Title: Substitution and Indel Distances to Infer Evolutionary
Relationships
Diff between sidier versions 3.0 dated 2014-11-18 and 3.0.1 dated 2015-02-27
Description: Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
Author: A. Jesus Muñoz Pajares
Maintainer: A.J. Muñoz-Pajares
DESCRIPTION | 12 +++++------
MD5 | 22 ++++++++++-----------
NEWS | 10 +++++++++
R/double.plot.R | 30 +++++++++++++++++-----------
R/mutation.network.R | 10 +++++----
R/perc.thr.R | 9 ++++----
R/pie.network.R | 8 ++++---
R/spatial.plot.R | 51 +++++++++++++++++++++++++++++++------------------
data/ex_alignment1.rda |binary
man/double.plot.Rd | 38 ++++++++++++++++++++++++------------
man/sidier-package.Rd | 6 ++---
man/spatial.plot.Rd | 14 +++++++------
12 files changed, 131 insertions(+), 79 deletions(-)
Title: R Object-Oriented Programming with or without References
Diff between R.oo versions 1.18.0 dated 2014-02-25 and 1.19.0 dated 2015-02-27
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.oo-1.18.0/R.oo/tests/Object.finalize,reentrant.R |only
R.oo-1.19.0/R.oo/DESCRIPTION | 14 -
R.oo-1.19.0/R.oo/MD5 | 75 +++++---
R.oo-1.19.0/R.oo/NAMESPACE | 7
R.oo-1.19.0/R.oo/NEWS | 44 ++++
R.oo-1.19.0/R.oo/R/050.Object.R | 58 +-----
R.oo-1.19.0/R.oo/R/060.Class.R | 22 +-
R.oo-1.19.0/R.oo/R/999.DEPRECATED.R | 86 +++++++++
R.oo-1.19.0/R.oo/R/ASCII.R | 8
R.oo-1.19.0/R.oo/R/Class.misc.R | 55 ++----
R.oo-1.19.0/R.oo/R/Package.R | 128 --------------
R.oo-1.19.0/R.oo/R/Rdoc.R | 46 ++++-
R.oo-1.19.0/R.oo/R/abort.R | 4
R.oo-1.19.0/R.oo/R/ll.default.R | 9
R.oo-1.19.0/R.oo/R/objectSize.default.R | 8
R.oo-1.19.0/R.oo/R/objectSize.environment.R | 40 +++-
R.oo-1.19.0/R.oo/R/zzz.R | 2
R.oo-1.19.0/R.oo/man/Class.Rd | 3
R.oo-1.19.0/R.oo/man/RccViolationException.Rd | 4
R.oo-1.19.0/R.oo/man/charToInt.Rd | 2
R.oo-1.19.0/R.oo/man/gc.Object.Rd | 16 +
R.oo-1.19.0/R.oo/man/intToChar.Rd | 2
R.oo-1.19.0/R.oo/man/ll.Rd | 5
R.oo-1.19.0/R.oo/man/registerFinalizer.Object.Rd | 8
R.oo-1.19.0/R.oo/man/update.Package.Rd | 16 -
R.oo-1.19.0/R.oo/tests/ASCII.R |only
R.oo-1.19.0/R.oo/tests/BasicObject.R |only
R.oo-1.19.0/R.oo/tests/Class.R |only
R.oo-1.19.0/R.oo/tests/Exception.R |only
R.oo-1.19.0/R.oo/tests/InternalErrorException.reportBug.R |only
R.oo-1.19.0/R.oo/tests/Object.R |only
R.oo-1.19.0/R.oo/tests/Object.finalize,noattach.R | 17 +
R.oo-1.19.0/R.oo/tests/Object.finalize,onoff.R | 34 ++-
R.oo-1.19.0/R.oo/tests/Object.finalize.R |only
R.oo-1.19.0/R.oo/tests/Package.R |only
R.oo-1.19.0/R.oo/tests/Package.unload.R |only
R.oo-1.19.0/R.oo/tests/StaticMethodsAndNamespaces.R | 3
R.oo-1.19.0/R.oo/tests/abort.R |only
R.oo-1.19.0/R.oo/tests/attachLocally.Object.R |only
R.oo-1.19.0/R.oo/tests/equals.R |only
R.oo-1.19.0/R.oo/tests/extend.default.R |only
R.oo-1.19.0/R.oo/tests/getConstructorS3.R |only
R.oo-1.19.0/R.oo/tests/isBeingCreated.Class.R |only
R.oo-1.19.0/R.oo/tests/ll.R |only
R.oo-1.19.0/R.oo/tests/local.R |only
R.oo-1.19.0/R.oo/tests/objectSize.R |only
R.oo-1.19.0/R.oo/tests/throw.R |only
R.oo-1.19.0/R.oo/tests/trim.R |only
R.oo-1.19.0/R.oo/tests/typeOfClass.R |only
R.oo-1.19.0/R.oo/tests/zzz.Object.finalize,reentrant.R |only
50 files changed, 417 insertions(+), 299 deletions(-)
Title: Basic Functions for Power Analysis
Diff between pwr versions 1.1.1 dated 2009-10-26 and 1.1-2 dated 2015-02-27
Description: Power analysis functions along the lines of Cohen (1988).
Author: Stephane Champely [aut],
Claus Ekstrom [ctb],
Peter Dalgaard [ctb],
Jeffrey Gill [ctb],
Helios De Rosario [cre]
Maintainer: Helios De Rosario
ChangeLog |only
DESCRIPTION | 32 ++++++----
MD5 |only
NAMESPACE |only
R/ES.h.R | 10 +--
R/ES.w1.R | 10 +--
R/ES.w2.R | 16 ++---
R/cohen.ES.R | 58 +++++++++---------
R/pwr.2p.test.R | 128 ++++++++++++++++++++---------------------
R/pwr.2p2n.test.R | 140 ++++++++++++++++++++++-----------------------
R/pwr.anova.test.R | 88 ++++++++++++++--------------
R/pwr.chisq.test.R | 76 ++++++++++++------------
R/pwr.f2.test.R | 86 +++++++++++++--------------
R/pwr.norm.test.R | 124 ++++++++++++++++++++--------------------
R/pwr.p.test.R | 124 ++++++++++++++++++++--------------------
R/pwr.r.test.R | 142 +++++++++++++++++++++++-----------------------
R/pwr.t.test.R | 144 +++++++++++++++++++++++-----------------------
R/pwr.t2n.test.R | 154 +++++++++++++++++++++++++-------------------------
man/ES.h.Rd | 72 +++++++++++------------
man/ES.w1.Rd | 64 ++++++++++----------
man/ES.w2.Rd | 66 ++++++++++-----------
man/cohen.ES.Rd | 60 ++++++++++---------
man/pwr-package.Rd | 121 +++++++++++++++++++--------------------
man/pwr.2p.test.Rd | 100 ++++++++++++++++----------------
man/pwr.2p2n.test.Rd | 103 ++++++++++++++++-----------------
man/pwr.anova.test.Rd | 94 +++++++++++++++---------------
man/pwr.chisq.test.Rd | 102 ++++++++++++++++-----------------
man/pwr.f2.test.Rd | 82 +++++++++++++-------------
man/pwr.norm.test.Rd | 130 +++++++++++++++++++++---------------------
man/pwr.p.test.Rd | 107 +++++++++++++++++-----------------
man/pwr.r.test.Rd | 112 ++++++++++++++++++------------------
man/pwr.t.test.Rd | 130 +++++++++++++++++++++---------------------
man/pwr.t2n.test.Rd | 94 +++++++++++++++---------------
33 files changed, 1393 insertions(+), 1376 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Diff between MAMS versions 0.3 dated 2014-05-07 and 0.4 dated 2015-02-27
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki
Maintainer: Thomas Jaki
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NAMESPACE | 9 +++++++++
R/mams.R | 12 ++++++++++--
inst/NEWS | 6 +++++-
man/generic.Rd | 8 ++------
man/mams.Rd | 9 ++++-----
man/new.bounds.Rd | 3 ++-
man/step_down_mams.Rd | 6 +++---
9 files changed, 47 insertions(+), 30 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Diff between BDgraph versions 2.15 dated 2015-01-23 and 2.16 dated 2015-02-27
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
BDgraph-2.15/BDgraph/src/bdmcmc.cpp |only
BDgraph-2.16/BDgraph/DESCRIPTION | 10 -
BDgraph-2.16/BDgraph/MD5 | 58 +++---
BDgraph-2.16/BDgraph/R/bdgraph.R | 258 ++++++++-------------------
BDgraph-2.16/BDgraph/R/bdgraph.npn.R | 24 +-
BDgraph-2.16/BDgraph/R/bdgraph.sim.R | 25 +-
BDgraph-2.16/BDgraph/R/compare.R | 60 ++++--
BDgraph-2.16/BDgraph/R/plotcoda.R | 2
BDgraph-2.16/BDgraph/R/select.R | 36 ++-
BDgraph-2.16/BDgraph/man/BDgraph-internal.Rd | 2
BDgraph-2.16/BDgraph/man/BDgraph-package.Rd | 8
BDgraph-2.16/BDgraph/man/I.g.Rd | 4
BDgraph-2.16/BDgraph/man/bdgraph.Rd | 10 -
BDgraph-2.16/BDgraph/man/bdgraph.npn.Rd | 6
BDgraph-2.16/BDgraph/man/bdgraph.sim.Rd | 6
BDgraph-2.16/BDgraph/man/compare.Rd | 33 +--
BDgraph-2.16/BDgraph/man/phat.Rd | 6
BDgraph-2.16/BDgraph/man/plot.bdgraph.Rd | 6
BDgraph-2.16/BDgraph/man/plot.simulate.Rd | 6
BDgraph-2.16/BDgraph/man/plotcoda.Rd | 6
BDgraph-2.16/BDgraph/man/plotroc.Rd | 8
BDgraph-2.16/BDgraph/man/print.bdgraph.Rd | 6
BDgraph-2.16/BDgraph/man/print.simulate.Rd | 6
BDgraph-2.16/BDgraph/man/prob.Rd | 6
BDgraph-2.16/BDgraph/man/rgwish.Rd | 8
BDgraph-2.16/BDgraph/man/rwish.Rd | 6
BDgraph-2.16/BDgraph/man/select.Rd | 6
BDgraph-2.16/BDgraph/man/summary.bdgraph.Rd | 11 -
BDgraph-2.16/BDgraph/man/surveyData.Rd | 8
BDgraph-2.16/BDgraph/man/traceplot.Rd | 6
BDgraph-2.16/BDgraph/src/BDgraph.cpp |only
31 files changed, 284 insertions(+), 353 deletions(-)
Title: Apache OpenNLP Tools Interface
Diff between openNLP versions 0.2-3 dated 2014-04-19 and 0.2-4 dated 2015-02-27
Description: An interface to the Apache OpenNLP tools (version 1.5.3).
