Title: like base::sets tools but keeps duplicate elements.
Diff between vecsets versions 1.0 dated 2014-02-11 and 1.1 dated 2014-10-24
Description: The base 'sets' tools follow the algebraic definition
that each element of a set must be unique.
Since it's often helpful to compare all elements of two vectors,
this toolset treats every element as unique for counting purposes.
For ease of use, all functions in vecsets have an argument
'multiple' which, when set to FALSE,
reverts them to the base::set tools functionality.
Author: Carl Witthoft
Maintainer: Carl Witthoft
ChangeLog |only
DESCRIPTION | 8 ++++----
MD5 | 5 +++--
R/vsetdiff.R | 8 ++++++--
4 files changed, 13 insertions(+), 8 deletions(-)
Title: Conditional logistic regression: A two-step estimation method
Diff between TwoStepCLogit versions 1.2.2 dated 2013-06-11 and 1.2.3 dated 2014-10-24
Description: Conditional logistic regression with longitudinal follow up and
individual-level random coefficients: A stable and efficient
two-step estimation method
Author: Radu V. Craiu, Thierry Duchesne, Daniel Fortin and Sophie Baillargeon
Maintainer: Thierry Duchesne
DESCRIPTION | 17 ++---
MD5 | 20 +++---
NAMESPACE | 3
R/Ts.estim.R | 12 +--
R/TwoStepCLogit.R | 4 -
R/internal.R | 2
inst/NEWS.Rd | 5 +
man/Ts.estim.Rd | 134 ++++++++++++++++++-------------------------
man/TwoStepCLogit-package.Rd | 35 +++++------
man/bison.Rd | 40 +++++-------
man/ddim.Rd | 44 ++++++--------
11 files changed, 146 insertions(+), 170 deletions(-)
Title: Evaluation of surrogate endpoints in clinical trials
Diff between Surrogate versions 0.1-2 dated 2014-07-30 and 0.1-3 dated 2014-10-24
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks (for normally distributed endpoints). Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst
Surrogate-0.1-2/Surrogate/R/ICABinBin.R |only
Surrogate-0.1-2/Surrogate/R/MarginalProbs.R |only
Surrogate-0.1-2/Surrogate/R/RandVec.R |only
Surrogate-0.1-2/Surrogate/R/SimDataCounterfactualsBinBin.R |only
Surrogate-0.1-2/Surrogate/R/SimDataSTSBinBin.R |only
Surrogate-0.1-2/Surrogate/R/minSurrBinBin.R |only
Surrogate-0.1-2/Surrogate/R/plot_ICABinBin.R |only
Surrogate-0.1-2/Surrogate/R/summary_ICABinBin.R |only
Surrogate-0.1-2/Surrogate/man/ICABinBin.Rd |only
Surrogate-0.1-2/Surrogate/man/MarginalProbs.Rd |only
Surrogate-0.1-2/Surrogate/man/MinSurrBinBin.Rd |only
Surrogate-0.1-2/Surrogate/man/RandVec.Rd |only
Surrogate-0.1-2/Surrogate/man/Sim.Data.CounterfactualsBinBin.Rd |only
Surrogate-0.1-2/Surrogate/man/Sim.Data.STSBinBin.Rd |only
Surrogate-0.1-2/Surrogate/man/plot.ICABinBin.Rd |only
Surrogate-0.1-3/Surrogate/DESCRIPTION | 10 -
Surrogate-0.1-3/Surrogate/INDEX | 74 ++++++++--
Surrogate-0.1-3/Surrogate/MD5 | 49 ++----
Surrogate-0.1-3/Surrogate/NEWS | 6
Surrogate-0.1-3/Surrogate/R/BifixedContCont.R | 17 +-
Surrogate-0.1-3/Surrogate/R/BimixedContCont.R | 10 -
Surrogate-0.1-3/Surrogate/R/FixedContContIT.r | 5
Surrogate-0.1-3/Surrogate/R/MixedContContIT.R | 2
Surrogate-0.1-3/Surrogate/R/plot.InfoTheoretic.R | 1
Surrogate-0.1-3/Surrogate/man/ARMD.Rd | 2
Surrogate-0.1-3/Surrogate/man/FixedContContIT.Rd | 3
Surrogate-0.1-3/Surrogate/man/ICAContCont.Rd | 5
Surrogate-0.1-3/Surrogate/man/MICAContCont.Rd | 6
Surrogate-0.1-3/Surrogate/man/MinSurrContCont.Rd | 2
Surrogate-0.1-3/Surrogate/man/MixedContContIT.Rd | 4
Surrogate-0.1-3/Surrogate/man/Sim.Data.Counterfactuals.Rd | 5
Surrogate-0.1-3/Surrogate/man/plot.CausalInference.Rd | 6
Surrogate-0.1-3/Surrogate/man/summary.gen.Rd | 4
33 files changed, 118 insertions(+), 93 deletions(-)
Title: The sparr package: SPAtial Relative Risk
Diff between sparr versions 0.3-5 dated 2014-05-30 and 0.3-6 dated 2014-10-24
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
NAMESPACE | 5 +++--
R/zzz.R | 2 +-
man/sparr-package.Rd | 7 +++----
5 files changed, 17 insertions(+), 16 deletions(-)
Title: SQLite Interface for R
Diff between RSQLite versions 0.11.4 dated 2013-05-26 and 1.0.0 dated 2014-10-24
Description: This package embeds the SQLite database engine in R and
provides an interface compliant with the DBI package.
