Title: Estimating Infection Rates from Serological Data
Description: Translates antibody levels measured in a (cross-sectional)
population sample into an estimate of the frequency with which
seroconversions (infections) occur in the sampled population.
Author: Peter Teunis [aut] (Author of the method and original code),
Daniel Lewandowski [com, ctb] (Creator of the R package),
Chantal Quinten [ctb, cre] (Project manager and the package maintainer)
Maintainer: Chantal Quinten <seroincidence@ecdc.europa.eu>
Diff between seroincidence versions 1.0.4 dated 2015-05-22 and 1.0.5 dated 2015-12-29
DESCRIPTION | 10 +++-- MD5 | 60 ++++++++++++++++---------------- NAMESPACE | 2 - NEWS | 8 ++++ R/campylobacterResponseParams.R | 6 +-- R/campylobacterSerologyData.R | 6 +-- R/estimateSeroincidence.R | 7 +-- R/logRhoCdf.R | 8 ++-- R/logRhoPdf.R | 8 ++-- R/rinvgamma.R | 2 - R/salmonellaSerologyData.R | 6 +-- R/seroincidence.R | 6 +-- R/simulateSalmonellaResponseParams.R | 6 +-- R/simulateSerologyData.R | 2 - inst/doc/cover.html | 8 ++-- inst/doc/installation.R | 8 ++-- inst/doc/installation.pdf |binary inst/doc/methodology.Rmd | 1 inst/doc/methodology.pdf |binary inst/doc/tutorial.pdf |binary man/campylobacterResponseParams.Rd | 4 +- man/campylobacterSerologyData.Rd | 4 +- man/estimateSeroincidence.Rd | 4 +- man/print.seroincidence.Rd | 4 +- man/print.summary.seroincidence.Rd | 4 +- man/salmonellaSerologyData.Rd | 4 +- man/seroincidence.Rd | 2 - man/simulateSalmonellaResponseParams.Rd | 4 +- man/simulateSerologyData.Rd | 4 +- man/summary.seroincidence.Rd | 4 +- vignettes/methodology.Rmd | 1 31 files changed, 105 insertions(+), 88 deletions(-)
Title: Crystallization Toolset
Description: This is the tool set for crystallographer to design and analyze crystallization experiments, especially for ribosome from Mycobacterium tuberculosis.
Author: Qingan Sun, Xiaojun Li
Maintainer: Qingan Sun <quinsun@gmail.com>
Diff between xtal versions 1.0 dated 2014-11-05 and 1.15 dated 2015-12-29
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/Design8Vertex.R | 2 +- man/xtal-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Total Operating Characteristic Curve and ROC Curve
Diff between TOC versions 0.0-3 dated 2015-08-05 and 0.0-4 dated 2015-12-29
Description: Construction of the Total Operating Characteristic (TOC) Curve and the Receiver (aka Relative) Operating Characteristic (ROC) Curve for spatial and non-spatial data. The TOC method is a modification of the ROC method which measures the ability of an index variable to diagnose either presence or absence of a characteristic. The diagnosis depends on whether the value of an index variable is above a threshold. Each threshold generates a two-by-two contingency table, which contains four entries: hits (H), misses (M), false alarms (FA), and correct rejections (CR). While ROC shows for each threshold only two ratios, H/(H + M) and FA/(FA + CR), TOC reveals the size of every entry in the contingency table for each threshold (Pontius Jr., R.G., Si, K. 2014. The total operating characteristic to measure diagnostic ability for multiple thresholds. Int. J. Geogr. Inf. Sci. 28 (3), 570-583).
Author: Robert G. Pontius
Maintainer: Alí Santacruz
DESCRIPTION | 9 +++++----
MD5 | 12 ++++++------
NAMESPACE | 2 +-
R/TOCnosp.R | 1 +
R/plotROC.R | 4 ++--
R/plotTOC.R | 4 ++--
man/TOC-package.Rd | 4 ++--
7 files changed, 19 insertions(+), 17 deletions(-)
Title: R Wrapper Around the Telegram Bot API
Description: R wrapper around the Telegram Bot API (http://core.telegram.org/bots/api) to access Telegram's messaging facilities with ease (e.g. you send messages, images, files from R to your smartphone).