The Apache OpenNLP library is a machine learning based toolkit for the
processing of natural language text written in Java.
It supports the most common NLP tasks, such as tokenization, sentence
segmentation, part-of-speech tagging, named entity extraction, chunking,
parsing, and coreference resolution.
See
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 8 +++++---
MD5 | 14 +++++++-------
R/chunk.R | 4 +++-
R/ner.R | 5 ++++-
R/pos.R | 4 +++-
R/sentdetect.R | 4 +++-
R/tokenize.R | 4 +++-
R/utils.R | 3 ---
8 files changed, 28 insertions(+), 18 deletions(-)
Title: Performing Continuous-Time Microsimulation
Diff between MicSim versions 1.0.6 dated 2014-07-02 and 1.0.7 dated 2015-02-27
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn
DESCRIPTION | 14 +++++++-------
MD5 | 12 ++++++------
NAMESPACE | 6 +++---
R/micSim.r | 8 ++++----
inst/NEWS.Rd | 6 ++++++
man/MicSim-package.Rd | 12 +++---------
man/micSim.Rd | 7 -------
7 files changed, 29 insertions(+), 36 deletions(-)
Title: Data Mangement for Hydrology and Beyond Using the Observations
Data Model
Diff between RObsDat versions 14.12 dated 2014-12-29 and 15.02 dated 2015-02-27
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser
DESCRIPTION | 10 ++++-----
MD5 | 36 ++++++++++++++++-----------------
R/addCV.R | 2 -
R/addDataValues.R | 2 -
R/addISOMetadata.R | 2 -
R/addOffsetType.R | 2 -
R/addQualityControlLevel.R | 2 -
R/addSite.R | 2 -
R/addSource.R | 2 -
R/addSpatialReferences.R | 2 -
R/addUnits.R | 2 -
R/addVariable.R | 2 -
R/class_stfdf.R | 4 +--
R/createST.R | 6 ++---
R/getDataValues.R | 2 -
R/h.m.R | 2 -
inst/doc/RObsDat_Einstiegstutorial.pdf |binary
inst/tests/test_various.R | 23 ++++++++++++++++++++-
vignettes/RObsDat.bib | 30 +++++++++++----------------
19 files changed, 75 insertions(+), 58 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Diff between lcmm versions 1.7.1 dated 2015-02-26 and 1.7.2 dated 2015-02-27
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
DESCRIPTION | 8 +++---
MD5 | 20 +++++++--------
NEWS | 2 -
R/Jointlcmm.R | 12 ++++++++-
R/epoce.R | 66 +++++++++++++++++++++++++++++++++++++++++++++++-----
R/plot.predictY.R | 8 +++++-
THANKS | 4 ++-
man/epoce.Rd | 3 +-
man/lcmm-package.Rd | 4 +--
src/Makevars | 13 ++++------
src/predictCont.f90 | 6 ++--
11 files changed, 109 insertions(+), 37 deletions(-)
Title: Normalisation of Psychometric Tests
Diff between NormPsy versions 1.0.2 dated 2014-11-27 and 1.0.3 dated 2015-02-27
Description: Functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). Functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores are also provided.
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima
DESCRIPTION | 16 ++++++++--------
MD5 | 6 +++---
R/predictMMSE.R | 6 +++---
man/NormPsy-package.Rd | 4 ++--
4 files changed, 16 insertions(+), 16 deletions(-)
Title: Finding Heterogeneous Treatment Effects
Diff between FindIt versions 0.4 dated 2015-02-07 and 0.5 dated 2015-02-27
Description: The heterogeneous treatment effect estimation procedure
proposed by Imai and Ratkovic (2013).
The proposed method is applicable, for
example, when selecting a small number of most (or least)
efficacious treatments from a large number of alternative
treatments as well as when identifying subsets of the
population who benefit (or are harmed by) a treatment of
interest. The method adapts the Support Vector Machine
classifier by placing separate LASSO constraints over the
pre-treatment parameters and causal heterogeneity parameters of
interest. This allows for the qualitative distinction between
causal and other parameters, thereby making the variable
selection suitable for the exploration of causal heterogeneity.
The package also contains the function, INT, which estimates
the average marginal treatment effect, the average treatment
combination effect, and the average marginal treatment interaction
effect proposed by Egami and Imai (2015).
Author: Naoki Egami
Maintainer: Naoki Egami
FindIt-0.4/FindIt/data/GerberGreen.tab.gz |only
FindIt-0.4/FindIt/data/LaLonde.tab.gz |only
FindIt-0.4/FindIt/data/datalist |only
FindIt-0.5/FindIt/DESCRIPTION | 20
FindIt-0.5/FindIt/MD5 | 36
FindIt-0.5/FindIt/NAMESPACE | 2
FindIt-0.5/FindIt/R/INT.R |only
FindIt-0.5/FindIt/R/SVMHet.R | 1839 ----------------------------
FindIt-0.5/FindIt/R/full.FindIt.R |only
FindIt-0.5/FindIt/R/makeallway.R |only
FindIt-0.5/FindIt/R/maketwoway.R |only
FindIt-0.5/FindIt/R/plot.PredictEffect.R |only
FindIt-0.5/FindIt/R/predict.FindIt.R |only
FindIt-0.5/FindIt/R/summary.FindIt.R |only
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FindIt-0.5/FindIt/data/LaLonde.rdata |only
FindIt-0.5/FindIt/data/Unifdata.rdata |only
FindIt-0.5/FindIt/man/FindIt.Rd | 312 ++--
FindIt-0.5/FindIt/man/GerberGreen.Rd | 103 -
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FindIt-0.5/FindIt/man/Immigration.Rd |only
FindIt-0.5/FindIt/man/LaLonde.Rd | 25
FindIt-0.5/FindIt/man/MakeTwoWay.Rd | 5
FindIt-0.5/FindIt/man/Predict.FindIt.Rd | 12
FindIt-0.5/FindIt/man/full.FindIt.Rd |only
FindIt-0.5/FindIt/man/plot.PredictFindIt.Rd | 16
28 files changed, 282 insertions(+), 2088 deletions(-)
Title: Cox Models with Dynamic Ridge Penalties
Diff between CoxRidge versions 0.9.1 dated 2013-06-26 and 0.9.2 dated 2015-02-27
Description: A package for fitting Cox models with penalized ridge-type partial likelihood. The package includes functions for fitting simple Cox models with all covariates controlled by a ridge penalty. The weight of the penalty is optimised by using a REML type-algorithm. Models with time varying effects of the covariates can also be fitted. Some of the covariates may be allowed to be fixed and thus not controlled by the penalty. There are three different penalty functions, ridge, dynamic and weighted dynamic. Time varying effects can be fitted without the need of an expanded dataset.
