Author: Adrian Baddeley
Diff between spatstat versions 1.16-3 dated 2009-10-13 and 1.17-0 dated 2009-10-22
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Contains
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, and pixel images. Point
process models can be fitted to point pattern data. Cluster
type models are fitted by the method of minimum contrast. Very
general Gibbs point process models can be fitted to point
pattern data using a function ppm similar to lm or glm. Models
may include dependence on covariates, interpoint interaction
and dependence on marks. Fitted models can be simulated
automatically. Also provides facilities for formal inference
(such as chi-squared tests) and model diagnostics (including
simulation envelopes, residuals, residual plots and Q-Q plots).
spatstat-1.16-3/spatstat/R/rmhseed.R |only
spatstat-1.16-3/spatstat/inst/ratfor/arand.r |only
spatstat-1.16-3/spatstat/inst/ratfor/areaint.r |only
spatstat-1.16-3/spatstat/inst/ratfor/aru.r |only
spatstat-1.16-3/spatstat/inst/ratfor/badgey.r |only
spatstat-1.16-3/spatstat/inst/ratfor/cif.h |only
spatstat-1.16-3/spatstat/inst/ratfor/cif.r |only
spatstat-1.16-3/spatstat/inst/ratfor/death.h |only
spatstat-1.16-3/spatstat/inst/ratfor/death.template |only
spatstat-1.16-3/spatstat/inst/ratfor/deathm.r |only
spatstat-1.16-3/spatstat/inst/ratfor/deathu.r |only
spatstat-1.16-3/spatstat/inst/ratfor/dgs.r |only
spatstat-1.16-3/spatstat/inst/ratfor/diggra.r |only
spatstat-1.16-3/spatstat/inst/ratfor/dist2.r |only
spatstat-1.16-3/spatstat/inst/ratfor/fexitf.r |only
spatstat-1.16-3/spatstat/inst/ratfor/geyer.r |only
spatstat-1.16-3/spatstat/inst/ratfor/initaux.r |only
spatstat-1.16-3/spatstat/inst/ratfor/lookup.r |only
spatstat-1.16-3/spatstat/inst/ratfor/methas.template |only
spatstat-1.16-3/spatstat/inst/ratfor/mh1.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh10.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh11.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh2.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh3.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh4.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh5.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh6.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh7.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh8.r |only
spatstat-1.16-3/spatstat/inst/ratfor/mh9.r |only
spatstat-1.16-3/spatstat/inst/ratfor/sftcr.r |only
spatstat-1.16-3/spatstat/inst/ratfor/straush.r |only
spatstat-1.16-3/spatstat/inst/ratfor/straushm.r |only
spatstat-1.16-3/spatstat/inst/ratfor/strauss.r |only
spatstat-1.16-3/spatstat/inst/ratfor/straussm.r |only
spatstat-1.16-3/spatstat/inst/ratfor/updaux.r |only
spatstat-1.16-3/spatstat/src/arand.f |only
spatstat-1.16-3/spatstat/src/areaint.f |only
spatstat-1.16-3/spatstat/src/aru.f |only
spatstat-1.16-3/spatstat/src/badgey.f |only
spatstat-1.16-3/spatstat/src/cif.f |only
spatstat-1.16-3/spatstat/src/deathm.f |only
spatstat-1.16-3/spatstat/src/deathu.f |only
spatstat-1.16-3/spatstat/src/dgs.f |only
spatstat-1.16-3/spatstat/src/diggra.f |only
spatstat-1.16-3/spatstat/src/dist2.f |only
spatstat-1.16-3/spatstat/src/fexitf.f |only
spatstat-1.16-3/spatstat/src/geyer.f |only
spatstat-1.16-3/spatstat/src/initaux.f |only
spatstat-1.16-3/spatstat/src/lookup.f |only
spatstat-1.16-3/spatstat/src/mh1.f |only
spatstat-1.16-3/spatstat/src/mh10.f |only
spatstat-1.16-3/spatstat/src/mh11.f |only
spatstat-1.16-3/spatstat/src/mh2.f |only
spatstat-1.16-3/spatstat/src/mh3.f |only
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spatstat-1.16-3/spatstat/src/mh6.f |only
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spatstat-1.16-3/spatstat/src/straussm.f |only
spatstat-1.16-3/spatstat/src/updaux.f |only
spatstat-1.17-0/spatstat/.Rbuildindex.7635 |only
spatstat-1.17-0/spatstat/DESCRIPTION | 32
spatstat-1.17-0/spatstat/INDEX | 1
spatstat-1.17-0/spatstat/R/Kinhom.S | 16
spatstat-1.17-0/spatstat/R/Kmulti.inhom.R | 39 -
spatstat-1.17-0/spatstat/R/density.ppp.R | 18
spatstat-1.17-0/spatstat/R/distances.psp.R | 61 +
spatstat-1.17-0/spatstat/R/mincontrast.R | 11
spatstat-1.17-0/spatstat/R/multipair.util.R | 24
spatstat-1.17-0/spatstat/R/multistrauss.S | 4
