- 1
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#'
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#' # Run with adjusted settings
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#' ccdr.run(data = dat, betas = init.betas, lambdas.length = 10, alpha = 10, verbose = TRUE)
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#' }
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#' ccdr.run(data = dat, betas = init.betas, lambdas.length = 20, alpha = 10, verbose = TRUE)
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#'
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#' @export
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ccdr.run <- function(data,
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# Still need to set start = 0, though.
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betas$start <- 0
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} # Type-checking for betas happens in ccdr_singleR
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# This parameter can be set by the user, but in order to prevent the algorithm from taking too long to run
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# it is a good idea to keep the threshold used by default which is O(sqrt(pp))
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if(is.null(max.iters)){

‎R/ccdrAlgorithm-mvn.R‎

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#' @param ivn List of interventions (see \code{\link[sparsebnUtils]{sparsebnData}}). Must be a \code{list} with exactly \code{n} components.
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#' @param ivn.rand If \code{TRUE}, random N(0,1) values will be drawn for each intervention. Otherwise, these values need to supplied manually in \code{ivn}.
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#'
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#' @examples
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#'
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#' ### Generate observational data
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#' gr <- sparsebnUtils::random.graph(5, 5) # use sparsebnUtils package to generate a random graph
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#' gr.params <- runif(10) # there are 5 coefficients + 5 variances
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#' data.obs <- ccdrAlgorithm::generate_mvn_data(graph = gr,
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#' n = 100,
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#' params = gr.params)
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#'
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#' ### Generate experimental data
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#' ivn <- as.list(c(rep("V1", 50), rep("V2", 50))) # 50 interventions on V1, 50 interventions on V2
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#' data.ivn <- ccdrAlgorithm::generate_mvn_data(graph = gr,
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#' n = 100,
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#' params = gr.params,
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#' ivn = ivn)
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#'
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#' @export
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generate_mvn_data <- function(graph, params, n = 1, ivn = NULL, ivn.rand = TRUE){
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‎man/ccdr.run.Rd‎

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‎man/generate_mvn_data.Rd‎

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‎revdep/README.md‎

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|setting |value |
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|:--------|:----------------------------|
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|version |R version 3.3.2 (2016-10-31) |
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|version |R version 3.3.3 (2017-03-06) |
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|system |x86_64, darwin13.4.0 |
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|ui |RStudio (1.0.44) |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|tz |America/New_York |
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|date |2016-11-19 |
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|date |2017-03-09 |
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## Packages
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|package |* |version |date |source |
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|:-------------|:--|:-------|:----------|:---------------------------------------------|
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|ccdrAlgorithm |* |0.0.2 |2016-11-19 |local (itsrainingdata/ccdrAlgorithm@NA) |
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|Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) |
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|sparsebnUtils |* |0.0.2 |2016-11-19 |Github (itsrainingdata/sparsebnUtils@db676a0) |
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|package |* |version |date |source |
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|:-------------|:--|:-------|:----------|:---------------------------------------|
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|ccdrAlgorithm | |0.0.3 |2017-03-09 |local (itsrainingdata/ccdrAlgorithm@NA) |
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# Check results
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1 packages
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## sparsebn (0.0.1)
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## sparsebn (0.0.2)
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Maintainer: Bryon Aragam <sparsebn@gmail.com>
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Bug reports: https://github.com/itsrainingdata/sparsebn/issues
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0 errors | 1 warning | 0 notes
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```
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checking re-building of vignette outputs ... WARNING
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Error in re-building vignettes:
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...
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Loading required package: sparsebnUtils
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Loading required package: ccdrAlgorithm
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Loading required package: discretecdAlgorithm
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sparsebn v0.0.1, Copyright (c) 2016
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Bryon Aragam, University of California, Los Angeles
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Jiaying Gu, University of California, Los Angeles
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... 6 lines ...
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---> Bugs? Please report any bugs at https://github.com/itsrainingdata/sparsebn/issues.
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A list of interventions was not specified: Assuming data is purely observational.
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Note: method with signature 'ddiMatrix#dMatrix' chosen for function '-',
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target signature 'ddiMatrix#dtCMatrix'.
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"diagonalMatrix#triangularMatrix" would also be valid
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A list of interventions was not specified: Assuming data is purely observational.
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Quitting from lines 144-153 (sparsebn-vignette.Rmd)
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Error: processing vignette 'sparsebn-vignette.Rmd' failed with diagnostics:
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could not find function "get.solution"
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Execution halted
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checking Rd cross-references ... WARNING
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Missing link or links in documentation object 'estimate.dag.Rd':
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‘[discretecdAlgorithm]{cd.run}’
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See section 'Cross-references' in the 'Writing R Extensions' manual.
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```
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‎revdep/checks.rds‎

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‎revdep/problems.md‎

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|setting |value |
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|:--------|:----------------------------|
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|version |R version 3.3.2 (2016-10-31) |
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|version |R version 3.3.3 (2017-03-06) |
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|system |x86_64, darwin13.4.0 |
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|ui |RStudio (1.0.44) |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|tz |America/New_York |
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|date |2016-11-19 |
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|date |2017-03-09 |
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## Packages
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|package |* |version |date |source |
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|:-------------|:--|:-------|:----------|:---------------------------------------------|
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|ccdrAlgorithm |* |0.0.2 |2016-11-19 |local (itsrainingdata/ccdrAlgorithm@NA) |
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|Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) |
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|sparsebnUtils |* |0.0.2 |2016-11-19 |Github (itsrainingdata/sparsebnUtils@db676a0) |
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|package |* |version |date |source |
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|:-------------|:--|:-------|:----------|:---------------------------------------|
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|ccdrAlgorithm | |0.0.3 |2017-03-09 |local (itsrainingdata/ccdrAlgorithm@NA) |
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# Check results
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1 packages with problems
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## sparsebn (0.0.1)
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## sparsebn (0.0.2)
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Maintainer: Bryon Aragam <sparsebn@gmail.com>
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Bug reports: https://github.com/itsrainingdata/sparsebn/issues
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```
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checking re-building of vignette outputs ... WARNING
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Error in re-building vignettes:
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...
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Loading required package: sparsebnUtils
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Loading required package: ccdrAlgorithm
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Loading required package: discretecdAlgorithm
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sparsebn v0.0.1, Copyright (c) 2016
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Bryon Aragam, University of California, Los Angeles
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Jiaying Gu, University of California, Los Angeles
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... 6 lines ...
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---> Bugs? Please report any bugs at https://github.com/itsrainingdata/sparsebn/issues.
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A list of interventions was not specified: Assuming data is purely observational.
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Note: method with signature 'ddiMatrix#dMatrix' chosen for function '-',
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target signature 'ddiMatrix#dtCMatrix'.
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"diagonalMatrix#triangularMatrix" would also be valid
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A list of interventions was not specified: Assuming data is purely observational.
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Quitting from lines 144-153 (sparsebn-vignette.Rmd)
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Error: processing vignette 'sparsebn-vignette.Rmd' failed with diagnostics:
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could not find function "get.solution"
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Execution halted
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checking Rd cross-references ... WARNING
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Missing link or links in documentation object 'estimate.dag.Rd':
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‘[discretecdAlgorithm]{cd.run}’
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See section 'Cross-references' in the 'Writing R Extensions' manual.
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```
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