Adjustments to pass R CMD check --as-cran

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index eb5e6f6..e1050a3 100644 (file)
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -16,6 +16,7 @@ Imports:
     methods,
     pracma
 Suggests:
     methods,
     pracma
 Suggests:

+    devtools,

     flexmix,
     parallel,
     testthat,
     flexmix,
     parallel,
     testthat,

diff --git a/pkg/R/A_NAMESPACE.R b/pkg/R/A_NAMESPACE.R
index ea2711e..0a45138 100644 (file)
--- a/pkg/R/A_NAMESPACE.R
+++ b/pkg/R/A_NAMESPACE.R
@@ -3,8 +3,8 @@
 #' @useDynLib morpheus
 #'
 #' @importFrom jointDiag ajd
 #' @useDynLib morpheus
 #'
 #' @importFrom jointDiag ajd

-#' @importFrom stats rbinom rmultinom rnorm pnorm runif integrate
-#' @importFrom graphics boxplot barplot hist par
+#' @importFrom stats rbinom rmultinom rnorm pnorm runif integrate sd
+#' @importFrom graphics boxplot barplot hist par matplot

 #' @importFrom methods new
 #' @importFrom pracma integral
 #'
 #' @importFrom methods new
 #' @importFrom pracma integral
 #'

diff --git a/pkg/R/multiRun.R b/pkg/R/multiRun.R
index 0a2a833..1cebaab 100644 (file)
--- a/pkg/R/multiRun.R
+++ b/pkg/R/multiRun.R
@@ -11,6 +11,7 @@
 #' @param prepareArgs Prepare arguments for the functions inside estimParams
 #' @param N Number of runs
 #' @param ncores Number of cores for parallel runs (<=1: sequential)
 #' @param prepareArgs Prepare arguments for the functions inside estimParams
 #' @param N Number of runs
 #' @param ncores Number of cores for parallel runs (<=1: sequential)

+#' @param agg Aggregation method (default: lapply)

 #' @param verbose TRUE to indicate runs + methods numbers
 #'
 #' @return A list of nf aggregates of N results (matrices).
 #' @param verbose TRUE to indicate runs + methods numbers
 #'
 #' @return A list of nf aggregates of N results (matrices).

diff --git a/pkg/R/optimParams.R b/pkg/R/optimParams.R
index 9185efb..1ef1494 100644 (file)
--- a/pkg/R/optimParams.R
+++ b/pkg/R/optimParams.R
@@ -56,11 +56,6 @@ optimParams = function(K, link=c("logit","probit"), optargs=list())
                M <- computeMoments(optargs$X,optargs$Y)
        }
 
                M <- computeMoments(optargs$X,optargs$Y)
        }
 

-       # TODO: field?!
-       exactComp <<- optargs$exact
-       if (is.null(exactComp))
-               exactComp <<- FALSE
-

        # Build and return optimization algorithm object
        methods::new("OptimParams", "li"=link, "M1"=as.double(M[[1]]),
                "M2"=as.double(M[[2]]), "M3"=as.double(M[[3]]), "K"=as.integer(K))
        # Build and return optimization algorithm object
        methods::new("OptimParams", "li"=link, "M1"=as.double(M[[1]]),
                "M2"=as.double(M[[2]]), "M3"=as.double(M[[3]]), "K"=as.integer(K))


@@ -249,6 +244,8 @@ setRefClass(
        # link="probit"; order=2; λ=c(531.8099,586.8893,523.5816); b=c(-118.512674,-3.488020,2.109969)
        # Switch to pracma package for that (but it seems slow...)
 
        # link="probit"; order=2; λ=c(531.8099,586.8893,523.5816); b=c(-118.512674,-3.488020,2.109969)
        # Switch to pracma package for that (but it seems slow...)
 

+       exactComp <- FALSE #TODO: global, or argument...
+

        if (exactComp && link == "probit")
        {
                # Use exact computations
        if (exactComp && link == "probit")
        {
                # Use exact computations

diff --git a/pkg/R/plot.R b/pkg/R/plot.R
index 0097607..265f1cd 100644 (file)
--- a/pkg/R/plot.R
+++ b/pkg/R/plot.R
@@ -115,6 +115,9 @@ plotCoefs <- function(mr, params)
 #' Draw 3D map of objective function values
 #'
 #' @param N Number of starting points
 #' Draw 3D map of objective function values
 #'
 #' @param N Number of starting points

+#' @param n Number of points in sample
+#' @param p Vector of proportions
+#' @param b Vector of biases

 #' @param β Regression matrix (target)
 #' @param link Link function (logit or probit)
 #'
 #' @param β Regression matrix (target)
 #' @param link Link function (logit or probit)
 #'

diff --git a/pkg/tests/testthat.R b/pkg/tests/testthat.R
index 539a565..3b28538 100644 (file)
--- a/pkg/tests/testthat.R
+++ b/pkg/tests/testthat.R
@@ -1,5 +1,10 @@
 library(testthat)
 library(testthat)

-#library(morpheus)
-load_all()
+
+# Locally:
+#library(devtools)
+#load_all("../")
+
+# With R CMD check:
+library(morpheus)

 
 test_check("morpheus")
 
 test_check("morpheus")

diff --git a/to-cran.sh b/to-cran.sh
index b7e0ccd..16d4407 100755 (executable)
--- a/to-cran.sh
+++ b/to-cran.sh
@@ -9,6 +9,7 @@ for file in `find -name *.R`; do
        if [ -f $file ]; then
                sed -i 's/μ/mu/g' $file
                sed -i 's/β/beta/g' $file
        if [ -f $file ]; then
                sed -i 's/μ/mu/g' $file
                sed -i 's/β/beta/g' $file

+               sed -i 's/ρ/rho/g' $file

                sed -i 's/λ/lambda/g' $file
                sed -i 's/Σ/Sigma/g' $file
        fi
                sed -i 's/λ/lambda/g' $file
                sed -i 's/Σ/Sigma/g' $file
        fi