spatstat-1.17-0/spatstat/R/rmh.default.R | 217 ++----
spatstat-1.17-0/spatstat/R/rmhmodel.R | 302 ++------
spatstat-1.17-0/spatstat/R/rmhmodel.ppm.R | 4
spatstat-1.17-0/spatstat/R/rmhstart.R | 20
spatstat-1.17-0/spatstat/R/tess.R | 3
spatstat-1.17-0/spatstat/R/util.S | 66 +
spatstat-1.17-0/spatstat/R/window.S | 106 ++
spatstat-1.17-0/spatstat/R/xypolygon.S | 11
spatstat-1.17-0/spatstat/data/bronzefilter.rda |only
spatstat-1.17-0/spatstat/demo/data.R | 3
spatstat-1.17-0/spatstat/inst/doc/shapefiles.pdf | 681 +++++++++----------
spatstat-1.17-0/spatstat/inst/ratfor/Makefile | 70 -
spatstat-1.17-0/spatstat/man/Kcross.inhom.Rd | 58 +
spatstat-1.17-0/spatstat/man/Kdot.inhom.Rd | 61 +
spatstat-1.17-0/spatstat/man/Kinhom.Rd | 2
spatstat-1.17-0/spatstat/man/Ldot.inhom.Rd | 2
spatstat-1.17-0/spatstat/man/as.mask.Rd | 7
spatstat-1.17-0/spatstat/man/as.owin.Rd | 7
spatstat-1.17-0/spatstat/man/bronzefilter.Rd |only
spatstat-1.17-0/spatstat/man/internal.Rd | 24
spatstat-1.17-0/spatstat/man/owin.Rd | 14
spatstat-1.17-0/spatstat/man/rmh.default.Rd | 47 -
spatstat-1.17-0/spatstat/man/rmhstart.Rd | 29
spatstat-1.17-0/spatstat/man/spatstat-package.Rd | 9
spatstat-1.17-0/spatstat/src/areaint.c |only
spatstat-1.17-0/spatstat/src/badgey.c |only
spatstat-1.17-0/spatstat/src/dgs.c |only
spatstat-1.17-0/spatstat/src/diggra.c |only
spatstat-1.17-0/spatstat/src/dist2.c |only
spatstat-1.17-0/spatstat/src/dist2.h |only
spatstat-1.17-0/spatstat/src/fexitc.c | 8
spatstat-1.17-0/spatstat/src/getcif.c |only
spatstat-1.17-0/spatstat/src/geyer.c |only
spatstat-1.17-0/spatstat/src/lookup.c |only
spatstat-1.17-0/spatstat/src/methas.c |only
spatstat-1.17-0/spatstat/src/methas.h |only
spatstat-1.17-0/spatstat/src/sftcr.c |only
spatstat-1.17-0/spatstat/src/straush.c |only
spatstat-1.17-0/spatstat/src/straushm.c |only
spatstat-1.17-0/spatstat/src/strauss.c |only
spatstat-1.17-0/spatstat/src/straussm.c |only
spatstat-1.17-0/spatstat/tests/rmhBasic.R | 4
spatstat-1.17-0/spatstat/tests/rmhmodel.ppm.R | 17
120 files changed, 1008 insertions(+), 970 deletions(-)
Author: Matthias Templ
Title: Statistical Disclosure Control methods for the generation of
public- and scientific-use files.
Description: Data from statistical agencies and other institutions are
mostly confidential. This package can be used for the
generation of save (micro)data, i.e. for the generation of
public- and scientific-use files. The package includes also a
graphical user interface.
Diff between sdcMicro versions 2.6.1 dated 2009-09-18 and 2.6.2 dated 2009-10-22
.project |only DESCRIPTION | 11 ++++++----- R/freqCalc.r | 5 +++-- inst/doc/Rplots.pdf | 4 ++-- inst/doc/sdcMicroPaper.pdf |binary man/freqCalc.Rd | 4 ++-- man/localSupp.Rd | 2 +- man/localSupp2.Rd | 2 +- man/localSupp2Wrapper.Rd | 2 +- man/microaggregation.Rd | 2 +- man/plot.indivRisk.Rd | 2 +- man/print.pram.Rd | 2 +- man/sdcMicro-package.Rd | 2 +- man/summary.micro.Rd | 2 +- man/summary.pram.Rd | 2 +- 15 files changed, 22 insertions(+), 20 deletions(-)
Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra
Taylor, Sandrine Dudoit
Title: Resampling-based multiple hypothesis testing
Description: Non-parametric bootstrap and permutation resampling-based
multiple testing procedures (including empirical Bayes methods)
for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the
proportion of false positives (TPPFP), and false discovery rate
(FDR). Several choices of bootstrap-based null distribution
are implemented (centered, centered and scaled,
quantile-transformed). Single-step and step-wise methods are
available. Tests based on a variety of t- and F-statistics
(including t-statistics based on regression parameters from
linear and survival models as well as those based on
correlation parameters) are included. When probing hypotheses
with t-statistics, users may also select a potentially faster
null distribution which is multivariate normal with mean zero
and variance covariance matrix derived from the vector
influence function. Results are reported in terms of adjusted
p-values, confidence regions and test statistic cutoffs. The
procedures are directly applicable to identifying
differentially expressed genes in DNA microarray experiments.