The source for the SQLite engine (version 3.8.6) is included.
Author: Hadley Wickham [aut, cre],
David A. James [aut],
Seth Falcon [aut],
SQLite Authors [ctb] (for the included SQLite sources),
Liam Healy [ctb] (for the include SQLite extensions),
RStudio [cph]
Maintainer: Hadley Wickham
RSQLite-0.11.4/RSQLite/R/S4R.R |only
RSQLite-0.11.4/RSQLite/R/SQLite.R |only
RSQLite-0.11.4/RSQLite/R/SQLiteSupport.R |only
RSQLite-0.11.4/RSQLite/R/dbObjectId.R |only
RSQLite-0.11.4/RSQLite/inst/HACKING |only
RSQLite-0.11.4/RSQLite/inst/INSTALL |only
RSQLite-0.11.4/RSQLite/inst/NEWS |only
RSQLite-0.11.4/RSQLite/inst/ONEWS |only
RSQLite-0.11.4/RSQLite/inst/README |only
RSQLite-0.11.4/RSQLite/inst/THANKS |only
RSQLite-0.11.4/RSQLite/inst/TODO |only
RSQLite-0.11.4/RSQLite/inst/UnitTests |only
RSQLite-0.11.4/RSQLite/inst/announce |only
RSQLite-0.11.4/RSQLite/inst/rsqlitePerf.txt |only
RSQLite-0.11.4/RSQLite/man/S4R.Rd |only
RSQLite-0.11.4/RSQLite/man/SQLite.Rd |only
RSQLite-0.11.4/RSQLite/man/SQLiteObject-class.Rd |only
RSQLite-0.11.4/RSQLite/man/dbBuildTableDefinition.Rd |only
RSQLite-0.11.4/RSQLite/man/dbCallProc-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbCommit-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbConnect-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbDataType-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbDriver-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbGetInfo-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbListTables-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbObjectId-class.Rd |only
RSQLite-0.11.4/RSQLite/man/dbReadTable-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbSendQuery-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/dbSetDataMappings-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/fetch-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/isIdCurrent.Rd |only
RSQLite-0.11.4/RSQLite/man/make.db.names-methods.Rd |only
RSQLite-0.11.4/RSQLite/man/safe.write.Rd |only
RSQLite-0.11.4/RSQLite/man/sqliteSupport.Rd |only
RSQLite-0.11.4/RSQLite/man/summary-methods.Rd |only
RSQLite-0.11.4/RSQLite/src/RS-DBI.c |only
RSQLite-0.11.4/RSQLite/src/RS-DBI.h |only
RSQLite-0.11.4/RSQLite/src/RS-SQLite.c |only
RSQLite-0.11.4/RSQLite/src/RS-SQLite.h |only
RSQLite-0.11.4/RSQLite/src/Rhelpers.h |only
RSQLite-0.11.4/RSQLite/src/param_binding.h |only
RSQLite-0.11.4/RSQLite/tests/RSQLite_unit_tests.R |only
RSQLite-0.11.4/RSQLite/tests/gc-tests.R |only
RSQLite-1.0.0/RSQLite/DESCRIPTION | 46
RSQLite-1.0.0/RSQLite/MD5 | 157
RSQLite-1.0.0/RSQLite/NAMESPACE | 150
RSQLite-1.0.0/RSQLite/R/Connect.R |only
RSQLite-1.0.0/RSQLite/R/Connection.R |only
RSQLite-1.0.0/RSQLite/R/ConnectionExtensions.R |only
RSQLite-1.0.0/RSQLite/R/ConnectionRead.R |only
RSQLite-1.0.0/RSQLite/R/ConnectionTransactions.R |only
RSQLite-1.0.0/RSQLite/R/ConnectionWrite.R |only
RSQLite-1.0.0/RSQLite/R/Constants.R |only
RSQLite-1.0.0/RSQLite/R/Driver.R |only
RSQLite-1.0.0/RSQLite/R/Escaping.R |only
RSQLite-1.0.0/RSQLite/R/Object.R |only
RSQLite-1.0.0/RSQLite/R/Result.R |only
RSQLite-1.0.0/RSQLite/R/Summary.R |only
RSQLite-1.0.0/RSQLite/R/Utils.R |only
RSQLite-1.0.0/RSQLite/R/datasetsDb.R |only
RSQLite-1.0.0/RSQLite/R/dbGetInfo.R |only
RSQLite-1.0.0/RSQLite/R/extensions.R |only
RSQLite-1.0.0/RSQLite/R/zzz.R | 59
RSQLite-1.0.0/RSQLite/README.md |only
RSQLite-1.0.0/RSQLite/configure | 3740
RSQLite-1.0.0/RSQLite/configure.in | 2
RSQLite-1.0.0/RSQLite/inst/db |only
RSQLite-1.0.0/RSQLite/inst/include/sqlite3.h | 1293