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between telegram versions 0.1 dated 2015-12-24 and 0.3.0 dated 2015-12-29
DESCRIPTION | 8 MD5 | 16 + NAMESPACE | 2 R/TGBot.R | 507 ++++++++++++++++++++++++++++++++++----------------- R/telegram-package.r | 1 README.md | 92 +++++++-- inst |only man/TGBot.Rd | 74 ++----- man/bot_token.Rd |only 9 files changed, 467 insertions(+), 233 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multi-type/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 over 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(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
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 <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.44-0 dated 2015-12-23 and 1.44-1 dated 2015-12-29
DESCRIPTION | 10 MD5 | 58 NAMESPACE | 16 NEWS | 59 R/anova.mppm.R | 274 ++ R/anova.ppm.R | 48 R/leverage.R | 7 R/mppm.R | 33 R/tess.R | 7 R/texture.R | 6 inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 4 inst/doc/updates.Rnw | 55 inst/doc/updates.pdf |binary man/anova.mppm.Rd | 100 - man/anova.ppm.Rd | 72 man/as.function.tess.Rd |only man/logLik.mppm.Rd | 109 - man/logLik.ppm.Rd | 6 man/plot.leverage.ppm.Rd | 36 man/spatstat-internal.Rd | 2 man/textureplot.Rd | 3 man/tileindex.Rd |only src/linSnncross.h | 6 src/linknnd.c | 6 tests/alltests.R | 4215 +++++++++++++++++++++++---------------------- vignettes/packagesizes.txt | 1 vignettes/updates.Rnw | 55 31 files changed, 2914 insertions(+), 2274 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.7-3 dated 2015-09-20 and 0.7-4 dated 2015-12-29
RDS-0.7-3/RDS/man/summary.svyglm.Rd |only RDS-0.7-4/RDS/DESCRIPTION | 13 +-- RDS-0.7-4/RDS/MD5 | 42 +++++----- RDS-0.7-4/RDS/NAMESPACE | 6 - RDS-0.7-4/RDS/R/bootstrap-intervals.R | 18 ++++ RDS-0.7-4/RDS/R/control.rds.estimates.R | 12 +++ RDS-0.7-4/RDS/R/data-export.R | 2 RDS-0.7-4/RDS/R/data-import.R | 3 RDS-0.7-4/RDS/R/estimate-plots.R | 113 ---------------------------- RDS-0.7-4/RDS/R/estimate-utils.R | 45 +++++++++++ RDS-0.7-4/RDS/R/gile-bootstrap.R | 8 ++ RDS-0.7-4/RDS/R/llmeC.R | 123 ++++++++++++++++--------------- RDS-0.7-4/RDS/R/me.impute.R | 37 ++++++--- RDS-0.7-4/RDS/R/rds-doc.R | 5 + RDS-0.7-4/RDS/R/rds.data.frame-plots.R | 17 ++-- RDS-0.7-4/RDS/R/rds.estimates.local.R | 1 RDS-0.7-4/RDS/R/summary.odds.R | 23 +++-- RDS-0.7-4/RDS/R/utils.R | 1 RDS-0.7-4/RDS/R/weights.R | 1 RDS-0.7-4/RDS/man/impute.visibility.Rd | 9 +- RDS-0.7-4/RDS/man/plot.rds.data.frame.Rd | 10 +- RDS-0.7-4/RDS/man/summary.svyglm.RDS.Rd |only RDS-0.7-4/RDS/src/llmeC.c | 20 +++-- 23 files changed, 261 insertions(+), 248 deletions(-)
Title: Generating Various Numerical Representation Schemes of Protein
Sequence
Description: Comprehensive toolkit for generating various numerical
representation schemes of protein sequence. The descriptors and similarity
scores included are extensively used in bioinformatics and chemogenomics.
For full functionality, the software 'ncbi-blast+' is needed, see
<http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
for more information.
Author: Nan Xiao <road2stat@gmail.com>, Qingsong Xu <dasongxu@gmail.com>,
Dongsheng Cao <oriental-cds@163.com>
Maintainer: Nan Xiao <road2stat@gmail.com>
Diff between protr versions 1.0-1 dated 2015-11-27 and 1.1-1 dated 2015-12-29
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 16 ++++++++++++++-- R/desc09CTDD.R | 18 +++++++++++++++--- R/desc13PAAC.R | 3 --- R/desc14APAAC.R | 3 --- R/protr-package.R | 4 ++-- README.md | 12 ++++++------ build/vignette.rds |binary inst/CITATION | 6 +++--- inst/doc/protr.R | 2 +- inst/doc/protr.Rnw | 19 ++++++++----------- inst/doc/protr.pdf |binary man/extractAPAAC.Rd | 3 --- man/extractPAAC.Rd | 3 --- man/protr-package.Rd | 4 ++-- vignettes/protr.Rnw | 19 ++++++++----------- 17 files changed, 79 insertions(+), 73 deletions(-)
Title: Population (and Individual) Optimal Experimental Design
Description: Optimal experimental designs for both population and individual
studies based on nonlinear mixed-effect models. Often this is based on a
computation of the Fisher Information Matrix (FIM). This package was developed
for pharmacometric problems, and examples and predefined models are available
for these types of systems.