Author: Aris Perperoglou
Maintainer: Aris Perperoglou
DESCRIPTION | 26 ++++++++------------------
MD5 | 4 ++--
NAMESPACE | 3 +++
3 files changed, 13 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-02 1.0.6
2014-08-20 0.0.4
Title: Quantitative Analysis Made Accessible
Diff between userfriendlyscience versions 0.1-2 dated 2014-04-22 and 0.2-0 dated 2015-02-27
More information about userfriendlyscience at CRAN
Description: Contains a number of functions that serve
two goals: first, make R more accessible to people migrating from
SPSS by adding a number of functions that behave roughly like their
SPSS equivalents; and second, make a number of slightly more
advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters
userfriendlyscience-0.1-2/userfriendlyscience/R/basicSPSStranslationFunctions.R |only
userfriendlyscience-0.1-2/userfriendlyscience/R/simpleFunctions.r |only
userfriendlyscience-0.1-2/userfriendlyscience/R/sysrev.r |only
userfriendlyscience-0.1-2/userfriendlyscience/man/userfriendlyscience-sysrev.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/ChangeLog | 7
userfriendlyscience-0.2-0/userfriendlyscience/DESCRIPTION | 18
userfriendlyscience-0.2-0/userfriendlyscience/MD5 | 70 +--
userfriendlyscience-0.2-0/userfriendlyscience/NAMESPACE | 39 +
userfriendlyscience-0.2-0/userfriendlyscience/NEWS | 18
userfriendlyscience-0.2-0/userfriendlyscience/R/associationMatrix.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/basicSPSStranslationFunctions.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/confIntV.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/didacticPlot.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/dlvPlot.r | 8
userfriendlyscience-0.2-0/userfriendlyscience/R/freq.r | 22
userfriendlyscience-0.2-0/userfriendlyscience/R/meanDiff.multi.r | 3
userfriendlyscience-0.2-0/userfriendlyscience/R/normalityAssessment.r | 231 +++++++++-
userfriendlyscience-0.2-0/userfriendlyscience/R/oneway.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/posthocTGH.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/regr.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/rnwString.r | 2
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleDiagnosis.r | 44 -
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleDiagnosisToPDF.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleInspection.r | 20
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleReliability.r | 12
userfriendlyscience-0.2-0/userfriendlyscience/R/scatterMatrix.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/userfriendlyscienceBasics.r | 40 +
userfriendlyscience-0.2-0/userfriendlyscience/data/testRetestSimData.rda |binary
userfriendlyscience-0.2-0/userfriendlyscience/inst |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-associationMatrix.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-associationMatrixHelperFunctions.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-confIntV.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-didacticPlot.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-dlvPlot.Rd | 4
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-freq.Rd | 5
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-normalityAssessment.Rd | 68 ++
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-oneway.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-package.Rd | 41 +
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-posthocTGH.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-printMethods.Rd | 47 +-
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-regr.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleDiagnosis.Rd | 21
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleDiagnosisToPDF.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleInspection.Rd | 5
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scatterMatrix.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-userfriendlyscienceBasics.Rd | 32 +
userfriendlyscience-0.2-0/userfriendlyscience/tests/reliabilityTest.r | 50 +-
userfriendlyscience-0.2-0/userfriendlyscience/tests/sysRevExampleTemplate.r |only
48 files changed, 640 insertions(+), 167 deletions(-)
Permanent link
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Diff between spatstat versions 1.40-0 dated 2014-12-31 and 1.41-1 dated 2015-02-27
Description: Comprehensive toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
spatstat-1.40-0/spatstat/man/markcorrint.Rd |only
spatstat-1.40-0/spatstat/src/dppll.f |only
spatstat-1.40-0/spatstat/src/inxypOld.f |only
spatstat-1.41-1/spatstat/DESCRIPTION | 22
spatstat-1.41-1/spatstat/MD5 | 590 ++++++------
spatstat-1.41-1/spatstat/NAMESPACE | 145 +++
spatstat-1.41-1/spatstat/NEWS | 878 +++++++++++++++++++
spatstat-1.41-1/spatstat/R/Iest.R | 4
spatstat-1.41-1/spatstat/R/Kcom.R | 12
spatstat-1.41-1/spatstat/R/Kest.R | 13
spatstat-1.41-1/spatstat/R/Kinhom.R | 10
spatstat-1.41-1/spatstat/R/Kmeasure.R | 89 +
spatstat-1.41-1/spatstat/R/Kmulti.R | 10
spatstat-1.41-1/spatstat/R/Kmulti.inhom.R | 10
spatstat-1.41-1/spatstat/R/Kscaled.R | 5
spatstat-1.41-1/spatstat/R/Math.im.R | 6
spatstat-1.41-1/spatstat/R/Math.linim.R |only
spatstat-1.41-1/spatstat/R/Tstat.R | 4
spatstat-1.41-1/spatstat/R/anova.ppm.R | 492 +++++-----
spatstat-1.41-1/spatstat/R/cdf.test.mppm.R | 5
spatstat-1.41-1/spatstat/R/clickpoly.R | 13
spatstat-1.41-1/spatstat/R/clickppp.R | 152 +--
spatstat-1.41-1/spatstat/R/closepairs.R | 86 +
spatstat-1.41-1/spatstat/R/clusterfunctions.R |only
spatstat-1.41-1/spatstat/R/clusterinfo.R |only
spatstat-1.41-1/spatstat/R/colourtools.R | 4
spatstat-1.41-1/spatstat/R/concom.R | 4
spatstat-1.41-1/spatstat/R/crossdistlpp.R | 6
spatstat-1.41-1/spatstat/R/deldir.R | 30
spatstat-1.41-1/spatstat/R/density.ppp.R | 81 +
spatstat-1.41-1/spatstat/R/diagnoseppm.R | 25
spatstat-1.41-1/spatstat/R/diagram.R | 51 -
spatstat-1.41-1/spatstat/R/distances.psp.R | 8
spatstat-1.41-1/spatstat/R/distbdry.R | 5
spatstat-1.41-1/spatstat/R/dummy.R | 2
spatstat-1.41-1/spatstat/R/envelope.R | 7
spatstat-1.41-1/spatstat/R/fgk3.R | 36
spatstat-1.41-1/spatstat/R/fv.R | 8
spatstat-1.41-1/spatstat/R/hierstrauss.R | 21
spatstat-1.41-1/spatstat/R/hyperframe.R | 104 +-
spatstat-1.41-1/spatstat/R/hypersub.R | 13
spatstat-1.41-1/spatstat/R/images.R | 27
spatstat-1.41-1/spatstat/R/intensity.R | 4
spatstat-1.41-1/spatstat/R/interactions.R | 8
spatstat-1.41-1/spatstat/R/iplot.R | 6
spatstat-1.41-1/spatstat/R/iplotlayered.R | 30
spatstat-1.41-1/spatstat/R/istat.R | 4
spatstat-1.41-1/spatstat/R/kppm.R | 436 +++++----
spatstat-1.41-1/spatstat/R/layered.R | 64 -
spatstat-1.41-1/spatstat/R/levelset.R | 10
spatstat-1.41-1/spatstat/R/leverage.R | 19
spatstat-1.41-1/spatstat/R/linalg.R | 5
spatstat-1.41-1/spatstat/R/linearK.R | 24
spatstat-1.41-1/spatstat/R/linearKmulti.R | 11
spatstat-1.41-1/spatstat/R/lineardisc.R | 4
spatstat-1.41-1/spatstat/R/linearmrkcon.R | 13
spatstat-1.41-1/spatstat/R/linearpcf.R | 28
spatstat-1.41-1/spatstat/R/linearpcfmulti.R | 8
spatstat-1.41-1/spatstat/R/linfun.R | 45
spatstat-1.41-1/spatstat/R/linim.R | 81 +
spatstat-1.41-1/spatstat/R/linnet.R | 231 ++++
spatstat-1.41-1/spatstat/R/lpp.R | 203 +++-
spatstat-1.41-1/spatstat/R/lppm.R | 49 -
spatstat-1.41-1/spatstat/R/markcorr.R | 66 +