RSQLite-1.0.0/RSQLite/inst/include/sqlite3ext.h | 91
RSQLite-1.0.0/RSQLite/man/SQLiteConnection-class.Rd | 65
RSQLite-1.0.0/RSQLite/man/SQLiteDriver-class.Rd | 104
RSQLite-1.0.0/RSQLite/man/SQLiteResult-class.Rd | 52
RSQLite-1.0.0/RSQLite/man/datasetsDb.Rd |only
RSQLite-1.0.0/RSQLite/man/dbBeginTransaction.Rd |only
RSQLite-1.0.0/RSQLite/man/dbConnect-SQLiteDriver-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbDataType-SQLiteConnection-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbExistsTable-SQLiteConnection-character-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbGetException-SQLiteConnection-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbGetInfo.Rd |only
RSQLite-1.0.0/RSQLite/man/dbIsValid.Rd |only
RSQLite-1.0.0/RSQLite/man/dbListFields-SQLiteConnection-character-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbListTables-SQLiteConnection-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbReadTable-SQLiteConnection-character-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbRemoveTable-SQLiteConnection-character-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbSendPreparedQuery.Rd |only
RSQLite-1.0.0/RSQLite/man/dbUnloadDriver-SQLiteDriver-method.Rd |only
RSQLite-1.0.0/RSQLite/man/dbWriteTable.Rd |only
RSQLite-1.0.0/RSQLite/man/initExtension.Rd |only
RSQLite-1.0.0/RSQLite/man/make.db.names-SQLiteConnection-character-method.Rd |only
RSQLite-1.0.0/RSQLite/man/query.Rd |only
RSQLite-1.0.0/RSQLite/man/sqlite-meta.Rd |only
RSQLite-1.0.0/RSQLite/man/sqliteBuildTableDefinition.Rd |only
RSQLite-1.0.0/RSQLite/man/sqliteCopyDatabase.Rd | 66
RSQLite-1.0.0/RSQLite/man/sqliteQuickColumn.Rd | 43
RSQLite-1.0.0/RSQLite/man/summary.Rd |only
RSQLite-1.0.0/RSQLite/man/transactions.Rd |only
RSQLite-1.0.0/RSQLite/src/connection.c |only
RSQLite-1.0.0/RSQLite/src/driver.c |only
RSQLite-1.0.0/RSQLite/src/exceptions.c |only
RSQLite-1.0.0/RSQLite/src/extension-functions.c |only
RSQLite-1.0.0/RSQLite/src/fetch.c |only
RSQLite-1.0.0/RSQLite/src/fields.c |only
RSQLite-1.0.0/RSQLite/src/importFile.c |only
RSQLite-1.0.0/RSQLite/src/param_binding.c | 299
RSQLite-1.0.0/RSQLite/src/quick_column.c |only
RSQLite-1.0.0/RSQLite/src/result.c |only
RSQLite-1.0.0/RSQLite/src/rsqlite.h |only
RSQLite-1.0.0/RSQLite/src/sqlite-all.c | 2
RSQLite-1.0.0/RSQLite/src/sqlite-all.o-68d98681 |only
RSQLite-1.0.0/RSQLite/src/sqlite/sqlite3.c |40210 ++++++----
RSQLite-1.0.0/RSQLite/src/sqlite/sqlite3.h | 575
RSQLite-1.0.0/RSQLite/src/sqlite/sqlite3ext.h | 3
RSQLite-1.0.0/RSQLite/src/test-dbDisconnect.R |only
RSQLite-1.0.0/RSQLite/src/utils.c |only
RSQLite-1.0.0/RSQLite/tests/testthat |only
RSQLite-1.0.0/RSQLite/tests/testthat.R |only
116 files changed, 28102 insertions(+), 18855 deletions(-)
Title: Replication Interval Functions
Diff between replicationInterval versions 0.1 dated 2014-08-27 and 0.2 dated 2014-10-24
More information about replicationInterval at CRAN
Description: A common problem faced by journal reviewers and authors is the
question of whether the results of a replication study are consistent with
the original published study. One solution to this problem is to examine
the effect size from the published study and generate the range of effect
sizes that could reasonably be obtained (due to random sampling) in a
replication attempt (i.e., calculate a replication interval). If a
replication effect size falls outside the replication interval then that
value could not have occurred to due the effects of sampling error alone.