Author: Andrew C. Hooker [aut, cre, trl, cph],
Sebastian Ueckert [aut] (MATLAB version),
Marco Foracchia [aut] (O-Matrix version),
Joakim Nyberg [aut] (MATLAB version),
Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker <andrew.hooker@farmbio.uu.se>
Diff between PopED versions 0.2.0 dated 2015-03-20 and 0.3.0 dated 2015-12-29
PopED-0.2.0/PopED/R/PopED-package.R |only PopED-0.2.0/PopED/man/PopED-internal.Rd |only PopED-0.2.0/PopED/man/PopED-package.Rd |only PopED-0.2.0/PopED/tests/test-all.R |only PopED-0.3.0/PopED/DESCRIPTION | 20 PopED-0.3.0/PopED/MD5 | 459 +++++----- PopED-0.3.0/PopED/NAMESPACE | 110 ++ PopED-0.3.0/PopED/NEWS | 14 PopED-0.3.0/PopED/R/Doptim.R | 90 + PopED-0.3.0/PopED/R/Dtrace.R | 4 PopED-0.3.0/PopED/R/LEDoptim.R | 3 PopED-0.3.0/PopED/R/LinMatrixH.R | 5 PopED-0.3.0/PopED/R/LinMatrixL.R | 2 PopED-0.3.0/PopED/R/LinMatrixLH.R | 2 PopED-0.3.0/PopED/R/LinMatrixL_occ.R | 2 PopED-0.3.0/PopED/R/PopED.R |only PopED-0.3.0/PopED/R/RS_opt.R | 2 PopED-0.3.0/PopED/R/RS_opt_gen.R | 2 PopED-0.3.0/PopED/R/a_line_search.R | 1 PopED-0.3.0/PopED/R/bfgsb_min.R | 4 PopED-0.3.0/PopED/R/blockexp.R | 6 PopED-0.3.0/PopED/R/blockfinal.R | 47 - PopED-0.3.0/PopED/R/blockheader.R | 64 - PopED-0.3.0/PopED/R/blockopt.R | 3 PopED-0.3.0/PopED/R/build_sfg.R | 25 PopED-0.3.0/PopED/R/calc_ofv_and_fim.R | 1 PopED-0.3.0/PopED/R/cell.R | 3 PopED-0.3.0/PopED/R/convert_variables.R | 3 PopED-0.3.0/PopED/R/create.poped.database.R | 60 - PopED-0.3.0/PopED/R/create_design.R | 2 PopED-0.3.0/PopED/R/create_design_space.R | 11 PopED-0.3.0/PopED/R/diag_matlab.R | 2 PopED-0.3.0/PopED/R/downsizing_general_design.R | 4 PopED-0.3.0/PopED/R/ed_laplace_ofv.R | 7 PopED-0.3.0/PopED/R/ed_mftot.R | 4 PopED-0.3.0/PopED/R/evaluate.e.ofv.fim.R | 1 PopED-0.3.0/PopED/R/evaluate.fim.R | 7 PopED-0.3.0/PopED/R/feval.R | 4 PopED-0.3.0/PopED/R/fileparts.R | 3 PopED-0.3.0/PopED/R/find.largest.index.R |only PopED-0.3.0/PopED/R/getTruncatedNormal.R |only PopED-0.3.0/PopED/R/get_all_params.R | 2 PopED-0.3.0/PopED/R/get_cv.R | 2 PopED-0.3.0/PopED/R/get_unfixed_params.R | 80 - PopED-0.3.0/PopED/R/get_vector_str.R | 6 PopED-0.3.0/PopED/R/getfulld.R | 5 PopED-0.3.0/PopED/R/inv.R | 10 PopED-0.3.0/PopED/R/isempty.R | 3 PopED-0.3.0/PopED/R/isfield.R | 3 PopED-0.3.0/PopED/R/log_prior_pdf.R | 3 PopED-0.3.0/PopED/R/mf.R | 2 PopED-0.3.0/PopED/R/mf3.R | 26 PopED-0.3.0/PopED/R/mf5.R | 2 PopED-0.3.0/PopED/R/mf6.R | 2 PopED-0.3.0/PopED/R/mf7.R | 2 PopED-0.3.0/PopED/R/mf8.R | 2 PopED-0.3.0/PopED/R/mfea.R | 2 PopED-0.3.0/PopED/R/mftot.R | 3 PopED-0.3.0/PopED/R/mftot0.R | 3 PopED-0.3.0/PopED/R/mftot1.R | 3 PopED-0.3.0/PopED/R/mftot2.R | 3 PopED-0.3.0/PopED/R/mftot3.R | 3 PopED-0.3.0/PopED/R/mftot4.R | 3 PopED-0.3.0/PopED/R/mftot5.R | 2 PopED-0.3.0/PopED/R/mftot6.R | 3 PopED-0.3.0/PopED/R/mftot7.R | 2 PopED-0.3.0/PopED/R/model_prediction.R | 9 PopED-0.3.0/PopED/R/models.R | 13 PopED-0.3.0/PopED/R/ofv_criterion.R | 1 PopED-0.3.0/PopED/R/ofv_fim.R | 6 PopED-0.3.0/PopED/R/ones.R | 2 PopED-0.3.0/PopED/R/optim_ARS.R |only PopED-0.3.0/PopED/R/optim_LS.R |only PopED-0.3.0/PopED/R/pargen.R | 30 PopED-0.3.0/PopED/R/plot_efficiency_of_windows.R | 4 PopED-0.3.0/PopED/R/plot_model_prediction.R | 7 PopED-0.3.0/PopED/R/poped_optim.R |only PopED-0.3.0/PopED/R/poped_optimize.R | 2 PopED-0.3.0/PopED/R/rand.R | 3 PopED-0.3.0/PopED/R/randn.R | 3 PopED-0.3.0/PopED/R/randperm.R | 3 PopED-0.3.0/PopED/R/size.R | 2 PopED-0.3.0/PopED/R/start_parallel.R |only PopED-0.3.0/PopED/R/test_for_max.R | 3 PopED-0.3.0/PopED/R/test_for_min.R | 3 PopED-0.3.0/PopED/R/test_for_zeros.R | 3 PopED-0.3.0/PopED/R/test_mat_size.R | 3 PopED-0.3.0/PopED/R/tic.R | 2 PopED-0.3.0/PopED/R/toc.R | 7 PopED-0.3.0/PopED/R/zeros.R | 2 PopED-0.3.0/PopED/README.md | 6 PopED-0.3.0/PopED/inst/examples/PopED_output_summary_D_cont_opt_1.txt |only PopED-0.3.0/PopED/inst/shinyapp/server.R | 13 PopED-0.3.0/PopED/inst/shinyapp/ui.R | 20 