spatstat-1.41-1/spatstat/R/measures.R | 10
spatstat-1.41-1/spatstat/R/mincontrast.R | 524 ++---------
spatstat-1.41-1/spatstat/R/mpl.R | 46
spatstat-1.41-1/spatstat/R/multihard.R | 17
spatstat-1.41-1/spatstat/R/multistrauss.R | 3
spatstat-1.41-1/spatstat/R/multistrhard.R | 43
spatstat-1.41-1/spatstat/R/nncorr.R | 4
spatstat-1.41-1/spatstat/R/nndistlpp.R | 15
spatstat-1.41-1/spatstat/R/options.R | 16
spatstat-1.41-1/spatstat/R/pairdistlpp.R | 4
spatstat-1.41-1/spatstat/R/pairwise.family.R | 4
spatstat-1.41-1/spatstat/R/pcf.R | 6
spatstat-1.41-1/spatstat/R/pcfmulti.R | 18
spatstat-1.41-1/spatstat/R/pcfmulti.inhom.R | 10
spatstat-1.41-1/spatstat/R/pixellate.R | 57 -
spatstat-1.41-1/spatstat/R/plot.anylist.R | 5
spatstat-1.41-1/spatstat/R/plot.owin.R | 4
spatstat-1.41-1/spatstat/R/plot.plotppm.R | 8
spatstat-1.41-1/spatstat/R/plot.ppm.R | 4
spatstat-1.41-1/spatstat/R/plot3d.R |only
spatstat-1.41-1/spatstat/R/pool.R |only
spatstat-1.41-1/spatstat/R/pp3.R | 58 -
spatstat-1.41-1/spatstat/R/ppp.R | 110 --
spatstat-1.41-1/spatstat/R/predict.ppm.R | 2
spatstat-1.41-1/spatstat/R/profilepl.R | 7
spatstat-1.41-1/spatstat/R/psp2pix.R | 59 -
spatstat-1.41-1/spatstat/R/pspcross.R | 74 +
spatstat-1.41-1/spatstat/R/psst.R | 2
spatstat-1.41-1/spatstat/R/psstG.R | 8
spatstat-1.41-1/spatstat/R/quadratmtest.R | 3
spatstat-1.41-1/spatstat/R/quadrattest.R | 23
spatstat-1.41-1/spatstat/R/quantess.R |only
spatstat-1.41-1/spatstat/R/rLGCP.R | 139 +--
spatstat-1.41-1/spatstat/R/random.R | 131 +-
spatstat-1.41-1/spatstat/R/randomNS.R | 198 ++--
spatstat-1.41-1/spatstat/R/randomlpp.R | 8
spatstat-1.41-1/spatstat/R/randommk.R | 57 -
spatstat-1.41-1/spatstat/R/rat.R | 4
spatstat-1.41-1/spatstat/R/reduceformula.R | 2
spatstat-1.41-1/spatstat/R/relrisk.ppm.R | 4
spatstat-1.41-1/spatstat/R/resid4plot.R | 34
spatstat-1.41-1/spatstat/R/residuals.mppm.R | 4
spatstat-1.41-1/spatstat/R/rhohat.R | 10
spatstat-1.41-1/spatstat/R/rlabel.R | 4
spatstat-1.41-1/spatstat/R/rmh.ppm.R | 13
spatstat-1.41-1/spatstat/R/rose.R | 2
spatstat-1.41-1/spatstat/R/segtest.R |only
spatstat-1.41-1/spatstat/R/simulatelppm.R | 11
spatstat-1.41-1/spatstat/R/slrm.R | 13
spatstat-1.41-1/spatstat/R/solist.R | 39
spatstat-1.41-1/spatstat/R/split.ppp.R | 16
spatstat-1.41-1/spatstat/R/subfits.R | 28
spatstat-1.41-1/spatstat/R/summary.im.R | 80 -
spatstat-1.41-1/spatstat/R/summary.mppm.R | 78 -
spatstat-1.41-1/spatstat/R/summary.ppm.R | 2
spatstat-1.41-1/spatstat/R/terse.R | 47 -
spatstat-1.41-1/spatstat/R/tess.R | 198 +++-
spatstat-1.41-1/spatstat/R/units.R | 8
spatstat-1.41-1/spatstat/R/util.R | 56 +
spatstat-1.41-1/spatstat/R/vcov.kppm.R | 180 ++-
spatstat-1.41-1/spatstat/R/weights.R | 132 +-
spatstat-1.41-1/spatstat/R/window.R | 84 +
spatstat-1.41-1/spatstat/R/wingeom.R | 4
spatstat-1.41-1/spatstat/R/xypolygon.R | 31
spatstat-1.41-1/spatstat/R/xysegment.R | 68 -
spatstat-1.41-1/spatstat/data/Kovesi.rda |binary
spatstat-1.41-1/spatstat/data/bdspots.rda |binary
spatstat-1.41-1/spatstat/data/bei.rda |binary
spatstat-1.41-1/spatstat/data/chicago.rda |binary
spatstat-1.41-1/spatstat/data/clmfires.rda |binary
spatstat-1.41-1/spatstat/data/datalist | 2
spatstat-1.41-1/spatstat/data/demohyper.rda |binary
spatstat-1.41-1/spatstat/data/dendrite.rda |only
spatstat-1.41-1/spatstat/data/flu.rda |binary
spatstat-1.41-1/spatstat/data/gorillas.rda |binary
spatstat-1.41-1/spatstat/data/heather.rda |binary
spatstat-1.41-1/spatstat/data/murchison.rda |binary
spatstat-1.41-1/spatstat/data/osteo.rda |binary
spatstat-1.41-1/spatstat/data/pyramidal.rda |binary
spatstat-1.41-1/spatstat/data/spiders.rda |only
spatstat-1.41-1/spatstat/data/waterstriders.rda |binary
spatstat-1.41-1/spatstat/demo/data.R | 9
spatstat-1.41-1/spatstat/demo/spatstat.R | 4
spatstat-1.41-1/spatstat/inst/doc/datasets.R | 164 ++-
spatstat-1.41-1/spatstat/inst/doc/datasets.Rnw | 101 ++
spatstat-1.41-1/spatstat/inst/doc/datasets.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/getstart.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/replicated.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/shapefiles.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/updates.R | 4
spatstat-1.41-1/spatstat/inst/doc/updates.Rnw | 250 +++++
spatstat-1.41-1/spatstat/inst/doc/updates.pdf |binary
spatstat-1.41-1/spatstat/inst/rawdata/osteo |only
spatstat-1.41-1/spatstat/inst/rawdata/sandholes |only
spatstat-1.41-1/spatstat/man/Emark.Rd | 10
spatstat-1.41-1/spatstat/man/K3est.Rd | 11
spatstat-1.41-1/spatstat/man/Kmark.Rd |only
spatstat-1.41-1/spatstat/man/Math.im.Rd | 4
spatstat-1.41-1/spatstat/man/Math.linim.Rd |only
spatstat-1.41-1/spatstat/man/anova.lppm.Rd | 29
spatstat-1.41-1/spatstat/man/anova.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/anova.ppm.Rd | 10
spatstat-1.41-1/spatstat/man/anylist.Rd | 4
spatstat-1.41-1/spatstat/man/as.function.im.Rd |only
spatstat-1.41-1/spatstat/man/as.linnet.linim.Rd |only
spatstat-1.41-1/spatstat/man/as.linnet.psp.Rd |only
spatstat-1.41-1/spatstat/man/as.lpp.Rd | 7
spatstat-1.41-1/spatstat/man/as.solist.Rd | 4
spatstat-1.41-1/spatstat/man/cauchy.estK.Rd | 6
spatstat-1.41-1/spatstat/man/cauchy.estpcf.Rd | 10
spatstat-1.41-1/spatstat/man/cdf.test.Rd | 4
spatstat-1.41-1/spatstat/man/clickbox.Rd | 5
spatstat-1.41-1/spatstat/man/clickdist.Rd |only
spatstat-1.41-1/spatstat/man/clickpoly.Rd | 11
spatstat-1.41-1/spatstat/man/clickppp.Rd | 15
spatstat-1.41-1/spatstat/man/closepairs.Rd | 12
spatstat-1.41-1/spatstat/man/clusterfield.Rd |only
spatstat-1.41-1/spatstat/man/clusterfit.Rd |only
spatstat-1.41-1/spatstat/man/clusterkernel.Rd |only
spatstat-1.41-1/spatstat/man/clusterradius.Rd |only
spatstat-1.41-1/spatstat/man/coef.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/colourtools.Rd | 2
spatstat-1.41-1/spatstat/man/crossdist.psp.Rd | 10
spatstat-1.41-1/spatstat/man/delaunay.Rd | 4
spatstat-1.41-1/spatstat/man/delaunay.distance.Rd | 3
spatstat-1.41-1/spatstat/man/delaunay.network.Rd |only
spatstat-1.41-1/spatstat/man/dendrite.Rd |only
spatstat-1.41-1/spatstat/man/density.ppp.Rd | 9
spatstat-1.41-1/spatstat/man/diagnose.ppm.Rd | 23
spatstat-1.41-1/spatstat/man/dirichlet.vertices.Rd | 36
spatstat-1.41-1/spatstat/man/fitted.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/identify.ppp.Rd | 6
spatstat-1.41-1/spatstat/man/identify.psp.Rd | 4
spatstat-1.41-1/spatstat/man/improve.kppm.Rd | 2
spatstat-1.41-1/spatstat/man/integral.im.Rd | 33
spatstat-1.41-1/spatstat/man/integral.linim.Rd |only
spatstat-1.41-1/spatstat/man/integral.msr.Rd | 11
spatstat-1.41-1/spatstat/man/intersect.tess.Rd | 15
spatstat-1.41-1/spatstat/man/iplot.Rd | 14
spatstat-1.41-1/spatstat/man/is.marked.ppm.Rd | 2
spatstat-1.41-1/spatstat/man/is.multitype.ppm.Rd | 2
spatstat-1.41-1/spatstat/man/is.multitype.ppp.Rd | 8
spatstat-1.41-1/spatstat/man/kppm.Rd | 37
spatstat-1.41-1/spatstat/man/lgcp.estK.Rd | 9
spatstat-1.41-1/spatstat/man/lgcp.estpcf.Rd | 10
spatstat-1.41-1/spatstat/man/linearKcross.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearKdot.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearKinhom.Rd | 6
spatstat-1.41-1/spatstat/man/linearpcfcross.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearpcfdot.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearpcfinhom.Rd | 5
