version 2.1-3

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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,23 +1,23 @@
 Package: DAKS
-Type: Package
+Version: 2.1-3
+Date: 2016-06-05
 Title: Data Analysis and Knowledge Spaces
-Version: 2.1-2
-Date: 2012-08-17
-Authors@R: c(person("Ali", "Uenlue", email = "ali.uenlue@tum.de", role
-        = c("aut", "cre")), person("Anatol", "Sargin", email =
-        "anatol.sargin@generali.de", role = c("aut")))
-Description: Functions and an example dataset for the psychometric
-        theory of knowledge spaces.  This package implements data
-        analysis methods and procedures for simulating data and quasi
-        orders and transforming different formulations in knowledge
-        space theory.
-Depends: R (>= 2.15.1), relations, sets
+Description: Functions and an example dataset for the psychometric theory of
+  knowledge spaces.  This package implements data analysis methods and
+  procedures for simulating data and quasi orders and transforming different
+  formulations in knowledge space theory.  See package?DAKS for an overview.
+Authors@R: c(person("Ali", "Uenlue", role = c("aut", "cre"),
+  email = "ali.uenlue@tum.de"),
+  person("Anatol", "Sargin", role = c("aut"),
+  email = "anatol.sargin@generali.de"))
+Author: Ali Uenlue [aut, cre], Anatol Sargin [aut]
+Maintainer: Ali Uenlue <ali.uenlue@tum.de>
+Depends: R (>= 3.3.0), relations, sets
 LazyLoad: yes
 LazyData: yes
 License: GPL (>= 2)
-URL: http://www.meb.edu.tum.de/
-Packaged: 2012-08-17 17:01:43 UTC; root
-Author: Ali Uenlue [aut, cre], Anatol Sargin [aut]
-Maintainer: Ali Uenlue <ali.uenlue@tum.de>
+URL: http://www.meb.edu.tum.de
+NeedsCompilation: no
+Packaged: 2016-06-05 21:30:37 UTC; Ali
 Repository: CRAN
-Date/Publication: 2012-08-17 17:40:21
+Date/Publication: 2016-06-06 13:14:35
diff --git a/MD5 b/MD5
@@ -1,7 +1,7 @@
 94d55d512a9ba36caa9b7df079bae19f *COPYING
-f11f4f97d89516d5b5637f3dcf489b60 *COPYRIGHTS
-30129eb3cc6f4dc7999ba7419df684ad *DESCRIPTION
-253a93634b7178a14bf2a3e66cf3c3dc *NAMESPACE
+e5c8f6cf57155564e6c024eda4d52d53 *DESCRIPTION
+ec28734c9607788aab23e172858a6bbd *NAMESPACE
+c4455b316e2140dd4975da18673ee97d *NEWS
 f24824d27ef436d38e3c3cb17bd71a88 *R/corr_iita.r
 22b1e6892174f1bd0c68582b027f5393 *R/hasse.r
 9ed1fff2876c220a6a9cc842823a2e1b *R/iita.r
@@ -24,36 +24,37 @@ e41963d64975cbf9ff0b0c4e9e9fbb59 *R/state2imp.r
 375a0838c4ae7eec82ce624605378e64 *R/summary.popiita.r
 7b35ee37aa58b3c6cd609813c60cca59 *R/variance.r
 71fa80fc1f624742d47d2691cf83e073 *R/z_test.r
+0bb39f78e6f861e74dfe5ad2eee970c5 *build/vignette.rds
 6b0ac16f909d3f7f4b46224f941796f8 *data/pisa.rda
-feb45a27bdaf7f9a78d9ad5c4dc3eedd *inst/CITATION
+0a105fb4f8beb11b0228f1073a2202a4 *inst/CITATION
+24f55471f8bc719ff22dd454702d7f50 *inst/COPYRIGHTS
+6765a2760f74a7dc2312bad8cdddf8b6 *inst/doc/DAKS.R
 ec6256fb9b59366a4af1088df7f7208c *inst/doc/DAKS.Rnw
-26739b6d836658699b2ce1376550ed50 *inst/doc/DAKS.pdf
-beac5be1510aca615119b3fe858ac8c9 *man/DAKS-package.Rd
+bcc12999bab44c9c5b96df96a9d4c088 *inst/doc/DAKS.pdf
+0a3303d9b29cf211b178dcab94a800b7 *man/DAKS-package.Rd
 63f382f06ff66b715c99a8b4e6df5441 *man/corr_iita.Rd
 91507a8414764f59568bf1bdccf81f1e *man/hasse.Rd
-5e954e70d90a3c7138f099ee5eba5639 *man/iita.Rd
+35f48c778df4d49f33125b851dc4320d *man/iita.Rd
 a166da7deed9b900537d8690107ecbb9 *man/imp2state.Rd
-e94fdfcc2506449a3d771dafa3851d90 *man/ind_gen.Rd
+7d43c47108eb6c65c932fcb514d186f7 *man/ind_gen.Rd
 79e3f5057311c88efb70e1d11c9069d6 *man/mini_iita.Rd
 ae99bf5226720ee75258c4d5ef2fefed *man/ob_counter.Rd
 09349db4d571b1c84c8101435fcaeccc *man/orig_iita.Rd
 9ecf369529a485ff2bbe30116841b6b4 *man/pattern.Rd
 5b359584eee8f9b7fb1be0cb505b4fab *man/pisa.Rd
-21faeb375de0cd861d02fd6933f3ee4f *man/pop_iita.Rd
-a6108f55efeea7bbbfb218b8c618e7c6 *man/pop_variance.Rd
+434e01dee13cda1879a174879de3bf41 *man/pop_iita.Rd
+d0af408ff1ad5fa198d2174a120c1ed5 *man/pop_variance.Rd
 59f94c5dfbf8d50fa258b3489703849c *man/print.iita.Rd
 710f5df155cfe2c94523c696662d4bc6 *man/print.pat.Rd
 2686d3f9a47676f271482d6087e73256 *man/print.popiita.Rd
 c09645d3bdfd689f3d89a40b9a724810 *man/print.summpopiita.Rd
 a7251d5a68bd2ef63f7a3d377ed03fb2 *man/print.ztest.Rd
-b11ef339ece2a38cecf6b854c6c2e457 *man/simu.Rd
+ad0eab1b49fcb2e43318f6c6c53bb60e *man/simu.Rd
 5b94f6da1294aab728491ea0318a1811 *man/state2imp.Rd
 0f6d2d258df0c7dcb8c13fd54abf3363 *man/summary.iita.Rd
 fe543b0c551b4242ee81659a0937f0d5 *man/summary.popiita.Rd
-8af9d0c6e2fefc961d651b2a260fbd13 *man/variance.Rd
-c1193810060d2b77a8738d0f5306e3bc *man/z_test.Rd
+551898286f5874c7b67d59fa3905b275 *man/variance.Rd
+da2837904fa95352590ae9df25c7d79f *man/z_test.Rd
 ec6256fb9b59366a4af1088df7f7208c *vignettes/DAKS.Rnw
 f54b72ddeac9e7f52e0c1093aff87617 *vignettes/hasse_pisa.pdf
-92e903f33d4067a7fbc89fa4e7571c92 *vignettes/jss.bst
-597d284e5204836c015463ad73e972ab *vignettes/jss.cls
 16c0dab6c8b4be112335a99235fd1166 *vignettes/kst.bib
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,17 +1,18 @@
 export(corr_iita, hasse, iita, imp2state, ind_gen, mini_iita,
        ob_counter, orig_iita, pattern, pop_iita, pop_variance, print.iita,
        print.pat, print.popiita, print.summpopiita, print.ztest, simu,
-       state2imp, summary.iita, summary.popiita, variance, z_test)
-
+       state2imp, summary.iita, summary.popiita, variance, z_test)
+
 # internal functions; not intended to be visible to users
 # export()
 