PopED-0.3.0/PopED/man/Doptim.Rd | 119 +- PopED-0.3.0/PopED/man/Dtrace.Rd | 21 PopED-0.3.0/PopED/man/LEDoptim.Rd | 79 + PopED-0.3.0/PopED/man/LinMatrixH.Rd | 50 - PopED-0.3.0/PopED/man/LinMatrixL.Rd | 26 PopED-0.3.0/PopED/man/LinMatrixLH.Rd | 52 - PopED-0.3.0/PopED/man/LinMatrixL_occ.Rd | 50 - PopED-0.3.0/PopED/man/PopED.Rd |only PopED-0.3.0/PopED/man/RS_opt.Rd | 72 - PopED-0.3.0/PopED/man/RS_opt_gen.Rd | 78 + PopED-0.3.0/PopED/man/a_line_search.Rd | 42 PopED-0.3.0/PopED/man/bfgsb_min.Rd | 38 PopED-0.3.0/PopED/man/blockexp.Rd | 26 PopED-0.3.0/PopED/man/blockfinal.Rd | 38 PopED-0.3.0/PopED/man/blockheader.Rd | 59 - PopED-0.3.0/PopED/man/blockopt.Rd | 26 PopED-0.3.0/PopED/man/calc_autofocus.Rd | 43 PopED-0.3.0/PopED/man/calc_ofv_and_fim.Rd | 88 + PopED-0.3.0/PopED/man/calc_ofv_and_grad.Rd | 43 PopED-0.3.0/PopED/man/cell.Rd | 16 PopED-0.3.0/PopED/man/convert_variables.Rd | 13 PopED-0.3.0/PopED/man/create.poped.database.Rd | 92 +- PopED-0.3.0/PopED/man/create_design.Rd | 20 PopED-0.3.0/PopED/man/create_design_space.Rd | 24 PopED-0.3.0/PopED/man/diag_matlab.Rd | 21 PopED-0.3.0/PopED/man/downsizing_general_design.Rd | 32 PopED-0.3.0/PopED/man/ed_laplace_ofv.Rd | 56 - PopED-0.3.0/PopED/man/ed_mftot.Rd | 79 + PopED-0.3.0/PopED/man/evaluate.e.ofv.fim.Rd | 95 +- PopED-0.3.0/PopED/man/evaluate.fim.Rd | 70 - PopED-0.3.0/PopED/man/feps.add.Rd | 30 PopED-0.3.0/PopED/man/feps.add.prop.Rd | 30 PopED-0.3.0/PopED/man/feps.prop.Rd | 45 PopED-0.3.0/PopED/man/feval.Rd | 15 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.md.CL.Rd | 28 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.md.KE.Rd | 28 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.sd.CL.Rd | 43 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.sd.KE.Rd | 28 PopED-0.3.0/PopED/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd | 28 PopED-0.3.0/PopED/man/ff.PKPD.1.comp.sd.CL.emax.Rd | 26 PopED-0.3.0/PopED/man/fileparts.Rd | 15 PopED-0.3.0/PopED/man/getTruncatedNormal.Rd | 5 PopED-0.3.0/PopED/man/get_all_params.Rd | 19 PopED-0.3.0/PopED/man/get_rse.Rd | 21 PopED-0.3.0/PopED/man/get_unfixed_params.Rd |only PopED-0.3.0/PopED/man/getfulld.Rd | 5 PopED-0.3.0/PopED/man/gradf_eps.Rd | 48 - PopED-0.3.0/PopED/man/inv.Rd |only PopED-0.3.0/PopED/man/isempty.Rd | 15 PopED-0.3.0/PopED/man/isfield.Rd | 15 PopED-0.3.0/PopED/man/log_prior_pdf.Rd | 38 PopED-0.3.0/PopED/man/mf.Rd | 47 - PopED-0.3.0/PopED/man/mf3.Rd | 49 - PopED-0.3.0/PopED/man/mf5.Rd | 57 - PopED-0.3.0/PopED/man/mf6.Rd | 49 - PopED-0.3.0/PopED/man/mf7.Rd | 47 - PopED-0.3.0/PopED/man/mf8.Rd | 51 - PopED-0.3.0/PopED/man/mfea.Rd | 65 - PopED-0.3.0/PopED/man/mftot.Rd | 46 - PopED-0.3.0/PopED/man/mftot0.Rd | 48 - PopED-0.3.0/PopED/man/mftot1.Rd | 50 - PopED-0.3.0/PopED/man/mftot2.Rd | 29 PopED-0.3.0/PopED/man/mftot3.Rd | 29 PopED-0.3.0/PopED/man/mftot4.Rd | 58 - PopED-0.3.0/PopED/man/mftot5.Rd | 50 - PopED-0.3.0/PopED/man/mftot6.Rd | 48 - PopED-0.3.0/PopED/man/mftot7.Rd | 52 - PopED-0.3.0/PopED/man/model_prediction.Rd | 30 PopED-0.3.0/PopED/man/ofv_criterion.Rd | 56 - PopED-0.3.0/PopED/man/ofv_fim.Rd | 66 - PopED-0.3.0/PopED/man/ones.Rd | 14 PopED-0.3.0/PopED/man/optim_ARS.Rd |only PopED-0.3.0/PopED/man/optim_LS.Rd |only PopED-0.3.0/PopED/man/pargen.Rd | 65 - PopED-0.3.0/PopED/man/plot_efficiency_of_windows.Rd | 37 PopED-0.3.0/PopED/man/plot_model_prediction.Rd | 16 PopED-0.3.0/PopED/man/poped.choose.Rd | 11 PopED-0.3.0/PopED/man/poped_optim.Rd |only PopED-0.3.0/PopED/man/poped_optimize.Rd | 70 - PopED-0.3.0/PopED/man/rand.Rd | 15 PopED-0.3.0/PopED/man/randn.Rd | 15 PopED-0.3.0/PopED/man/randperm.Rd | 15 PopED-0.3.0/PopED/man/size.Rd | 14 PopED-0.3.0/PopED/man/start_parallel.Rd |only PopED-0.3.0/PopED/man/test_for_max.Rd | 9 PopED-0.3.0/PopED/man/test_for_min.Rd | 9 PopED-0.3.0/PopED/man/test_for_zeros.Rd | 9 PopED-0.3.0/PopED/man/test_mat_size.Rd | 3 PopED-0.3.0/PopED/man/tic.Rd | 16 PopED-0.3.0/PopED/man/toc.Rd | 16 PopED-0.3.0/PopED/man/zeros.Rd | 16 PopED-0.3.0/PopED/tests/testthat.R |only PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_D_cont_opt_1.txt | 328 +++---- PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_ED_Laplace_opt.txt | 118 +- PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_RS_1.txt | 112 +- PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_mfea_opt_1.txt | 74 - PopED-0.3.0/PopED/tests/testthat/Rplots.pdf |binary PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_Doptim.