Alternatively, if a replication effect size falls within the replication
interval then the replication results could have reasonably occurred due to
the effects of sampling error alone. This package has functions that
calculate the replication interval for two different types of effect sizes,
namely correlation (i.e., r) and the standardized mean difference
(i.e.,d-value).
Author: David Stanley
Maintainer: David Stanley
DESCRIPTION | 13 +++++++------
MD5 | 12 ++++++------
NAMESPACE | 2 +-
R/replicationInterval.R | 35 +++++++++++++++++++++++------------
man/replicationInterval-package.Rd | 16 ++++++++--------
man/ri.d.Rd | 8 ++++++--
man/ri.r.Rd | 2 +-
7 files changed, 52 insertions(+), 36 deletions(-)
Permanent link
Title: Analysis of subjective perspectives using Q methodology
Diff between qmethod versions 1.1 dated 2014-06-23 and 1.2 dated 2014-10-24
Description: Analysis of Q methodology data to identify the distinct perspectives existing within a group. This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org). The function qmethod() runs the full analysis. Each step can be run separately using the corresponding functions: qflag() for automatic flagging of Q-sorts (manual flagging is optional), qzscores() for scores for statements, qda() for distinguishing and consensus statements, and qfcharact() for general characteristics of the factors. Additional functions import data from PQMethod software, export plain text data for interpretation in two flavours, print and plot Q method results in a syntethic manner. The package uses principal components and it offers the following choices: manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
Author: Aiora Zabala [aut, cre]
Maintainer: Aiora Zabala
DESCRIPTION | 10 +-
MD5 | 37 ++++-----
NAMESPACE | 1
R/plot.QmethodRes.R | 2
R/print.QmethodRes.R |only
R/qdc.R | 1
R/qfcharact.R | 8 +
R/qflag.R | 8 +
R/qmethod.R | 37 +++++++--
R/qzscores.R | 186 +++++++++++++++++++++++-----------------------
R/summary.QmethodRes.R |only
man/QmethodRes-class.Rd | 2
man/plot.QmethodRes.Rd | 3
man/print.QmethodRes.Rd |only
man/qdc.Rd | 3
man/qfcharact.Rd | 32 ++++---
man/qflag.Rd | 7 -
man/qmethod-package.Rd | 9 --
man/qmethod.Rd | 24 +----
man/qzscores.Rd | 10 --
man/summary.QmethodRes.Rd | 3
21 files changed, 203 insertions(+), 180 deletions(-)
Title: Model and Analyse Interval Data
Diff between MAINT.Data versions 0.2 dated 2011-11-07 and 0.3 dated 2014-10-24
Description: MAINT.Data implements methodologies for modelling interval data, considering appropriate parameterizations of the variance-covariance matrix that take into account the intrinsic nature of interval data, and lead to five different possible configuration structures.
Author: Pedro Duarte Silva
Maintainer: Pedro Duarte Silva
CHANGELOG | 11 ++
DESCRIPTION | 16 +--
MD5 | 44 ++++-----
NAMESPACE | 1
R/IData.R | 2
R/IdtMaxLikNC2.R | 67 ++++++--------
R/lqda.R | 2
R/mle.R | 210 ++++++++++++++++++++++++---------------------
man/ConfTests-class.Rd | 15 +--
man/IData-class.Rd | 16 +--
man/IdtClMANOVA-class.Rd | 9 +
man/IdtE-class.Rd | 11 +-
man/IdtHetNMANOVA-class.Rd | 7 -
man/IdtMANOVA-class.Rd | 10 +-
man/IdtMxE-class.Rd | 7 -
man/IdtMxNDE-class.Rd | 9 -
man/IdtNDE-class.Rd | 17 +--
man/IdtSngDE-class.Rd | 11 +-
man/IdtSngNDE-class.Rd | 9 -
man/Idtlda-class.Rd | 7 +
man/Idtqda-class.Rd | 6 -
man/MAINT.Data-package.Rd | 29 +++---
man/testMod-methods.Rd | 20 ++--
23 files changed, 281 insertions(+), 255 deletions(-)
Title: Cubature over Polygonal Domains
Diff between polyCub versions 0.5-0 dated 2014-05-07 and 0.5-1 dated 2014-10-24
Description: A package providing methods for cubature (numerical integration)
over polygonal domains.
Currently, four cubature methods are implemented:
the two-dimensional midpoint rule as a simple wrapper around
as.im.function() from package spatstat (Baddeley and Turner, 2005),
the product Gauss cubature by Sommariva and Vianello (2007),
an adaptive cubature for isotropic functions via line integrate()
along the boundary (Meyer and Held, 2014),
and quasi-exact methods specific to the integration of the
bivariate Gaussian density over polygonal and circular domains
(based on formulae from the Abramowitz and Stegun (1972) handbook).
For cubature over simple hypercubes, the packages "cubature" and
"R2Cuba" are more appropriate.
