Title: Add Gate Information to Your Tibble
Description: It interactively or programmatically label points within custom gates on two dimensions <https://github.com/stemangiola/tidygate>.
The information is added to your tibble. It is based on the package 'gatepoints' from Wajid Jawaid (who is also author of this package). The code of 'gatepoints' was nto integrated in 'tidygate'.
The benefits are (i) in interactive mode you can draw your gates on extensive 'ggplot'-like scatter plots;
(ii) you can draw multiple gates; and (iii) you can save your gates and apply the programmatically.
Author: Stefano Mangiola [aut, cre],
Wajid Jawaid [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidygate versions 0.4.9 dated 2022-01-20 and 0.4.10 dated 2024-01-22
DESCRIPTION | 8 MD5 | 63 +- NAMESPACE | 85 +-- R/data.R | 26 - R/fhs.R | 170 +++---- R/functions_OLD.R | 870 +++++++++++++++++++-------------------- R/functions_chr_int.R | 505 +++++++++++----------- R/gatepoints.R | 60 +- R/methods.R | 11 R/methods_OLD.R | 1 R/nanny.R | 244 +++++----- R/utilities.R | 222 +++++---- README.md | 76 +-- build/stage23.rdb |only build/tidygate.pdf |binary build/vignette.rds |binary inst/doc/introdution.R | 6 inst/doc/introdution.html | 380 ++++++----------- man/add_attr.Rd | 44 - man/fhs.Rd | 88 +-- man/gate-methods.Rd | 246 +++++------ man/gate_chr-methods.Rd | 206 ++++----- man/gate_chr.numeric.Rd | 92 ++-- man/gate_int.numeric.Rd | 92 ++-- man/gate_interactive.Rd | 100 ++-- man/gate_interactive_chr_int.Rd | 94 ++-- man/gate_list.Rd | 32 - man/gate_programmatic.Rd | 58 +- man/gate_programmatic_chr_int.Rd | 50 +- man/quo_names.Rd | 48 +- man/tidygate_data.Rd | 32 - tests/testthat.R | 8 tests/testthat/test-methods.R | 24 - 33 files changed, 1948 insertions(+), 1993 deletions(-)
Title: QTL Mapping and Hotspots Detection
Description: For QTL mapping, it consists of several functions to perform various tasks, including
simulating or analyzing data, computing the significance thresholds and visualizing the
QTL mapping results. The single-QTL or multiple-QTL method that allows a host of
statistical models to be fitted and compared is applied to analyze the data for the
estimation of QTL parameters. The models include the linear regression, permutation test,
normal mixture model and truncated normal mixture model. The Gaussian stochastic process
is implemented to compute the significance thresholds for QTL detection onto a genetic
linkage map in the experimental populations. Two types of data, the complete genotyping
or selective genotyping data, from various experimental populations, including backcross,
F2, recombinant inbred (RI) populations, and advanced intercrossed (AI) populations, are
considered in the QTL mapping analysis. For QTL hotspot detection, the statistical methods
can be developed based on either usin [...truncated...]
Author: Ping-Yuan Chung [cre],
Chen-Hung Kao [aut],
Y.-T. Guo [aut],
H.-N. Ho [aut],
H.-I. Lee [aut],
P.-Y. Wu [aut],
M.-H. Yang [aut],
M.-H. Zeng [aut]
Maintainer: Ping-Yuan Chung <pychung@webmail.stat.sinica.edu.tw>
Diff between QTLEMM versions 1.4.1 dated 2023-10-23 and 1.5.0 dated 2024-01-22
DESCRIPTION | 6 +++--- MD5 | 16 +++++++++------- NAMESPACE | 1 + R/EM.MIM.R | 26 +++++++++++++------------- R/EM.MIM2.R | 5 +++++ R/EM.MIMv.R |only R/Q.make.R | 6 +++--- R/progeny.R | 25 ++++++++++++------------- man/EM.MIM.Rd | 1 + man/EM.MIMv.Rd |only 10 files changed, 47 insertions(+), 39 deletions(-)
Title: Composite Grid Gaussian Processes
Description: Run computer experiments using the adaptive composite grid
algorithm with a Gaussian process model.
The algorithm works best when running an experiment that can evaluate thousands
of points from a deterministic computer simulation.
This package is an implementation of a forthcoming paper by Plumlee,
Erickson, Ankenman, et al. For a preprint of the paper,
contact the maintainer of this package.