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_Dtrace.R | 2 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixH.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixL.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixLH.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixL_occ.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt_gen.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_a_line_search.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_bfgsb_min.R | 2 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_blockexp.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_blockfinal.R | 2 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_blockheader.R | 21 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_blockopt.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_build_sfg.R |only PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_calc_autofocus.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_calc_ofv_and_fim.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_calc_ofv_and_grad.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_downsizing_general_design.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_ed_mftot.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_evaluate.e.ofv.fim.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_get_all_params.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_gradf_eps.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_log_prior_pdf.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf3.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf5.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf6.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf7.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf8.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mfea.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot0.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot1.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot4.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot5.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot6.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot7.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_optim_ARS.R |only PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_optim_LS.R |only PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_pargen.R | 26 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_poped-package.R | 16 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_poped_optim.R |only PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_poped_optimize.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/warfarin_basic.R | 15 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/warfarin_ed.R | 20 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/warfarin_optimize.R | 18 PopED-0.3.0/PopED/tests/testthat/helper_functions.R |only PopED-0.3.0/PopED/tests/testthat/helper_options.R |only PopED-0.3.0/PopED/tests/testthat/test_create_databases.R | 10 PopED-0.3.0/PopED/tests/testthat/test_distributions.R | 81 - PopED-0.3.0/PopED/tests/testthat/test_examples.R | 2 PopED-0.3.0/PopED/tests/testthat/test_optimization.R |only 244 files changed, 3133 insertions(+), 2290 deletions(-)
Title: Statistical Inference of Variables Driving Systematic Variation
Description: Significance test for association between variables
and their estimated latent variables.