Author: Sebastian Meyer [aut, cre, trl],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer
DESCRIPTION | 12 +--
MD5 | 70 ++++++++++----------
NAMESPACE | 6 -
R/coerce-gpc-methods.R | 83 +++++++++++++++++-------
R/plotpolyf.R | 29 +++++---
R/polyCub.SV.R | 147 ++++++++++++++++++++++--------------------
R/polyCub.iso.R | 35 ++++++----
R/polyCub.midpoint.R | 7 --
R/sysdata.rda |binary
R/tools.R | 11 +--
R/xylist.R | 33 +++------
R/zzz.R | 11 +--
inst/CITATION | 11 +--
inst/NEWS.Rd | 18 +++++
inst/examples/polyCub.R | 22 +++---
man/checkintrfr.Rd | 65 ++++++++----------
man/circleCub.Gauss.Rd | 39 +++++------
man/coerce-gpc-methods.Rd | 54 +++++++--------
man/coerce-sp-methods.Rd | 7 +-
man/dotprod.Rd | 3
man/gpclibPermit.Rd | 11 +--
man/isClosed.Rd | 9 +-
man/isScalar.Rd | 6 -
man/makegrid.Rd | 17 ++--
man/plot_polyregion.Rd | 23 +++---
man/plotpolyf.Rd | 78 ++++++++++------------
man/polyCub-package.Rd | 105 +++++++++++++++---------------
man/polyCub.Rd | 79 +++++++++++-----------
man/polyCub.SV.Rd | 138 +++++++++++++++++++---------------------
man/polyCub.exact.Gauss.Rd | 93 +++++++++++++--------------
man/polyCub.iso.Rd | 155 ++++++++++++++++++++-------------------------
man/polyCub.midpoint.Rd | 49 +++++++-------
man/polygauss.Rd | 85 +++++++++++-------------
man/vecnorm.Rd | 3
man/xylist.Rd | 99 +++++++++++++---------------
tests/testthat/test-NWGL.R | 12 ++-
36 files changed, 826 insertions(+), 799 deletions(-)
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Diff between spatstat versions 1.39-0 dated 2014-10-23 and 1.39-1 dated 2014-10-24
Description: A package 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
DESCRIPTION | 10 -
MD5 | 332 ++++++++++++++++++++++-----------------------
NEWS | 22 ++
R/First.R | 2
R/Gcom.R | 2
R/Gest.R | 2
R/Gmulti.R | 2
R/Jinhom.R | 12 -
R/Jmulti.R | 2
R/Kcom.R | 2
R/Kest.R | 41 +----
R/Kinhom.R | 2
R/Kmeasure.R | 2
R/Kmulti.R | 2
R/Kmulti.inhom.R | 2
R/Kscaled.R | 2
R/Ksector.R | 2
R/Tstat.R | 2
R/adaptive.density.R | 2
R/affine.R | 2
R/applynbd.R | 2
R/areadiff.R | 11 -
R/areainter.R | 10 -
R/beginner.R | 2
R/blur.R | 2
R/bw.diggle.R | 6
R/clarkevans.R | 2
R/clip.psp.R | 7
R/closepairs.R | 19 --
R/clusterset.R | 2
R/compareFit.R | 2
R/compileK.R | 2
R/connected.R | 9 -
R/crossdistlpp.R | 7
R/cut.ppp.R | 2
R/deldir.R | 2
R/deltametric.R | 2
R/density.ppp.R | 40 +----
R/derivfv.R | 2
R/dg.R | 7
R/dgs.R | 7
R/diagnoseppm.R | 2
R/discarea.R | 7
R/dist2dpath.R | 6
R/distan3D.R | 32 +---
R/distances.R | 16 --
R/distances.psp.R | 2
R/distanxD.R | 22 --
R/distcdf.R | 2
R/distfun.R | 2
R/distfunlpp.R | 2
R/distmap.R | 12 -
R/edgeRipley.R | 10 -
R/edgeTrans.R | 2
R/edges2triangles.R | 2
R/eval.fasp.R | 2
R/exactPdt.R | 7
R/exactdt.R | 6
R/fardist.R | 9 -
R/fgk3.R | 38 +----
R/fiksel.R | 7
R/fryplot.R | 2
R/funxy.R | 2
R/geyer.R | 7
R/hardcore.R | 2
R/hyperframe.R | 2
R/idw.R | 12 -
R/images.R | 2
R/intensity.R | 2
R/interp.im.R | 2
R/iplotlayered.R | 2
R/is.subset.owin.R | 2
R/istat.R | 2
R/lennard.R | 2
R/linalg.R | 29 ---
R/linearK.R | 2
R/linearKmulti.R | 2
R/lineardisc.R | 7
R/linearpcf.R | 2
R/linearpcfmulti.R | 2