-import(graphics, relations, sets)
+import(graphics, stats)
+import(relations, sets)
 
 S3method(print, iita)
 S3method(print, popiita)
-S3method(summary, popiita)
 S3method(summary, iita)
+S3method(summary, popiita)
+S3method(print, pat)
 S3method(print, summpopiita)
 S3method(print, ztest)
-S3method(print, pat)
diff --git a/NEWS b/NEWS
@@ -0,0 +1,5 @@
+Changes in Version 2.1-3
+
+  o CRAN package check results have been addressed and fixed.
+
+  o This file NEWS has been added.
diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/inst/CITATION b/inst/CITATION
@@ -2,18 +2,17 @@ citHeader("To cite DAKS in publications use:")
 
 citEntry(entry = "Article",
   title        = "{DAKS}: An {R} Package for Data Analysis Methods in Knowledge Space Theory",
-  author       = personList(as.person("Ali \\\"Unl\\\"u"),
-                   as.person("Anatol Sargin")),
+  author       = personList(as.person("Ali \\\"Unl\\\"u"), as.person("Anatol Sargin")),
   journal      = "Journal of Statistical Software",
   year         = "2010",
   volume       = "37",
   number       = "2",
   pages        = "1--31",
-  url          = "http://www.jstatsoft.org/v37/i02/",
+  url          = "https://www.jstatsoft.org/article/view/v037i02",
 