Latent variables may be estimated by principal component analysis (PCA),
logistic factor analysis (LFA), and other techniques.
Author: Neo Christopher Chung <nchchung@gmail.com>, Wei Hao <whao@princeton.edu>, John D. Storey <jstorey@princeton.edu>
Maintainer: Neo Christopher Chung <nchchung@gmail.com>
Diff between jackstraw versions 1.0 dated 2014-01-31 and 1.1 dated 2015-12-29
DESCRIPTION | 25 +- MD5 | 31 ++- NAMESPACE | 12 + R/generic.R | 52 ++--- R/jackstraw.R | 449 +++++++++++++++++++++++++++++++++++++++----- R/jackstraw_parametric.R |only R/lfacorpcor.R |only R/likelihood.R |only R/permutationPA.R | 89 ++++---- man/dev.R.Rd |only man/devdiff.Rd |only man/devdiff_parallel.Rd |only man/efron_Rsq.Rd |only man/jackstraw.FUN.Rd |only man/jackstraw.LFA.Rd |only man/jackstraw.PCA.Rd |only man/jackstraw.Rd | 127 ++++-------- man/jackstraw.parametric.Rd |only man/lfa.corpcor.Rd |only man/permutationPA.Rd | 37 +-- man/pseudo_Rsq.Rd |only vignettes |only 22 files changed, 582 insertions(+), 240 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Diff between doBy versions 4.5-13 dated 2014-12-11 and 4.5-14 dated 2015-12-29
Description: The facilities can roughly be grouped as:
1) Facilities for groupwise computations of summary statistics and
other facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 6
DESCRIPTION | 18
MD5 | 48 +-
NAMESPACE | 83 ++++
R/BY-lmBy.R | 6
R/LSmeans.R | 6
R/linest.R | 28 +
R/linestGet.R | 37 +
R/linestMatrix.R | 14
build/vignette.rds |binary
data/beets.txt.gz |binary
data/budworm.txt.gz |binary
data/carcass.txt.gz |binary
data/carcassall.txt.gz |binary
data/crimeRate.txt.gz |binary
data/datalist | 23 -
data/haldCement.txt.gz |binary
data/potatoes.txt.gz |only
inst/doc/LSmeans.R | 822 ++++++++++++++++++++++----------------------
inst/doc/LSmeans.pdf |binary
inst/doc/doBy.R | 912 ++++++++++++++++++++++++-------------------------
inst/doc/doBy.pdf |binary
man/DATA-potatoes.Rd |only
man/LSmeans.Rd | 5
man/doBy-internal.Rd | 2
man/lmBy.Rd | 2
26 files changed, 1079 insertions(+), 933 deletions(-)
Title: Metrics of Difference for Comparing Pairs of Maps
Diff between diffeR versions 0.0-3 dated 2015-07-07 and 0.0-4 dated 2015-12-29
Description: Metrics of difference for comparing pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr.
Maintainer: Alí Santacruz
DESCRIPTION | 9 +++++----
MD5 | 8 ++++----
NAMESPACE | 2 +-
R/overallComponentsPlot.R | 2 +-
man/diffeR-package.Rd | 4 ++--
5 files changed, 13 insertions(+), 12 deletions(-)
Title: A Data Analysis GUI for R
Description: An intuitive, cross-platform graphical data analysis system. It uses menus and dialogs to guide the user efficiently through the data manipulation and analysis process, and has an excel like spreadsheet for easy data frame visualization and editing. Deducer works best when used with the Java based R GUI JGR, but the dialogs can be called from the command line. Dialogs have also been integrated into the Windows Rgui.
Author: Ian Fellows with contributions from others (see documentation).
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between Deducer versions 0.7-7 dated 2014-04-30 and 0.7-9 dated 2015-12-29
Deducer-0.7-7/Deducer/java/deducer |only Deducer-0.7-7/Deducer/java/projects |only Deducer-0.7-7/Deducer/man/summary.lm.Rd |only Deducer-0.7-9/Deducer/DESCRIPTION | 11 Deducer-0.7-9/Deducer/MD5 | 801 +++++++++++++-------------- Deducer-0.7-9/Deducer/NAMESPACE | 101 +++ Deducer-0.7-9/Deducer/NEWS | 6 Deducer-0.7-9/Deducer/R/contingency.tables.R | 4 Deducer-0.7-9/Deducer/R/ggcorplot.R | 64 -- Deducer-0.7-9/Deducer/R/perm.t.test.R | 9 Deducer-0.7-9/Deducer/R/summary.lm.R | 2 Deducer-0.7-9/Deducer/R/zzz.R | 56 - Deducer-0.7-9/Deducer/inst/java/deducer.jar |binary Deducer-0.7-9/Deducer/java/org |only Deducer-0.7-9/Deducer/man/summarylm.Rd |only 15 files changed, 558 insertions(+), 496 deletions(-)
Title: Inferring Disease Networks via Differential Network Inference
Description: Performs differential network analysis to infer disease specific gene networks.