R/linfun.R | 2
R/linnet.R | 2
R/localK.R | 2
R/localpcf.R | 11 -
R/logistic.R | 4
R/lppm.R | 2
R/measures.R | 2
R/minnndist.R | 16 --
R/morisita.R | 2
R/mpl.R | 4
R/multihard.R | 2
R/nearestsegment.R | 13 -
R/nncross.R | 10 -
R/nncross3D.R | 11 -
R/nndensity.R | 2
R/nndist.R | 18 --
R/nnfun.R | 2
R/nnfunlpp.R | 2
R/nnmap.R | 10 -
R/options.R | 8 -
R/ord.R | 2
R/pairdistlpp.R | 7
R/pairwise.R | 2
R/parres.R | 2
R/pcf.R | 2
R/pcfinhom.R | 2
R/pcfmulti.R | 2
R/pcfmulti.inhom.R | 2
R/pixellate.R | 7
R/plot.owin.R | 2
R/plot.ppp.R | 2
R/pp3.R | 2
R/ppm.R | 2
R/ppx.R | 2
R/primefactors.R | 2
R/psp2pix.R | 12 -
R/pspcross.R | 27 ---
R/psst.R | 2
R/psstA.R | 2
R/psstG.R | 2
R/quadclass.R | 2
R/quadratcount.R | 2
R/quadrattest.R | 2
R/quasirandom.R | 6
R/random.R | 2
R/randomNS.R | 2
R/rat.R | 2
R/relrisk.R | 2
R/rescale.R | 2
R/resid4plot.R | 2
R/rho2hat.R | 2
R/rhohat.R | 2
R/ripras.R | 2
R/rmh.default.R | 2
R/rmh.ppm.R | 2
R/rmhcontrol.R | 2
R/rmhexpand.R | 2
R/rmhmodel.R | 2
R/rmhsnoop.R | 2
R/rotate.R | 2
R/saturated.R | 2
R/scanstat.R | 6
R/simplepanel.R | 2
R/smooth.ppp.R | 28 +--
R/spatialcdf.R | 2
R/split.ppp.R | 2
R/strauss.R | 11 -
R/strausshard.R | 2
R/summary.im.R | 2
R/symbolmap.R | 2
R/terse.R | 2
R/tess.R | 2
R/triplets.R | 2
R/update.ppm.R | 2
R/vcov.ppm.R | 2
R/versions.R | 2
R/weights.R | 2
R/wingeom.R | 12 -
R/xypolygon.R | 16 --
R/xysegment.R | 12 -
inst/doc/getstart.pdf |binary
inst/doc/replicated.pdf |binary
inst/doc/shapefiles.pdf |binary
inst/doc/updates.pdf |binary
man/spatstat.options.Rd | 7
tests/alltests.R | 20 ++
vignettes/packagesizes.txt | 1
167 files changed, 506 insertions(+), 754 deletions(-)
Title: Matrix-based Partial Least Squares estimation
Diff between matrixpls versions 0.3.0 dated 2014-04-30 and 0.4.0 dated 2014-10-24
Description: matrixpls is implements Partial Least Squares Path Modeling
algorithm and related algorithms. The algorithm implementations aim for
computational efficiency using matrix algebra and covariance data. The
package is designed toward Monte Carlo simulations and includes functions
to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö
matrixpls-0.3.0/matrixpls/man/matrixpls.weights.Rd |only
matrixpls-0.4.0/matrixpls/DESCRIPTION | 14
matrixpls-0.4.0/matrixpls/MD5 | 85 +
matrixpls-0.4.0/matrixpls/NAMESPACE | 35
matrixpls-0.4.0/matrixpls/R/matrixpls.R | 610 +++++++++++---
matrixpls-0.4.0/matrixpls/R/matrixpls.boot.R | 96 ++
matrixpls-0.4.0/matrixpls/R/matrixpls.plsc.R | 171 +++
matrixpls-0.4.0/matrixpls/R/matrixpls.plspm.R | 12
matrixpls-0.4.0/matrixpls/R/matrixpls.postestimation.R | 102 +-
matrixpls-0.4.0/matrixpls/R/matrixpls.sempls.R | 11
matrixpls-0.4.0/matrixpls/R/matrixpls.sim.R | 120 ++
matrixpls-0.4.0/matrixpls/man/AVE.Rd | 36
matrixpls-0.4.0/matrixpls/man/CR.Rd | 33
matrixpls-0.4.0/matrixpls/man/GoF.Rd | 31
matrixpls-0.4.0/matrixpls/man/R2.Rd | 27
matrixpls-0.4.0/matrixpls/man/convCheck.absolute.Rd |only
matrixpls-0.4.0/matrixpls/man/convCheck.relative.Rd |only
matrixpls-0.4.0/matrixpls/man/convCheck.square.Rd |only
matrixpls-0.4.0/matrixpls/man/effects.matrixpls.Rd | 34