spatstat-1.41-1/spatstat/man/linfun.Rd | 30
spatstat-1.41-1/spatstat/man/linim.Rd | 3
spatstat-1.41-1/spatstat/man/linnet.Rd | 25
spatstat-1.41-1/spatstat/man/logLik.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/lpp.Rd | 5
spatstat-1.41-1/spatstat/man/markcorr.Rd | 6
spatstat-1.41-1/spatstat/man/marks.tess.Rd |only
spatstat-1.41-1/spatstat/man/matclust.estK.Rd | 11
spatstat-1.41-1/spatstat/man/matclust.estpcf.Rd | 9
spatstat-1.41-1/spatstat/man/methods.linfun.Rd | 5
spatstat-1.41-1/spatstat/man/methods.linnet.Rd | 50 -
spatstat-1.41-1/spatstat/man/methods.lppm.Rd | 4
spatstat-1.41-1/spatstat/man/mppm.Rd | 1
spatstat-1.41-1/spatstat/man/nestsplit.Rd |only
spatstat-1.41-1/spatstat/man/nndist.psp.Rd | 9
spatstat-1.41-1/spatstat/man/osteo.Rd | 2
spatstat-1.41-1/spatstat/man/pairdist.psp.Rd | 9
spatstat-1.41-1/spatstat/man/panel.contour.Rd | 2
spatstat-1.41-1/spatstat/man/paracou.Rd | 3
spatstat-1.41-1/spatstat/man/pixellate.Rd | 1
spatstat-1.41-1/spatstat/man/pixellate.psp.Rd | 18
spatstat-1.41-1/spatstat/man/plot.anylist.Rd | 12
spatstat-1.41-1/spatstat/man/plot.cdftest.Rd | 4
spatstat-1.41-1/spatstat/man/plot.fv.Rd | 4
spatstat-1.41-1/spatstat/man/plot.hyperframe.Rd | 11
spatstat-1.41-1/spatstat/man/plot.im.Rd | 11
spatstat-1.41-1/spatstat/man/plot.kppm.Rd | 39
spatstat-1.41-1/spatstat/man/plot.linim.Rd | 10
spatstat-1.41-1/spatstat/man/plot.linnet.Rd | 9
spatstat-1.41-1/spatstat/man/plot.listof.Rd | 12
spatstat-1.41-1/spatstat/man/plot.lpp.Rd | 11
spatstat-1.41-1/spatstat/man/plot.pp3.Rd | 68 -
spatstat-1.41-1/spatstat/man/plot.yardstick.Rd | 32
spatstat-1.41-1/spatstat/man/pool.Rd | 3
spatstat-1.41-1/spatstat/man/pool.anylist.Rd |only
spatstat-1.41-1/spatstat/man/pool.fv.Rd |only
spatstat-1.41-1/spatstat/man/pool.rat.Rd | 1
spatstat-1.41-1/spatstat/man/predict.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/print.owin.Rd | 3
spatstat-1.41-1/spatstat/man/quadrat.test.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/quantess.Rd |only
spatstat-1.41-1/spatstat/man/rCauchy.Rd | 68 +
spatstat-1.41-1/spatstat/man/rGaussPoisson.Rd | 8
spatstat-1.41-1/spatstat/man/rMatClust.Rd | 55 -
spatstat-1.41-1/spatstat/man/rMaternI.Rd | 8
spatstat-1.41-1/spatstat/man/rMaternII.Rd | 8
spatstat-1.41-1/spatstat/man/rNeymanScott.Rd | 33
spatstat-1.41-1/spatstat/man/rPoissonCluster.Rd | 41
spatstat-1.41-1/spatstat/man/rSSI.Rd | 8
spatstat-1.41-1/spatstat/man/rThomas.Rd | 47 -
spatstat-1.41-1/spatstat/man/rVarGamma.Rd | 69 -
spatstat-1.41-1/spatstat/man/rcell.Rd | 8
spatstat-1.41-1/spatstat/man/residuals.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/rjitter.Rd | 7
spatstat-1.41-1/spatstat/man/rmpoint.Rd | 24
spatstat-1.41-1/spatstat/man/rmpoispp.Rd | 22
spatstat-1.41-1/spatstat/man/rpoint.Rd | 7
spatstat-1.41-1/spatstat/man/rpoislpp.Rd | 5
spatstat-1.41-1/spatstat/man/rpoispp.Rd | 39
spatstat-1.41-1/spatstat/man/rpoisppOnLines.Rd | 2
spatstat-1.41-1/spatstat/man/rstrat.Rd | 7
spatstat-1.41-1/spatstat/man/rsyst.Rd | 8
spatstat-1.41-1/spatstat/man/rthin.Rd | 7
spatstat-1.41-1/spatstat/man/runifdisc.Rd | 7
spatstat-1.41-1/spatstat/man/runifpoint.Rd | 8
spatstat-1.41-1/spatstat/man/segregation.test.Rd |only
spatstat-1.41-1/spatstat/man/selfcut.psp.Rd |only
spatstat-1.41-1/spatstat/man/simulate.kppm.Rd | 8
spatstat-1.41-1/spatstat/man/simulate.lppm.Rd | 10
spatstat-1.41-1/spatstat/man/simulate.ppm.Rd | 10
spatstat-1.41-1/spatstat/man/simulate.slrm.Rd | 7
spatstat-1.41-1/spatstat/man/solapply.Rd |only
spatstat-1.41-1/spatstat/man/solist.Rd | 27
spatstat-1.41-1/spatstat/man/solutionset.Rd | 27
spatstat-1.41-1/spatstat/man/spatstat-internal.Rd | 99 +-
spatstat-1.41-1/spatstat/man/spatstat-package.Rd | 22
spatstat-1.41-1/spatstat/man/spatstat.options.Rd | 12
spatstat-1.41-1/spatstat/man/spiders.Rd |only
spatstat-1.41-1/spatstat/man/split.ppp.Rd | 13
spatstat-1.41-1/spatstat/man/spokes.Rd | 12
spatstat-1.41-1/spatstat/man/subfits.Rd | 1
spatstat-1.41-1/spatstat/man/subset.hyperframe.Rd |only
spatstat-1.41-1/spatstat/man/tess.Rd | 28
spatstat-1.41-1/spatstat/man/thomas.estK.Rd | 27
spatstat-1.41-1/spatstat/man/thomas.estpcf.Rd | 29
spatstat-1.41-1/spatstat/man/vargamma.estK.Rd | 19
spatstat-1.41-1/spatstat/man/vargamma.estpcf.Rd | 19
spatstat-1.41-1/spatstat/man/vcov.kppm.Rd | 7
spatstat-1.41-1/spatstat/man/vcov.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/vertices.Rd | 13
spatstat-1.41-1/spatstat/man/waka.Rd | 2
spatstat-1.41-1/spatstat/src/close3pair.c | 8
spatstat-1.41-1/spatstat/src/closefuns.h | 162 ++-
spatstat-1.41-1/spatstat/src/closepair.c | 19
spatstat-1.41-1/spatstat/src/seg2pix.c | 151 ---
spatstat-1.41-1/spatstat/src/seg2pix.h |only
spatstat-1.41-1/spatstat/tests/alltests.R | 59 -
spatstat-1.41-1/spatstat/vignettes/datasets.Rnw | 101 ++
spatstat-1.41-1/spatstat/vignettes/packagesizes.txt | 2
spatstat-1.41-1/spatstat/vignettes/updates.Rnw | 250 +++++
315 files changed, 6877 insertions(+), 3297 deletions(-)
Title: Rcpp Integration for the Eigen Templated Linear Algebra Library
Diff between RcppEigen versions 0.3.2.3.0 dated 2014-12-23 and 0.3.2.4.0 dated 2015-02-27
Description: R and Eigen integration using Rcpp.
Eigen is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on Lapack and level-3 BLAS.
The RcppEigen package includes the header files from the Eigen C++
template library (currently version 3.2.3). Thus users do not need to
install Eigen itself in order to use RcppEigen.
Since version 3.1.1, Eigen is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. RcppEigen (the Rcpp bindings/bridge to Eigen) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel
RcppEigen-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/Core/Product.h |only
RcppEigen-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/CoreIterators.h |only
RcppEigen-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseAssign.h |only
RcppEigen-0.3.2.4.0/RcppEigen/ChangeLog | 24 +++
RcppEigen-0.3.2.4.0/RcppEigen/DESCRIPTION | 12 -
RcppEigen-0.3.2.4.0/RcppEigen/MD5 | 36 ++---
RcppEigen-0.3.2.4.0/RcppEigen/R/RcppEigen.package.skeleton.R | 45 ++++--
RcppEigen-0.3.2.4.0/RcppEigen/README.md | 25 +--
RcppEigen-0.3.2.4.0/RcppEigen/inst/NEWS.Rd | 11 +
RcppEigen-0.3.2.4.0/RcppEigen/inst/doc/RcppEigen-Introduction.pdf |binary
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h | 70 ----------
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/MapBase.h | 11 -
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/Complex.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/util/Macros.h | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/util/Memory.h | 5
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealQZ.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Geometry/Rotation2D.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/Makevars | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/Makevars.win | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/rcppeigen_hello_world.Rd |only
21 files changed, 118 insertions(+), 143 deletions(-)
Title: Multi-Analysis Distance Sampling
Diff between mads versions 0.1.1 dated 2014-12-23 and 0.1.2 dated 2015-02-27
Description: Performs distance sampling analyses on a number of species
accounting for unidentified sightings, model uncertainty and covariate
uncertainty.