Author: Gokmen Altay
Maintainer: Gokmen Altay <altayscience@gmail.com>
Diff between dc3net versions 1.0 dated 2015-10-01 and 1.0.1 dated 2015-12-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- R/dc3net.R | 16 +++++----------- data/datalist |only data/geneNames.csv.gz |only data/normalData.csv.gz |only data/tumorData.csv.gz |only inst/doc/dc3net-manual.pdf |binary man/dc3net.Rd | 7 +++---- 9 files changed, 20 insertions(+), 23 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.48 dated 2015-10-29 and 1.49 dated 2015-12-29
Changelog | 27 +++++++++++++++++++++++++ DESCRIPTION | 8 +++---- MD5 | 19 +++++++++--------- NAMESPACE | 4 +-- R/Functions.R | 48 ++++++++++++++++++++++++++++++---------------- R/plotDendrogram.R |only man/WGCNA-package.Rd | 4 +-- man/goodGenes.Rd | 7 ++++++ man/goodGenesMS.Rd | 8 +++++++ man/goodSamplesGenes.Rd | 8 +++++++ man/goodSamplesGenesMS.Rd | 8 +++++++ 11 files changed, 108 insertions(+), 33 deletions(-)
Title: Profile Analysis of Multivariate Data in R
Description: Fit profile analytic models. This includes the multivariate methods
and data visualization tools to implement profile analysis and cross-validation
techniques described in Davison & Davenport (2002) and Bulut (2013).
Author: Okan Bulut <okanbulut84@gmail.com>, Christopher David Desjardins
<cddesjardins@gmail.com>
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>
Diff between profileR versions 0.3-1 dated 2015-10-19 and 0.3-2 dated 2015-12-29
profileR-0.3-1/profileR/inst/doc/jss_profileR.rnw |only profileR-0.3-1/profileR/vignettes/jss_profileR.rnw |only profileR-0.3-2/profileR/DESCRIPTION | 21 +++--- profileR-0.3-2/profileR/MD5 | 67 ++++++++++---------- profileR-0.3-2/profileR/NAMESPACE | 49 +++++++++++--- profileR-0.3-2/profileR/R/anova.critpat.R | 8 ++ profileR-0.3-2/profileR/R/cpa.R | 3 profileR-0.3-2/profileR/R/mpa.R | 1 profileR-0.3-2/profileR/R/pams.R | 29 ++++++++ profileR-0.3-2/profileR/R/paos.R | 1 profileR-0.3-2/profileR/R/pbg.R | 2 profileR-0.3-2/profileR/R/pcv.R | 1 profileR-0.3-2/profileR/R/plot.critpat.R | 1 profileR-0.3-2/profileR/R/plot.prof.R | 13 +++ profileR-0.3-2/profileR/R/pr.R | 34 +++++++++- profileR-0.3-2/profileR/R/print.critpat.R | 6 + profileR-0.3-2/profileR/R/print.prof.R | 3 profileR-0.3-2/profileR/R/print.profg.R | 4 - profileR-0.3-2/profileR/R/profileplot.R | 15 ++-- profileR-0.3-2/profileR/R/summary.profg.R | 3 profileR-0.3-2/profileR/build/vignette.rds |binary profileR-0.3-2/profileR/inst/doc/jss_profileR.Rnw |only profileR-0.3-2/profileR/inst/doc/jss_profileR.pdf |binary profileR-0.3-2/profileR/man/anova.critpat.Rd |only profileR-0.3-2/profileR/man/cpa.Rd | 5 - profileR-0.3-2/profileR/man/mpa.Rd | 3 profileR-0.3-2/profileR/man/pams.Rd | 36 ++++------ profileR-0.3-2/profileR/man/paos.Rd | 4 - profileR-0.3-2/profileR/man/pbg.Rd | 57 +++++------------ profileR-0.3-2/profileR/man/pcv.Rd | 8 +- profileR-0.3-2/profileR/man/plot.critpat.Rd | 2 profileR-0.3-2/profileR/man/plot.prof.Rd |only profileR-0.3-2/profileR/man/pr.Rd | 70 +++++---------------- profileR-0.3-2/profileR/man/print.critpat.Rd |only profileR-0.3-2/profileR/man/profileplot.Rd | 49 +++++--------- profileR-0.3-2/profileR/man/summary.critpat.Rd | 2 profileR-0.3-2/profileR/man/wprifm.Rd | 2 profileR-0.3-2/profileR/vignettes/jss_profileR.Rnw |only 38 files changed, 278 insertions(+), 221 deletions(-)
Title: Tools for HTML
Description: Tools for HTML generation and output.