   textVersion  =
   paste("Ali Uenlue, Anatol Sargin (2010).",
         "DAKS: An R Package for Data Analysis Methods in Knowledge Space Theory.",
         "Journal of Statistical Software, 37(2), 1-31.",
-        "URL http://www.jstatsoft.org/v37/i02/.")
-)
+        "URL https://www.jstatsoft.org/article/view/v037i02.")
+)
diff --git a/COPYRIGHTS → inst/COPYRIGHTS b/COPYRIGHTS → inst/COPYRIGHTS
@@ -5,6 +5,5 @@ This code is
 
   Copyright (C) 2010 Anatol Sargin and Ali Uenlue
 
-All code is subject to the GNU General Public License, Version 2.  See
-the file COPYING for the exact conditions under which you may
-redistribute it.
+All code is subject to the GNU General Public License, Version 2.  See the file
+COPYING for the exact conditions under which you may redistribute it.
diff --git a/inst/doc/DAKS.R b/inst/doc/DAKS.R
@@ -0,0 +1,55 @@
+### R code from vignette source 'DAKS.Rnw'
+
+###################################################
+### code chunk number 1: preliminaries
+###################################################
+library("DAKS")
+library("relations")
+library("sets")
+options(prompt="R> ", continue="R+", width=70)
+
+
+###################################################
+### code chunk number 2: integer
+###################################################
+1 == 1L
+
+
+###################################################
+### code chunk number 3: pisa1
+###################################################
+head(pisa)
+pat <- pattern(pisa)
+pat
+sum(pat$response.patterns)
+
+
+###################################################
+### code chunk number 4: pisa2
+###################################################
+apply(pisa, 2, table)
+
+
+###################################################
+### code chunk number 5: iita
+###################################################
+mini <- iita(pisa, v = 1)
+corr <- iita(pisa, v = 2)
+orig <- iita(pisa, v = 3)
+summary(mini)
+summary(corr)
+summary(orig)
+
+
+###################################################
+### code chunk number 6: set-operations1
+###################################################
+set_symdiff(orig$implications, mini$implications)
+
+
+###################################################
+### code chunk number 7: set-operations2
+###################################################
+set_is_proper_subset(orig$implications, mini$implications)
+
+
diff --git a/inst/doc/DAKS.pdf b/inst/doc/DAKS.pdf
diff --git a/man/DAKS-package.Rd b/man/DAKS-package.Rd
@@ -21,8 +21,8 @@
   \tabular{ll}{
     Package: \tab \pkg{DAKS}\cr
     Type: \tab Package\cr
-    Version: \tab 2.1-2\cr
-    Date: \tab 2012-08-17\cr
+    Version: \tab 2.1-3\cr
+    Date: \tab 2016-06-05\cr
     License: \tab \acronym{GPL} (>= 2)
   }
   Knowledge space theory is a recent psychometric test theory based on
@@ -76,9 +76,5 @@
   analysis methods in knowledge space theory. \emph{Journal of Statistical
   Software}, \bold{37}(2), 1--31.
   URL \url{http://www.jstatsoft.org/v37/i02/}.
-
-   Uenlue, A. and Sargin, A. (2010) Maximum likelihood methodology for
-  \emph{diff} fit measures for quasi orders.  Manuscript submitted for
-  publication.
 }
 \keyword{package}
diff --git a/man/iita.Rd b/man/iita.Rd
@@ -39,8 +39,7 @@ iita(dataset, v)
   interpretation of \eqn{(i, j)} as `mastering item \eqn{j} implies
   mastering item \eqn{i}.') The algorithms are described in the paper
   about the \pkg{DAKS} package by \cite{Uenlue and Sargin (2010)}, and
-  in the papers by \cite{Sargin and Uenlue (2009)} and
-  \cite{Uenlue and Sargin (2010)}.
+  in the paper by \cite{Sargin and Uenlue (2009)}.
 