Diff between multtest versions 2.1.1 dated 2009-06-14 and 2.1.3 dated 2009-10-22
DESCRIPTION | 6 +++--- R/EBMTP.R | 5 ++++- R/nulldistn_c.R | 8 ++++---- R/test.R | 10 ++++++++-- man/MTP.Rd | 2 +- 5 files changed, 20 insertions(+), 11 deletions(-)
Author: Mario Hasler
Title: Simultaneous Comparisons for Multiple Endpoints
Description: Simultaneous tests and confidence intervals for one-way
experimental designs with one or many normally distributed,
primary response variables (endpoints). The procedure of Hasler
(2009) is applied for differences or ratios of means. Various
contrasts can be chosen, unbalanced sample sizes are allowed as
well as heterogeneous covariance matrices.
Diff between SimComp versions 1.4.1 dated 2009-10-14 and 1.4.2 dated 2009-10-22
DESCRIPTION | 21 +++++++++----------- man/SimCiDiff.Rd | 8 +------ man/SimCiRat.Rd | 12 +++-------- man/SimComp-package.Rd | 50 ++++++++++++++++++++++++++++++++++--------------- man/SimTestDiff.Rd | 8 +------ man/SimTestRat.Rd | 8 +------ 6 files changed, 55 insertions(+), 52 deletions(-)
Author: Jouni Helske
Diff between KFAS versions 0.4.5 dated 2009-10-19 and 0.4.6 dated 2009-10-22
Title: Multivariate Kalman filter and smoother, simulation smoother and
forecasting of state space models. Approximate likelihood of
linear non-gaussian state space models.
Description: Package KFAS provides functions for fast Kalman filtering,
state and disturbance smoothing, forecasting and simulation of
multivariate time-variant state space models. All functions can
use exact diffuse initialisation when distributions of some or
all elements of initial state vector are unknown. Filtering,
state smoothing and simulation functions use sequential
processing algorithm, which is faster than standard approach,
and it also allows singularity of prediction error variance
matrix. KFAS also contains function which computes approximate
likelihood of exponential family state space model.
DESCRIPTION | 18 ++++-----
R/KFAS.R | 107 ++++++++++++++++++++++++++++++++++++++++++++++++++++++---
elinankoodeja |only
man/expflik.Rd | 33 ++++++++++++-----
man/kf.Rd | 2 -
src/expf.f90 | 21 ++++++++---
6 files changed, 152 insertions(+), 29 deletions(-)
Author: Material from the book's webpage, R port and packaging by
Kjetil Halvorsen
Title: Data sets, functions and examples from the book: "The Elements
of Statistical Learning, Data Mining, Inference, and
Prediction" by Trevor Hastie, Robert Tibshirani and Jerome
Friedman.
Description: Useful when reading the book above mentioned, in the
documentation referred to as `the book'.
Diff between ElemStatLearn versions 0.1-6 dated 2009-02-12 and 0.1-7 dated 2009-10-22
DESCRIPTION | 40 +++++++++++++++++++++------------------- data/SAheart.RData |binary data/bone.RData |binary data/countries.RData |binary data/galaxy.RData |binary data/marketing.RData |binary data/mixture.example.RData |binary data/nci.RData |binary data/orange10.test.RData |binary data/orange10.train.RData |binary data/orange4.test.RData |binary data/orange4.train.RData |binary data/ozone.RData |binary data/phoneme.RData |binary data/prostate.RData |binary data/spam.RData |binary data/vowel.test.RData |binary data/vowel.train.RData |binary data/waveform.test.RData |binary data/waveform.train.RData |binary data/zip.test.RData |binary data/zip.train.RData |binary man/mixture.example.Rd | 25 +++++++++++++++++++++---- 23 files changed, 42 insertions(+), 23 deletions(-)
Author: Søren Højsgaard
Diff between doBy versions 4.0.4 dated 2009-10-19 and 4.0.5 dated 2009-10-22
Title: Groupwise computations of summary statistics, general linear
contrasts and other utilities
Description: Facilities for groupwise computations of summary
statistics and other facilities for working with grouped data.