matrixpls-0.4.0/matrixpls/man/fitSummary.Rd | 12
matrixpls-0.4.0/matrixpls/man/inner.GSCA.Rd | 65 -
matrixpls-0.4.0/matrixpls/man/inner.centroid.Rd | 39
matrixpls-0.4.0/matrixpls/man/inner.factor.Rd | 40
matrixpls-0.4.0/matrixpls/man/inner.identity.Rd | 45 -
matrixpls-0.4.0/matrixpls/man/inner.path.Rd | 37
matrixpls-0.4.0/matrixpls/man/loadings.matrixpls.Rd | 23
matrixpls-0.4.0/matrixpls/man/matrixpls-package.Rd | 7
matrixpls-0.4.0/matrixpls/man/matrixpls.Rd | 198 +---
matrixpls-0.4.0/matrixpls/man/matrixpls.boot.Rd | 55 -
matrixpls-0.4.0/matrixpls/man/matrixpls.plspm.Rd | 74 -
matrixpls-0.4.0/matrixpls/man/matrixpls.sempls.Rd | 161 +--
matrixpls-0.4.0/matrixpls/man/matrixpls.sim.Rd | 249 -----
matrixpls-0.4.0/matrixpls/man/optim.maximizeInnerR2.Rd |only
matrixpls-0.4.0/matrixpls/man/optim.maximizePrediction.Rd |only
matrixpls-0.4.0/matrixpls/man/outer.GSCA.Rd | 92 --
matrixpls-0.4.0/matrixpls/man/outer.factor.Rd | 39
matrixpls-0.4.0/matrixpls/man/outer.fixedWeights.Rd | 25
matrixpls-0.4.0/matrixpls/man/outer.modeA.Rd | 28
matrixpls-0.4.0/matrixpls/man/outer.modeB.Rd | 28
matrixpls-0.4.0/matrixpls/man/params.plsc.Rd | 136 +--
matrixpls-0.4.0/matrixpls/man/params.plsregression.Rd | 54 -
matrixpls-0.4.0/matrixpls/man/params.regression.Rd | 62 -
matrixpls-0.4.0/matrixpls/man/params.tsls.Rd |only
matrixpls-0.4.0/matrixpls/man/predict.matrixpls.Rd |only
matrixpls-0.4.0/matrixpls/man/residuals.matrixpls.Rd | 48 -
matrixpls-0.4.0/matrixpls/man/signChange.construct.Rd |only
matrixpls-0.4.0/matrixpls/man/signChange.individual.Rd |only
matrixpls-0.4.0/matrixpls/man/weight.fixed.Rd |only
matrixpls-0.4.0/matrixpls/man/weight.optim.Rd |only
matrixpls-0.4.0/matrixpls/man/weight.pls.Rd |only
50 files changed, 1686 insertions(+), 1248 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-21 2.1-2
2014-10-15 2.1-1
Title: Wilcox Robust Estimation and Testing.
Diff between WRS2 versions 0.1-0 dated 2014-10-03 and 0.2-0 dated 2014-10-24
Description: A user-friendly version of Wilcox' robust statistics functions (WRS package on GitHub). It implements robust tests for ANOVA and ANCOVA as described in R. Wilcox (2012) 'Introduction to Robust Estimation and Hypothesis Testing'.
Author: Patrick Mair [cre, aut],
Felix Schoenbrodt [aut],
Rand Wilcox [aut]
Maintainer: Patrick Mair
DESCRIPTION | 10 +++++-----
MD5 | 41 ++++++++++++++++++++++++++++++++++-------
NAMESPACE | 8 ++++++--
R/ancboot.R |only
R/ancova.R |only
R/covmtrim.R |only
R/idealf.R |only
R/johansp.R |only
R/lincon.R |only
R/linconb.R |only
R/med1way.R | 5 +++--
R/med2way.R |only
R/msmedse.R | 7 ++++---
R/near.R |only
R/print.ancova.R |only
R/print.t2way.R | 2 +-
R/smmcrit.R |only
R/smmcrit01.R |only
R/smmval.R |only
R/smmvalv2.R |only
R/trimpartt.R |only
R/tsplit.R |only
R/yuen1.R |only
data/invisibility.rda |only
data/picture.rda |only
inst |only
man/ancova.Rd |only
man/invisibility.Rd |only
man/med1way.Rd | 7 ++-----
man/med2way.Rd |only
man/picture.Rd |only
man/t2way.Rd | 2 +-
man/tsplit.Rd |only
33 files changed, 56 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-15 1.0
Title: R Interface to Many Species Occurrence Data Sources.