Author: Collin Erickson [aut, cre],
Matthew Plumlee [aut]
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between CGGP versions 1.0.3 dated 2021-05-08 and 1.0.4 dated 2024-01-22
DESCRIPTION | 8 MD5 | 188 +-- NAMESPACE | 122 +- NEWS.md | 54 - R/CGGP.R | 19 R/CGGP_S3_methods.R | 142 +- R/CGGP_append_fs.R | 1096 +++++++++++----------- R/CGGP_calc_lS_cholS_valo_etc.R | 494 +++++----- R/CGGP_calc_supp_pw_sigma2_Sti.R | 256 ++--- R/CGGP_corr_fs.R | 1120 +++++++++++----------- R/CGGP_create_fs.R | 580 +++++------ R/CGGP_fastcalcassist_fs.R | 648 ++++++------- R/CGGP_fit_fs.R | 1306 +++++++++++++------------- R/CGGP_fitwithonlysupp.R | 454 ++++----- R/CGGP_gneglogpost.R | 842 ++++++++--------- R/CGGP_impute_fs.R | 724 +++++++------- R/CGGP_neglogpost.R | 444 ++++----- R/CGGP_plot.R | 1666 +++++++++++++++++----------------- R/CGGP_postvarcalc.R | 166 +-- R/CGGP_pred_fs.R | 688 +++++++------- R/CGGP_predwithonlysupp.R | 296 +++--- R/CGGP_sharedfunctions.R | 312 +++--- R/RcppExports.R | 116 +- README.md | 522 +++++----- build/vignette.rds |binary inst/doc/CGGP.R | 108 +- inst/doc/CGGP.Rmd | 434 ++++---- inst/doc/CGGP.html | 818 +++++++++++----- man/CGGP.Rd | 29 man/CGGP_internal_CorrMatCauchy.Rd | 112 +- man/CGGP_internal_CorrMatCauchySQ.Rd | 112 +- man/CGGP_internal_CorrMatCauchySQT.Rd | 112 +- man/CGGP_internal_CorrMatGaussian.Rd | 120 +- man/CGGP_internal_CorrMatMatern32.Rd | 112 +- man/CGGP_internal_CorrMatMatern52.Rd | 112 +- man/CGGP_internal_CorrMatPowerExp.Rd | 112 +- man/CGGP_internal_CorrMatWendland0.Rd | 112 +- man/CGGP_internal_CorrMatWendland1.Rd | 112 +- man/CGGP_internal_CorrMatWendland2.Rd | 112 +- man/CGGP_internal_MSEpredcalc.Rd | 54 - man/CGGP_internal_calcMSE.Rd | 52 - man/CGGP_internal_calcMSEde.Rd | 62 - man/CGGP_internal_calcpw.Rd | 60 - man/CGGP_internal_calcpwanddpw.Rd | 56 - man/CGGP_internal_gneglogpost.Rd | 98 +- man/CGGP_internal_neglogpost.Rd | 96 - man/CGGP_internal_set_corr.Rd | 46 man/CGGPappend.Rd | 92 - man/CGGPcreate.Rd | 110 +- man/CGGPfit.Rd | 126 +- man/CGGPplotblocks.Rd | 88 - man/CGGPplotblockselection.Rd | 70 - man/CGGPplotcorr.Rd | 118 +- man/CGGPplotheat.Rd | 108 +- man/CGGPplothist.Rd | 96 - man/CGGPplotsamplesneglogpost.Rd | 72 - man/CGGPplotslice.Rd | 130 +- man/CGGPplottheta.Rd | 72 - man/CGGPplotvariogram.Rd | 84 - man/CGGPpred.Rd | 100 +- man/CGGPvalplot.Rd | 90 - man/CGGPvalstats.Rd | 100 +- man/plot.CGGP.Rd | 60 - man/print.CGGP.Rd | 54 - man/rcpp_fastmatclcr.Rd | 50 - man/rcpp_fastmatclcranddclcr.Rd | 62 - man/rcpp_gkronDBS.Rd | 52 - man/rcpp_kronDBS.Rd | 42 man/valplot.Rd | 74 - man/valstats.Rd | 156 +-- src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 tests/testthat.R | 8 tests/testthat/testS3.R | 46 tests/testthat/testappend.R | 136 +- tests/testthat/testcorr.R | 1106 +++++++++++----------- tests/testthat/testcreate.R | 40 tests/testthat/testfastcalcassist.R | 170 +-- tests/testthat/testfit.R | 376 +++---- tests/testthat/testimputation.R | 108 +- tests/testthat/testoutputparamdim.R | 256 ++--- tests/testthat/testplot.R | 368 +++---- tests/testthat/testpred.R | 588 ++++++------ tests/testthat/testsupponly.R | 690 +++++++------- tools/README-corrplot-1.png |binary tools/README-heat-1.png |binary tools/README-hist-1.png |binary tools/README-plotblocks-1.png |binary tools/README-plotslice-1.png |binary tools/README-plotslice2-1.png |binary tools/README-plottheta-1.png |binary tools/README-samplesneglogpost-1.png |binary tools/README-vario-1.png |binary vignettes/CGGP.Rmd | 434 ++++---- 95 files changed, 10958 insertions(+), 10687 deletions(-)
Title: Repeated Evaluation
Description: Provide simple mechanism to repeatedly evaluate an expression until either it succeeds or timeout exceeded. It is useful in situations that random failures could happen.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between retry versions 0.1.0 dated 2020-04-23 and 0.1.1 dated 2024-01-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/retry.R | 1 - README.md | 9 +++++---- man/retry-package.Rd | 1 + 5 files changed, 15 insertions(+), 14 deletions(-)
Title: One Time Password Generation and Verification
Description: Generating and validating One-time Password based on
Hash-based Message Authentication Code (HOTP)
and Time Based One-time Password (TOTP)
according to RFC 4226 <https://datatracker.ietf.org/doc/html/rfc4226> and
RFC 6238 <https://datatracker.ietf.org/doc/html/rfc6238>.