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between htmltools versions 0.2.6 dated 2014-09-08 and 0.3 dated 2015-12-29
DESCRIPTION | 13 +- MD5 | 71 +++++++----- NAMESPACE | 11 +- NEWS | 28 +++++ R/html_dependency.R | 76 ++++++++++++- R/tags.R | 177 ++++++++++++++++++++++++++++---- R/template.R |only inst/tests/template-document.html |only inst/tests/test-tags.r | 209 ++++++++++++++++++++++++++++++++++++++ inst/tests/test-template.R |only man/HTML.Rd | 4 man/as.tags.Rd | 3 man/browsable.Rd | 3 man/builder.Rd | 3 man/copyDependencyToDir.Rd | 7 - man/css.Rd |only man/findDependencies.Rd | 3 man/htmlDependencies.Rd | 13 +- man/htmlDependency.Rd | 28 +++-- man/htmlEscape.Rd | 3 man/htmlPreserve.Rd | 4 man/htmlTemplate.Rd |only man/html_print.Rd | 5 man/include.Rd | 7 - man/knitr_methods.Rd | 3 man/makeDependencyRelative.Rd | 7 - man/print.html.Rd | 3 man/renderDependencies.Rd | 5 man/renderDocument.Rd |only man/renderTags.Rd | 5 man/resolveDependencies.Rd | 3 man/save_html.Rd | 7 - man/singleton.Rd | 3 man/singleton_tools.Rd | 3 man/subtractDependencies.Rd | 9 - man/suppressDependencies.Rd |only man/tag.Rd | 29 +++-- man/urlEncodePath.Rd | 3 man/validateCssUnit.Rd | 3 man/withTags.Rd | 5 40 files changed, 630 insertions(+), 126 deletions(-)
Title: Gene Set Uncertainty in Enrichment Analysis
Description: Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets.
Author: Florian Schmid, Christoph Müssel, Johann M. Kraus, Hans A. Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between GiANT versions 1.1 dated 2015-09-08 and 1.2 dated 2015-12-29
DESCRIPTION | 8 +-- MD5 | 21 ++++---- R/evaluateGeneSetUncertainty.R | 71 ++++++++++++++++++++++++++--- R/significance.R | 56 ++++++++++++++++++++++ build/vignette.rds |binary inst/doc/giant_package_vignette.R | 41 ++++++++++++---- inst/doc/giant_package_vignette.Snw | 48 +++++++++++++++++-- inst/doc/giant_package_vignette.pdf |binary man/GiANT-package.Rd | 3 - man/evaluateGeneSetUncertainty.Rd | 4 + vignettes/giant_package_vignette.Snw | 48 +++++++++++++++++-- vignettes/vignette_randomGeneSetValues.pdf |only 12 files changed, 260 insertions(+), 40 deletions(-)
Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices within a bayesian hierarchical framework as described by Culpepper and Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package contains the datasets used within the analysis of the paper.
Author: Steve Culpepper [aut, cph],
James Balamuta [aut, cre, ctb, com, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between cIRT versions 1.0.0 dated 2015-12-06 and 1.1.0 dated 2015-12-29
DESCRIPTION | 10 MD5 | 54 +-- NAMESPACE | 10 R/RcppExports.R | 612 +++++++++++++++++++------------------- R/cIRT-package.R | 54 +-- R/choice_matrix.R | 32 + R/payout_matrix.R | 26 - R/survey_data.R | 34 +- R/trial_matrix.R | 80 ++-- data/choice_matrix.rda |binary inst/CITATION | 40 +- man/Generate_Choice.Rd | 96 ++--- man/Total_Tabulate.Rd | 50 +-- man/TwoPLChoicemcmc.Rd | 138 ++++---- man/cIRT.Rd | 236 +++++++------- man/cIRT_package.Rd | 70 ++-- man/center_matrix.Rd | 70 ++-- man/choice_matrix.Rd | 56 +-- man/direct_sum.Rd | 72 ++-- man/payout_matrix.Rd | 50 +-- man/probitHLM.Rd | 150 ++++----- man/riwishart.Rd | 60 +-- man/rmvnorm.Rd | 66 ++-- man/rwishart.Rd | 88 ++--- man/survey_data.Rd | 58 +-- man/trial_matrix.Rd | 104 +++--- vignettes/parse_results.R | 254 +++++++-------- vignettes/simulation_CIRT_beta2.R | 192 +++++------ 28 files changed, 1381 insertions(+), 1381 deletions(-)