Diff between spocc versions 0.2.0 dated 2014-08-06 and 0.2.2 dated 2014-10-24
Description: A programmatic interface to many species occurrence data sources,
including GBIF, USGS's BISON, iNaturalist, Berkeley Ecoinformatics Engine
eBird, AntWeb, and more as they sources become easily available.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain
spocc-0.2.0/spocc/inst/doc/spocc_vignette.pdf |only
spocc-0.2.0/spocc/man/plot.occdat.Rd |only
spocc-0.2.0/spocc/man/print.occdat.Rd |only
spocc-0.2.0/spocc/man/print.occdatind.Rd |only
spocc-0.2.0/spocc/man/spocc_commas_to_periods.Rd |only
spocc-0.2.0/spocc/man/spocc_parseresults.Rd |only
spocc-0.2.0/spocc/vignettes/spocc_vignette.html |only
spocc-0.2.0/spocc/vignettes/spocc_vignette.md |only
spocc-0.2.2/spocc/DESCRIPTION | 21 -
spocc-0.2.2/spocc/MD5 | 111 +++---
spocc-0.2.2/spocc/NAMESPACE | 10
spocc-0.2.2/spocc/NEWS | 18 +
spocc-0.2.2/spocc/R/clean_spocc.r | 188 +++++++----
spocc-0.2.2/spocc/R/methods.r | 121 ++++---
spocc-0.2.2/spocc/R/occ.r | 36 +-
spocc-0.2.2/spocc/R/occ_coverage.R |only
spocc-0.2.2/spocc/R/occ_names.R |only
spocc-0.2.2/spocc/R/occ_names_options.R |only
spocc-0.2.2/spocc/R/occ_options.r | 63 ++-
spocc-0.2.2/spocc/R/occ_to_sp.r | 35 +-
spocc-0.2.2/spocc/R/plugins.r | 79 ++--
spocc-0.2.2/spocc/R/spocc-package.R |only
spocc-0.2.2/spocc/R/spocc_duplicates.R |only
spocc-0.2.2/spocc/R/startup.r |only
spocc-0.2.2/spocc/R/zzz.r | 196 ++++++++---
spocc-0.2.2/spocc/README.md | 5
spocc-0.2.2/spocc/build/vignette.rds |binary
spocc-0.2.2/spocc/inst/doc/spocc_vignette.Rmd | 354 ++++++++++++---------
spocc-0.2.2/spocc/inst/doc/spocc_vignette.html |only
spocc-0.2.2/spocc/man/basemaps.Rd | 2
spocc-0.2.2/spocc/man/bbox2wkt.Rd | 2
spocc-0.2.2/spocc/man/clean_spocc.Rd | 54 ++-
spocc-0.2.2/spocc/man/fixnames.Rd | 2
spocc-0.2.2/spocc/man/get_colors.Rd | 2
spocc-0.2.2/spocc/man/get_palette.Rd | 2
spocc-0.2.2/spocc/man/handle_sp.Rd | 2
spocc-0.2.2/spocc/man/mapggplot.Rd | 2
spocc-0.2.2/spocc/man/mapgist.Rd | 2
spocc-0.2.2/spocc/man/mapleaflet.Rd | 6
spocc-0.2.2/spocc/man/occ.Rd | 75 +++-
spocc-0.2.2/spocc/man/occ2df.Rd | 2
spocc-0.2.2/spocc/man/occ2sp.Rd | 4
spocc-0.2.2/spocc/man/occ_coverage.Rd |only
spocc-0.2.2/spocc/man/occ_names.Rd |only
spocc-0.2.2/spocc/man/occ_names_options.Rd |only
spocc-0.2.2/spocc/man/occ_options.Rd | 26 +
spocc-0.2.2/spocc/man/occ_to_sp.Rd | 20 -
spocc-0.2.2/spocc/man/palettes.Rd | 2
spocc-0.2.2/spocc/man/spocc-package.Rd |only
spocc-0.2.2/spocc/man/spocc_blanktheme.Rd | 2
spocc-0.2.2/spocc/man/spocc_capwords.Rd | 2
spocc-0.2.2/spocc/man/spocc_colClasses.Rd | 2
spocc-0.2.2/spocc/man/spocc_create_gist.Rd | 2
spocc-0.2.2/spocc/man/spocc_duplicates.Rd |only
spocc-0.2.2/spocc/man/spocc_gbifxmlToDataFrame.Rd | 2
spocc-0.2.2/spocc/man/spocc_get_credentials.Rd | 2
spocc-0.2.2/spocc/man/spocc_gist.Rd | 2
spocc-0.2.2/spocc/man/spocc_objects.Rd |only
spocc-0.2.2/spocc/man/spocc_rcharts_togeojson.Rd | 2
spocc-0.2.2/spocc/man/spocc_stylegeojson.Rd | 2
spocc-0.2.2/spocc/man/spocc_togeojson.Rd | 2
spocc-0.2.2/spocc/man/spocc_type_sum.Rd | 2
spocc-0.2.2/spocc/man/wkt_vis.Rd | 2
spocc-0.2.2/spocc/tests/testthat/test-ggmap.R | 4
spocc-0.2.2/spocc/tests/testthat/test-mapleaflet.R | 4
spocc-0.2.2/spocc/tests/testthat/test-occ.R | 57 +--
spocc-0.2.2/spocc/vignettes/spocc_vignette.Rmd | 354 ++++++++++++---------
67 files changed, 1206 insertions(+), 679 deletions(-)