Author: Laura Marshall
Maintainer: Laura Marshall
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NEWS | 11 +++++++++++
R/calculate.dht.R | 5 +++--
R/check.bootstrap.options.r | 6 +++---
R/check.ddf.models.R | 1 -
R/execute.multi.analysis.R | 9 +++++----
R/fit.ddf.models.R | 19 ++++++++++---------
R/mae.warning.R | 6 +++---
R/process.warnings.R | 5 ++++-
10 files changed, 52 insertions(+), 36 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Diff between geostatsp versions 1.1.9 dated 2015-01-23 and 1.2.1 dated 2015-02-27
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation..
Author: Patrick Brown
Maintainer: Patrick Brown
geostatsp-1.1.9/geostatsp/src/maternLogLgr.c |only
geostatsp-1.2.1/geostatsp/DESCRIPTION | 12
geostatsp-1.2.1/geostatsp/MD5 | 100 ++-
geostatsp-1.2.1/geostatsp/NAMESPACE | 9
geostatsp-1.2.1/geostatsp/R/RFsimulate.R | 45 -
geostatsp-1.2.1/geostatsp/R/excProb.R | 2
geostatsp-1.2.1/geostatsp/R/informationLgm.R | 72 +-
geostatsp-1.2.1/geostatsp/R/krige.R | 150 +++-
geostatsp-1.2.1/geostatsp/R/lgm.R | 55 -
geostatsp-1.2.1/geostatsp/R/lgm.Raster.R | 2
geostatsp-1.2.1/geostatsp/R/loglikGmrf.R | 321 ++++++++--
geostatsp-1.2.1/geostatsp/R/loglikLgm.R | 675 ++++++++++++----------
geostatsp-1.2.1/geostatsp/R/matern.R | 17
geostatsp-1.2.1/geostatsp/R/maternGmrfPrec.R | 17
geostatsp-1.2.1/geostatsp/R/param.R | 11
geostatsp-1.2.1/geostatsp/R/profLlgm.R | 150 ++--
geostatsp-1.2.1/geostatsp/R/spdfToBrick.R |only
geostatsp-1.2.1/geostatsp/R/variog.R | 8
geostatsp-1.2.1/geostatsp/data/datalist | 4
geostatsp-1.2.1/geostatsp/data/murder.RData |binary
geostatsp-1.2.1/geostatsp/data/torontoPop.RData |binary
geostatsp-1.2.1/geostatsp/inst/extdata |only
geostatsp-1.2.1/geostatsp/man/krige.Rd | 22
geostatsp-1.2.1/geostatsp/man/likfitLgm.Rd | 37 -
geostatsp-1.2.1/geostatsp/man/maternGmrfPrec.Rd | 10
geostatsp-1.2.1/geostatsp/man/murder.Rd | 199 ++++++
geostatsp-1.2.1/geostatsp/man/profLlgm.Rd | 2
geostatsp-1.2.1/geostatsp/man/stackRasterList.Rd | 19
geostatsp-1.2.1/geostatsp/man/variog.Rd | 12
geostatsp-1.2.1/geostatsp/src/geostatsp.h | 16
geostatsp-1.2.1/geostatsp/src/matern.c | 20
geostatsp-1.2.1/geostatsp/src/maternLogL.c | 203 +++---
geostatsp-1.2.1/geostatsp/src/maternLogLopt.c |only
geostatsp-1.2.1/geostatsp/src/sparseLogL.c |only
geostatsp-1.2.1/geostatsp/tests/RFsimulate.R | 39 -
geostatsp-1.2.1/geostatsp/tests/krige.R | 11
geostatsp-1.2.1/geostatsp/tests/lgm.R | 14
geostatsp-1.2.1/geostatsp/tests/lgmRaster.R | 76 --
geostatsp-1.2.1/geostatsp/tests/likfitLgm.R | 80 ++
geostatsp-1.2.1/geostatsp/tests/maternGmrfPrec.R | 4
geostatsp-1.2.1/geostatsp/tests/profLlgm.R | 111 ++-
geostatsp-1.2.1/geostatsp/tests/stackRasterList.R |only
42 files changed, 1635 insertions(+), 890 deletions(-)
Title: Distance Sampling Simulations
Diff between DSsim versions 1.0.2 dated 2014-12-23 and 1.0.3 dated 2015-02-27
Description: Performs distance sampling simulations. It repeatedly
generates instances of a user defined population within a given survey
region, generates realisations of a survey design (currently these must
be pre-generated using Distance software) and simulates the detection
process. The data are then analysed so that the results can be compared for
accuracy and precision across all replications. This will allow users to
select survey designs which will give them the best accuracy and precision
given their expectations about population distribution. Any uncertainty in
population distribution or population parameters can be included by running
the different survey designs for a number of different population
descriptions. An example simulation can be found in the help file
for make.simulation.
Author: Laura Marshall
Maintainer: Laura Marshall
DESCRIPTION | 8 +-
MD5 | 37 ++++-----
NEWS | 71 +++++++++++-------
R/Class.Constructors.R | 20 +++--
R/DDF.Analysis.R | 14 +--
R/Density.R | 156 +++++++++++++++++++++++++++++------------
R/LT.Design.R | 10 +-
R/Population.Description.R | 4 -
R/Region.R | 29 ++++---
R/Simulation.R | 2
R/add.dist.error.R | 2
R/check.intersection.R | 4 -
R/get.sampler.info.R | 4 -
R/is.gap.R | 2
R/single.simulation.loop.R | 10 --
inst/tests/test_Constructors.R |only
man/Density-class.Rd | 16 ++--
man/Region-class.Rd | 11 +-
man/make.density.Rd | 10 ++
man/make.simulation.Rd | 2
20 files changed, 256 insertions(+), 156 deletions(-)
Title: Biological Structure Analysis
Diff between bio3d versions 2.1-3 dated 2014-10-27 and 2.2-1 dated 2015-02-27
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant
bio3d-2.1-3/bio3d/R/cmap.filter.R |only
bio3d-2.1-3/bio3d/R/combine.sel.R |only
bio3d-2.1-3/bio3d/R/dssp.trj.R |only
bio3d-2.1-3/bio3d/R/ide.filter.R |only
bio3d-2.1-3/bio3d/R/pdbs.filter.R |only
bio3d-2.1-3/bio3d/R/plot.bio3d.R |only
bio3d-2.1-3/bio3d/R/plot.dccm2.R |only
bio3d-2.1-3/bio3d/R/rmsd.filter.R |only
bio3d-2.1-3/bio3d/data/aa.mass.rda |only
bio3d-2.1-3/bio3d/man/aa.mass.Rd |only
bio3d-2.1-3/bio3d/man/cmap.filter.Rd |only
bio3d-2.1-3/bio3d/man/combine.sel.Rd |only
bio3d-2.1-3/bio3d/man/dssp.pdbs.Rd |only
bio3d-2.1-3/bio3d/man/dssp.trj.Rd |only
bio3d-2.1-3/bio3d/man/ide.filter.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.enma.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.nma.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.pca.Rd |only