   \code{iita} calls \code{\link{ind_gen}} for constructing the set of
   competing quasi orders according to the inductive generation
@@ -90,10 +89,6 @@ iita(dataset, v)
   analysis methods in knowledge space theory. \emph{Journal of Statistical
   Software}, \bold{37}(2), 1--31.
   URL \url{http://www.jstatsoft.org/v37/i02/}.
-
- Uenlue, A. and Sargin, A. (2010) Maximum likelihood methodology for
-  \emph{diff} fit measures for quasi orders.  Manuscript submitted for
-  publication.
 }
 \author{
   Anatol Sargin, Ali Uenlue

diff --git a/man/ind_gen.Rd b/man/ind_gen.Rd
@@ -53,7 +53,8 @@ Sargin, A. and Uenlue, A. (2009) Inductive item tree analysis:
 \seealso{
   \code{\link{ob_counter}} for computation of numbers of
   counterexamples; \code{\link{iita}}, the interface that provides the
-  three inductive item tree analysis methods under one umbrella\code{\link{z_test}} for one- and two-sample Z-tests.  See
+  three inductive item tree analysis methods under one umbrella;
+  \code{\link{z_test}} for one- and two-sample Z-tests.  See
   also \code{\link{DAKS-package}} for general information about this
   package.
 }

diff --git a/man/pop_iita.Rd b/man/pop_iita.Rd
@@ -49,8 +49,7 @@ pop_iita(imp, ce, lg, items, dataset = NULL, A = NULL, v)
   the expected numbers of counterexamples.  For details see
   \code{\link{iita}}.  The algorithms are described in the paper about
   the \pkg{DAKS} package by \cite{Uenlue and Sargin (2010)}, and in
-  the papers by \cite{Sargin and Uenlue (2009)} and
-  \cite{Uenlue and Sargin (2010)}.
+  the paper by \cite{Sargin and Uenlue (2009)}.
 
   Compared to \code{\link{iita}}, the function \code{pop_iita}
   implements the three inductive item tree analysis algorithms in
@@ -105,10 +104,6 @@ Sargin, A. and Uenlue, A. (2009) Inductive item tree analysis:
   analysis methods in knowledge space theory. \emph{Journal of Statistical
   Software}, \bold{37}(2), 1--31.
   URL \url{http://www.jstatsoft.org/v37/i02/}.
-  
- Uenlue, A. and Sargin, A. (2010) Maximum likelihood methodology for
-  \emph{diff} fit measures for quasi orders.  Manuscript submitted for
-  publication.
 }
 \author{
   Anatol Sargin, Ali Uenlue

diff --git a/man/pop_variance.Rd b/man/pop_variance.Rd
@@ -59,10 +59,6 @@ Sargin, A. and Uenlue, A. (2009) Inductive item tree analysis:
   analysis methods in knowledge space theory. \emph{Journal of Statistical
   Software}, \bold{37}(2), 1--31.
   URL \url{http://www.jstatsoft.org/v37/i02/}.
-
- Uenlue, A. and Sargin, A. (2010) Maximum likelihood methodology for
-  \emph{diff} fit measures for quasi orders.  Manuscript submitted for
-  publication. 
 }
 \author{
   Anatol Sargin, Ali Uenlue

diff --git a/man/simu.Rd b/man/simu.Rd
@@ -100,10 +100,6 @@ Sargin, A. and Uenlue, A. (2009) Inductive item tree analysis:
   analysis methods in knowledge space theory. \emph{Journal of Statistical
   Software}, \bold{37}(2), 1--31.
   URL \url{http://www.jstatsoft.org/v37/i02/}.
-
- Uenlue, A. and Sargin, A. (2010) Maximum likelihood methodology for
-  \emph{diff} fit measures for quasi orders.  Manuscript submitted for
-  publication. 
 }
 \author{
   Anatol Sargin, Ali Uenlue

diff --git a/man/variance.Rd b/man/variance.Rd
@@ -61,10 +61,6 @@ Sargin, A. and Uenlue, A. (2009) Inductive item tree analysis:
   analysis methods in knowledge space theory. \emph{Journal of Statistical
   Software}, \bold{37}(2), 1--31.
   URL \url{http://www.jstatsoft.org/v37/i02/}.
-
- Uenlue, A. and Sargin, A. (2010) Maximum likelihood methodology for
-  \emph{diff} fit measures for quasi orders.  Manuscript submitted for
-  publication. 
 }
 \author{
   Anatol Sargin, Ali Uenlue

diff --git a/man/z_test.Rd b/man/z_test.Rd
@@ -48,10 +48,6 @@ z_test(dataset, imp, imp_alt = NULL,
   analysis methods in knowledge space theory. \emph{Journal of Statistical
   Software}, \bold{37}(2), 1--31.
   URL \url{http://www.jstatsoft.org/v37/i02/}.
-
-   Uenlue, A. and Sargin, A. (2010) Maximum likelihood methodology for
-  \emph{diff} fit measures for quasi orders.  Manuscript submitted for
-  publication. 
 }
 \author{
   Anatol Sargin, Ali Uenlue