ChangeLog | 9 +
DESCRIPTION | 6
R/orderBy.R | 2
inst/doc/doBy.pdf | 365 +++++++++++++++++++++++++++---------------------------
4 files changed, 195 insertions(+), 187 deletions(-)
Author: Daniela Witten and Rob Tibshirani and Sam Gross
Title: Penalized Multivariate Analysis
Description: Performs Penalized Multivariate Analysis: a penalized
matrix decomposition, sparse principal components analysis, and
sparse canonical correlation analysis, described in the
following papers: (1) Witten, Tibshirani and Hastie (2009) A
penalized matrix decomposition, with applications to sparse
principal components and canonical correlation analysis.
Biostatistics 10(3):515-534. (2) Witten and Tibshirani (2009)
Extensions of sparse canonical correlation analysis, with
applications to genomic data. Statistical Applications in
Genetics and Molecular Biology 8(1): Article 28.
Diff between PMA versions 1.0.2 dated 2009-04-15 and 1.0.4 dated 2009-10-22
PMA-1.0.2/PMA/R/CGH.SparseCCA.R |only PMA-1.0.2/PMA/R/MultiSparseCCA.R |only PMA-1.0.4/PMA/DESCRIPTION | 18 ++- PMA-1.0.4/PMA/NAMESPACE | 2 PMA-1.0.4/PMA/R/CCA.R |only PMA-1.0.4/PMA/R/CCA.xlfuns.R |only PMA-1.0.4/PMA/R/MultiCCA.R |only PMA-1.0.4/PMA/R/PMD.CGH.R | 43 ++++++- PMA-1.0.4/PMA/R/PMD.R | 100 ++++++++++++------ PMA-1.0.4/PMA/R/PlotFusedLasso.R | 6 - PMA-1.0.4/PMA/R/SamrFunctions.R |only PMA-1.0.4/PMA/man/CCA.Rd | 184 +++++++++++++++++----------------- PMA-1.0.4/PMA/man/CCA.permute.Rd | 120 ++++++++++++---------- PMA-1.0.4/PMA/man/MultiCCA.Rd |only PMA-1.0.4/PMA/man/MultiCCA.permute.Rd |only PMA-1.0.4/PMA/man/PMA-internal.Rd | 42 +++++-- PMA-1.0.4/PMA/man/PMA-package.Rd | 4 PMA-1.0.4/PMA/man/PMD.Rd | 14 ++ PMA-1.0.4/PMA/man/PMD.cv.Rd | 10 + PMA-1.0.4/PMA/man/PlotCGH.Rd | 3 PMA-1.0.4/PMA/man/SPC.Rd | 5 PMA-1.0.4/PMA/man/SPC.cv.Rd | 4 PMA-1.0.4/PMA/man/notusing |only 23 files changed, 342 insertions(+), 213 deletions(-)
Author: Marc J. Mazerolle
Diff between AICcmodavg versions 1.02 dated 2009-09-30 and 1.03 dated 2009-10-22
Title: Model selection and multimodel inference based on (Q)AIC(c)
Description: This package includes functions to create model selection
tables based on Akaike's information criterion (AIC) and the
second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc). Tables are printed with delta AIC
and Akaike weights. The package also includes functions to
conduct model averaging (multimodel inference) for a given
parameter of interest or predicted values. Other handy
functions enable the computation of relative variable
importance, evidence ratios, and confidence sets for the best
model. The present version works with linear models ('lm'
class), generalized linear models ('glm' class), linear mixed
models ('lme' class), multinomial and ordinal logistic
regressions ('multinom' and 'polr' classes).
DESCRIPTION | 14 +--
R/AICc.R | 26 ++---
R/AICc.glm.R | 23 ++---
R/AICc.lme.R | 22 ++--
R/AICc.mult.R | 36 ++++----
R/AICc.polr.R |only
R/aictab.R | 69 ++++++++-------
R/aictab.glm.R | 49 +++++++---
R/aictab.lme.R | 51 +++++++----
R/aictab.mult.R | 16 ++-
R/aictab.polr.R |only
R/c_hat.R | 30 +++---
R/confset.R | 190 +++++++++++++++++++++---------------------
R/evidence.R | 22 ++--
R/importance.R | 68 +++++++--------
R/modavg.R | 26 ++++-
R/modavg.glm.R | 191 ++++++++++++++++++++++++++++++------------
R/modavg.lme.R | 6 -
R/modavg.mult.R | 205 +++++++++++++++++++++++++++++++---------------
R/modavg.polr.R |only
R/modavgpred.R | 2
man/AICc.Rd | 74 +++++++++-------
man/AICcmodavg-package.Rd | 10 +-
man/aictab.Rd | 32 ++++---
man/modavg.Rd | 180 +++++++++++++++++++++++++++++++---------
25 files changed, 846 insertions(+), 496 deletions(-)