bio3d-2.1-3/bio3d/man/pdbs.filter.Rd |only
bio3d-2.1-3/bio3d/man/plot.blast.Rd |only
bio3d-2.1-3/bio3d/man/rmsd.filter.Rd |only
bio3d-2.1-3/bio3d/tests/test-all.R |only
bio3d-2.2-1/bio3d/DESCRIPTION | 6
bio3d-2.2-1/bio3d/MD5 | 453 ++++++++++----------
bio3d-2.2-1/bio3d/NAMESPACE | 100 ++++
bio3d-2.2-1/bio3d/NEWS | 78 ++-
bio3d-2.2-1/bio3d/R/aa2mass.R | 44 +
bio3d-2.2-1/bio3d/R/aa321.R | 43 +
bio3d-2.2-1/bio3d/R/amsm.xyz.R | 2
bio3d-2.2-1/bio3d/R/as.fasta.R |only
bio3d-2.2-1/bio3d/R/as.pdb.R |only
bio3d-2.2-1/bio3d/R/as.pdb.mol2.R |only
bio3d-2.2-1/bio3d/R/as.pdb.prmtop.R |only
bio3d-2.2-1/bio3d/R/as.select.R |only
bio3d-2.2-1/bio3d/R/as.xyz.R | 2
bio3d-2.2-1/bio3d/R/atom.select.R | 287 ------------
bio3d-2.2-1/bio3d/R/atom.select.pdb.R |only
bio3d-2.2-1/bio3d/R/atom.select.prmtop.R |only
bio3d-2.2-1/bio3d/R/basename.pdb.R |only
bio3d-2.2-1/bio3d/R/binding.site.R | 164 ++++---
bio3d-2.2-1/bio3d/R/biounit.R |only
bio3d-2.2-1/bio3d/R/bounds.sse.R |only
bio3d-2.2-1/bio3d/R/cat.pdb.R |only
bio3d-2.2-1/bio3d/R/chain.pdb.R | 15
bio3d-2.2-1/bio3d/R/clean.pdb.R |only
bio3d-2.2-1/bio3d/R/cmap.R | 12
bio3d-2.2-1/bio3d/R/cmap.pdb.R |only
bio3d-2.2-1/bio3d/R/cna.dccm.R | 10
bio3d-2.2-1/bio3d/R/cna.ensmb.R | 2
bio3d-2.2-1/bio3d/R/cnapath.R |only
bio3d-2.2-1/bio3d/R/com.R | 31 -
bio3d-2.2-1/bio3d/R/com.pdb.R |only
bio3d-2.2-1/bio3d/R/com.xyz.R | 23 -
bio3d-2.2-1/bio3d/R/combine.select.R |only
bio3d-2.2-1/bio3d/R/convert.pdb.R | 38 +
bio3d-2.2-1/bio3d/R/core.find.R | 114 +++--
bio3d-2.2-1/bio3d/R/dccm.pca.R | 38 +
bio3d-2.2-1/bio3d/R/dm.R | 36 -
bio3d-2.2-1/bio3d/R/dm.xyz.R | 77 +++
bio3d-2.2-1/bio3d/R/dssp.R | 274 ------------
bio3d-2.2-1/bio3d/R/dssp.pdb.R |only
bio3d-2.2-1/bio3d/R/dssp.pdbs.R | 47 +-
bio3d-2.2-1/bio3d/R/dssp.xyz.R |only
bio3d-2.2-1/bio3d/R/filter.cmap.R |only
bio3d-2.2-1/bio3d/R/filter.dccm.R | 7
bio3d-2.2-1/bio3d/R/filter.identity.R |only
bio3d-2.2-1/bio3d/R/filter.rmsd.R |only
bio3d-2.2-1/bio3d/R/fit.xyz.R | 36 -
bio3d-2.2-1/bio3d/R/geostas.R | 188 ++++++--
bio3d-2.2-1/bio3d/R/hmmer.R | 9
bio3d-2.2-1/bio3d/R/inspect.connectivity.R | 7
bio3d-2.2-1/bio3d/R/is.gap.R | 8
bio3d-2.2-1/bio3d/R/mktrj.R | 5
bio3d-2.2-1/bio3d/R/mktrj.enma.R | 30 -
bio3d-2.2-1/bio3d/R/mktrj.nma.R | 16
bio3d-2.2-1/bio3d/R/mktrj.pca.R | 14
bio3d-2.2-1/bio3d/R/mustang.R | 30 +
bio3d-2.2-1/bio3d/R/nma.pdbs.R | 40 -
bio3d-2.2-1/bio3d/R/pca.xyz.R | 37 +
bio3d-2.2-1/bio3d/R/pdb2aln.R | 37 -
bio3d-2.2-1/bio3d/R/pdb2aln.ind.R | 24 -
bio3d-2.2-1/bio3d/R/pdb2sse.R |only
bio3d-2.2-1/bio3d/R/pdbfit.R | 26 +
bio3d-2.2-1/bio3d/R/pdbsplit.R | 29 -
bio3d-2.2-1/bio3d/R/plot.cmap.R |only
bio3d-2.2-1/bio3d/R/plot.enma.R | 129 +++--
bio3d-2.2-1/bio3d/R/plot.fluct.R |only
bio3d-2.2-1/bio3d/R/plot.geostas.R |only
bio3d-2.2-1/bio3d/R/plot.pca.R | 49 +-
bio3d-2.2-1/bio3d/R/plotb3.R |only
bio3d-2.2-1/bio3d/R/print.fasta.R | 30 +
bio3d-2.2-1/bio3d/R/print.geostas.R |only
bio3d-2.2-1/bio3d/R/print.pdb.R | 4
bio3d-2.2-1/bio3d/R/print.prmtop.R |only
bio3d-2.2-1/bio3d/R/read.all.R | 2
bio3d-2.2-1/bio3d/R/read.crd.R | 56 --
bio3d-2.2-1/bio3d/R/read.crd.amber.R |only
bio3d-2.2-1/bio3d/R/read.crd.charmm.R |only
bio3d-2.2-1/bio3d/R/read.dcd.R | 6
bio3d-2.2-1/bio3d/R/read.fasta.pdb.R | 80 ++-
bio3d-2.2-1/bio3d/R/read.mol2.R | 100 +++-
bio3d-2.2-1/bio3d/R/read.pdb.R | 150 +++++-
bio3d-2.2-1/bio3d/R/read.prmtop.R |only
bio3d-2.2-1/bio3d/R/rmsf.R | 13
bio3d-2.2-1/bio3d/R/seq2aln.R | 45 -
bio3d-2.2-1/bio3d/R/seqaln.R | 15
bio3d-2.2-1/bio3d/R/seqaln.pair.R | 12
bio3d-2.2-1/bio3d/R/seqbind.R | 9
bio3d-2.2-1/bio3d/R/store.atom.R | 6
bio3d-2.2-1/bio3d/R/summary.cnapath.R |only
bio3d-2.2-1/bio3d/R/summary.pdb.R | 72 ++-
bio3d-2.2-1/bio3d/R/trim.pdb.R | 154 ++----
bio3d-2.2-1/bio3d/R/trim.pdbs.R |only
bio3d-2.2-1/bio3d/R/trim.xyz.R |only
bio3d-2.2-1/bio3d/R/unbound.R | 7
bio3d-2.2-1/bio3d/R/view.cnapath.R |only
bio3d-2.2-1/bio3d/R/wrap.tor.R | 9
bio3d-2.2-1/bio3d/R/write.pdb.R | 16
bio3d-2.2-1/bio3d/README.md | 8
bio3d-2.2-1/bio3d/build/vignette.rds |binary
bio3d-2.2-1/bio3d/data/aa.table.rda |only
bio3d-2.2-1/bio3d/data/kinesin.RData |binary
bio3d-2.2-1/bio3d/data/transducin.RData |binary
bio3d-2.2-1/bio3d/inst/CITATION | 2
bio3d-2.2-1/bio3d/inst/doc/bio3d_vignettes.Rmd | 18
bio3d-2.2-1/bio3d/inst/doc/bio3d_vignettes.html | 14
bio3d-2.2-1/bio3d/inst/examples/test.pdb |only
bio3d-2.2-1/bio3d/inst/staticdocs/index.r | 49 +-
bio3d-2.2-1/bio3d/man/aa.index.Rd | 4
bio3d-2.2-1/bio3d/man/aa.table.Rd |only
bio3d-2.2-1/bio3d/man/aa123.Rd | 18
bio3d-2.2-1/bio3d/man/aln2html.Rd | 2
bio3d-2.2-1/bio3d/man/angle.xyz.Rd | 8
bio3d-2.2-1/bio3d/man/as.fasta.Rd |only
bio3d-2.2-1/bio3d/man/as.pdb.Rd |only
bio3d-2.2-1/bio3d/man/as.select.Rd |only
bio3d-2.2-1/bio3d/man/atom.select.Rd | 180 ++++---
bio3d-2.2-1/bio3d/man/atom2ele.Rd | 2
bio3d-2.2-1/bio3d/man/atom2mass.Rd | 1
bio3d-2.2-1/bio3d/man/basename.pdb.Rd |only
bio3d-2.2-1/bio3d/man/bhattacharyya.Rd | 6
bio3d-2.2-1/bio3d/man/binding.site.Rd | 60 +-
bio3d-2.2-1/bio3d/man/bio3d.package.Rd | 232 ----------
bio3d-2.2-1/bio3d/man/biounit.Rd |only
bio3d-2.2-1/bio3d/man/blast.pdb.Rd | 86 +++
bio3d-2.2-1/bio3d/man/bounds.sse.Rd |only
bio3d-2.2-1/bio3d/man/bwr.colors.Rd | 4
bio3d-2.2-1/bio3d/man/cat.pdb.Rd |only
bio3d-2.2-1/bio3d/man/chain.pdb.Rd | 2
bio3d-2.2-1/bio3d/man/clean.pdb.Rd |only
bio3d-2.2-1/bio3d/man/cmap.Rd | 31 +
bio3d-2.2-1/bio3d/man/cna.Rd | 5
bio3d-2.2-1/bio3d/man/cnapath.Rd |only
bio3d-2.2-1/bio3d/man/com.Rd | 36 +
bio3d-2.2-1/bio3d/man/combine.select.Rd |only
bio3d-2.2-1/bio3d/man/community.tree.Rd | 1
bio3d-2.2-1/bio3d/man/conserv.Rd | 2
bio3d-2.2-1/bio3d/man/convert.pdb.Rd | 4
bio3d-2.2-1/bio3d/man/core.find.Rd | 32 +
bio3d-2.2-1/bio3d/man/covsoverlap.Rd | 5
bio3d-2.2-1/bio3d/man/dccm.enma.Rd | 2
bio3d-2.2-1/bio3d/man/dccm.nma.Rd | 2
bio3d-2.2-1/bio3d/man/dccm.pca.Rd | 21
bio3d-2.2-1/bio3d/man/dccm.xyz.Rd | 4
bio3d-2.2-1/bio3d/man/deformation.nma.Rd | 2
bio3d-2.2-1/bio3d/man/difference.vector.Rd | 3
bio3d-2.2-1/bio3d/man/dist.xyz.Rd | 2
bio3d-2.2-1/bio3d/man/dm.Rd | 28 -
bio3d-2.2-1/bio3d/man/dssp.Rd | 57 ++
bio3d-2.2-1/bio3d/man/filter.cmap.Rd |only
bio3d-2.2-1/bio3d/man/filter.dccm.Rd | 2
bio3d-2.2-1/bio3d/man/filter.identity.Rd |only
bio3d-2.2-1/bio3d/man/filter.rmsd.Rd |only
bio3d-2.2-1/bio3d/man/fit.xyz.Rd | 12
bio3d-2.2-1/bio3d/man/geostas.Rd | 134 ++++-
bio3d-2.2-1/bio3d/man/get.pdb.Rd | 1
bio3d-2.2-1/bio3d/man/get.seq.Rd | 12
bio3d-2.2-1/bio3d/man/hclustplot.Rd | 7
bio3d-2.2-1/bio3d/man/hmmer.Rd | 122 ++++-
bio3d-2.2-1/bio3d/man/identify.cna.Rd | 3
bio3d-2.2-1/bio3d/man/inspect.connectivity.Rd | 2
bio3d-2.2-1/bio3d/man/is.gap.Rd | 20
bio3d-2.2-1/bio3d/man/layout.cna.Rd | 4
bio3d-2.2-1/bio3d/man/lmi.Rd | 5
bio3d-2.2-1/bio3d/man/load.enmff.Rd | 1
bio3d-2.2-1/bio3d/man/mktrj.Rd | 93 ++--
bio3d-2.2-1/bio3d/man/motif.find.Rd | 2
bio3d-2.2-1/bio3d/man/mustang.Rd | 23 -
bio3d-2.2-1/bio3d/man/network.amendment.Rd | 1
bio3d-2.2-1/bio3d/man/nma.Rd | 80 ++-
bio3d-2.2-1/bio3d/man/nma.pdb.Rd | 55 +-
bio3d-2.2-1/bio3d/man/nma.pdbs.Rd | 27 -
bio3d-2.2-1/bio3d/man/orient.pdb.Rd | 4
bio3d-2.2-1/bio3d/man/overlap.Rd | 6
bio3d-2.2-1/bio3d/man/pca.Rd | 5
bio3d-2.2-1/bio3d/man/pca.pdbs.Rd | 2
bio3d-2.2-1/bio3d/man/pca.xyz.Rd | 53 +-
bio3d-2.2-1/bio3d/man/pdb.annotate.Rd | 1
bio3d-2.2-1/bio3d/man/pdb2aln.Rd | 83 +--
bio3d-2.2-1/bio3d/man/pdb2aln.ind.Rd | 90 ++-
bio3d-2.2-1/bio3d/man/pdb2sse.Rd |only
bio3d-2.2-1/bio3d/man/pdbfit.Rd | 28 -
bio3d-2.2-1/bio3d/man/pdbseq.Rd | 11
bio3d-2.2-1/bio3d/man/pdbsplit.Rd | 4
bio3d-2.2-1/bio3d/man/pfam.Rd | 2
bio3d-2.2-1/bio3d/man/plot.bio3d.Rd | 90 +++
bio3d-2.2-1/bio3d/man/plot.cmap.Rd |only
bio3d-2.2-1/bio3d/man/plot.cna.Rd | 4
bio3d-2.2-1/bio3d/man/plot.dccm.Rd | 9
bio3d-2.2-1/bio3d/man/plot.dmat.Rd | 14
bio3d-2.2-1/bio3d/man/plot.enma.Rd | 1
bio3d-2.2-1/bio3d/man/plot.fluct.Rd |only
bio3d-2.2-1/bio3d/man/plot.geostas.Rd |only
bio3d-2.2-1/bio3d/man/plot.hmmer.Rd | 1
bio3d-2.2-1/bio3d/man/plot.nma.Rd | 5
bio3d-2.2-1/bio3d/man/plot.pca.Rd | 28 -
bio3d-2.2-1/bio3d/man/print.cna.Rd | 2
bio3d-2.2-1/bio3d/man/print.fasta.Rd | 6
bio3d-2.2-1/bio3d/man/prune.cna.Rd | 3
bio3d-2.2-1/bio3d/man/read.all.Rd | 1
bio3d-2.2-1/bio3d/man/read.crd.Rd | 82 +--
bio3d-2.2-1/bio3d/man/read.crd.amber.Rd |only
bio3d-2.2-1/bio3d/man/read.crd.charmm.Rd |only
bio3d-2.2-1/bio3d/man/read.dcd.Rd | 6
bio3d-2.2-1/bio3d/man/read.fasta.pdb.Rd | 3
bio3d-2.2-1/bio3d/man/read.mol2.Rd | 36 +
bio3d-2.2-1/bio3d/man/read.ncdf.Rd | 2
bio3d-2.2-1/bio3d/man/read.pdb.Rd | 27 -
bio3d-2.2-1/bio3d/man/read.pdcBD.Rd | 2
bio3d-2.2-1/bio3d/man/read.pqr.Rd | 2
bio3d-2.2-1/bio3d/man/read.prmtop.Rd |only
bio3d-2.2-1/bio3d/man/rgyr.Rd | 2
bio3d-2.2-1/bio3d/man/rle2.Rd | 2
bio3d-2.2-1/bio3d/man/rmsd.Rd | 25 -
bio3d-2.2-1/bio3d/man/rmsf.Rd | 8
bio3d-2.2-1/bio3d/man/rmsip.Rd | 7
bio3d-2.2-1/bio3d/man/sdENM.Rd | 2
bio3d-2.2-1/bio3d/man/seq2aln.Rd | 5
bio3d-2.2-1/bio3d/man/seqaln.Rd | 12
bio3d-2.2-1/bio3d/man/seqaln.pair.Rd | 9
bio3d-2.2-1/bio3d/man/seqbind.Rd | 8
bio3d-2.2-1/bio3d/man/seqidentity.Rd | 5
bio3d-2.2-1/bio3d/man/sip.Rd | 4
bio3d-2.2-1/bio3d/man/struct.aln.Rd | 2
bio3d-2.2-1/bio3d/man/torsion.pdb.Rd | 8
bio3d-2.2-1/bio3d/man/torsion.xyz.Rd | 4
bio3d-2.2-1/bio3d/man/trim.pdb.Rd | 21
bio3d-2.2-1/bio3d/man/trim.pdbs.Rd |only
bio3d-2.2-1/bio3d/man/trim.xyz.Rd |only
bio3d-2.2-1/bio3d/man/unbound.Rd | 16
bio3d-2.2-1/bio3d/man/uniprot.Rd | 2
bio3d-2.2-1/bio3d/man/view.cna.Rd | 3
bio3d-2.2-1/bio3d/man/write.fasta.Rd | 2
bio3d-2.2-1/bio3d/man/write.ncdf.Rd | 2
bio3d-2.2-1/bio3d/man/write.pdb.Rd | 1
bio3d-2.2-1/bio3d/man/write.pir.Rd | 2
bio3d-2.2-1/bio3d/man/write.pqr.Rd | 1
bio3d-2.2-1/bio3d/tests/testthat.R |only
bio3d-2.2-1/bio3d/tests/testthat/test-atom.select.R |only
bio3d-2.2-1/bio3d/tests/testthat/test-atom2mass.R | 6
bio3d-2.2-1/bio3d/tests/testthat/test-clean.pdb.R |only
bio3d-2.2-1/bio3d/tests/testthat/test-core.find.R | 3
bio3d-2.2-1/bio3d/tests/testthat/test-fitting.R | 4
bio3d-2.2-1/bio3d/tests/testthat/test-nma.R | 6
bio3d-2.2-1/bio3d/tests/testthat/test-nma.pdbs.R | 10
bio3d-2.2-1/bio3d/tests/testthat/test-overlap.R | 8
bio3d-2.2-1/bio3d/tests/testthat/test-pca.R | 2
bio3d-2.2-1/bio3d/tests/testthat/test-read.pdb.R | 34 +
bio3d-2.2-1/bio3d/tests/testthat/test-rmsd.R | 3
bio3d-2.2-1/bio3d/vignettes/bio3d_vignettes.Rmd | 18
270 files changed, 3382 insertions(+), 2420 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-17 1.2-6