Author: Randy Lai [aut, cre, cph]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between otp versions 0.1.0 dated 2020-05-05 and 0.1.1 dated 2024-01-22
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- R/otp.R | 5 ++--- R/utils.R | 30 ++---------------------------- README.md | 50 ++++++++++++++++++++++++++++++++------------------ man/HOTP.Rd | 2 +- man/TOTP.Rd | 2 +- man/otp-package.Rd | 8 +++----- 8 files changed, 55 insertions(+), 70 deletions(-)
Title: Fit GLD Regression/Quantile/AFT Model to Data
Description: Owing to the rich shapes of Generalised Lambda Distributions (GLDs), GLD standard/quantile/Accelerated Failure Time (AFT) regression is a competitive flexible model compared to standard/quantile/AFT regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. For AFT model, it also eliminates the needs to try several different AFT models, owing to the flexible shapes of GLD. The goodness of fit of the proposed model can be assessed via QQ plots and Kolmogorov-Smirnov tests and data driven smooth test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly fro [...truncated...]
Author: Steve Su [aut, cre, cph] ,
R Core Team [aut]
Maintainer: Steve Su <allegro.su@gmail.com>
Diff between GLDreg versions 1.1.0 dated 2022-05-13 and 1.1.1 dated 2024-01-22
DESCRIPTION | 11 ++++++----- MD5 | 10 ++++++---- data |only man/GLD.lm.full.surv.Rd | 9 ++++----- man/GLD.lm.surv.Rd | 18 +++++++++++++----- man/GLDreg-package.Rd | 16 +++++++--------- man/actg.Rd |only 7 files changed, 36 insertions(+), 28 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.4.1 dated 2023-12-21 and 1.4.2 dated 2024-01-22
odbc-1.4.1/odbc/build/odbc.pdf |only odbc-1.4.1/odbc/build/stage23.rdb |only odbc-1.4.1/odbc/man/odbcConnectionCatalogs.Rd |only odbc-1.4.1/odbc/man/odbcConnectionSchemas.Rd |only odbc-1.4.1/odbc/man/odbcConnectionTableTypes.Rd |only odbc-1.4.1/odbc/man/odbcConnectionTables.Rd |only odbc-1.4.2/odbc/DESCRIPTION | 12 odbc-1.4.2/odbc/MD5 | 98 +- odbc-1.4.2/odbc/NAMESPACE | 6 odbc-1.4.2/odbc/NEWS.md | 45 + odbc-1.4.2/odbc/R/connection-pane.R | 33 odbc-1.4.2/odbc/R/dbi-connection.R | 16 odbc-1.4.2/odbc/R/dbi-driver.R | 6 odbc-1.4.2/odbc/R/dbi-table.R | 120 +-- odbc-1.4.2/odbc/R/driver-oracle.R | 13 odbc-1.4.2/odbc/R/driver-spark.R | 19 odbc-1.4.2/odbc/R/driver-sql-server.R | 46 - odbc-1.4.2/odbc/R/driver-teradata.R | 6 odbc-1.4.2/odbc/R/odbc-connection.R | 266 ++++--- odbc-1.4.2/odbc/R/odbc-package.R | 5 odbc-1.4.2/odbc/R/odbc.R | 5 odbc-1.4.2/odbc/R/utils.R | 63 + odbc-1.4.2/odbc/R/zzz.R | 2 odbc-1.4.2/odbc/inst/doc/develop.Rmd | 35 odbc-1.4.2/odbc/inst/doc/develop.html | 46 + odbc-1.4.2/odbc/man/DBI-tables.Rd | 17 odbc-1.4.2/odbc/man/OdbcConnection.Rd | 5 odbc-1.4.2/odbc/man/OdbcResult.Rd | 5 odbc-1.4.2/odbc/man/Oracle.Rd | 19 odbc-1.4.2/odbc/man/SQLServer.Rd | 12 odbc-1.4.2/odbc/man/dbConnect-OdbcDriver-method.Rd | 6 odbc-1.4.2/odbc/man/figures/lifecycle-archived.svg |only odbc-1.4.2/odbc/man/figures/lifecycle-defunct.svg |only odbc-1.4.2/odbc/man/figures/lifecycle-deprecated.svg |only odbc-1.4.2/odbc/man/figures/lifecycle-experimental.svg |only odbc-1.4.2/odbc/man/figures/lifecycle-maturing.svg |only odbc-1.4.2/odbc/man/figures/lifecycle-questioning.svg |only odbc-1.4.2/odbc/man/figures/lifecycle-soft-deprecated.svg |only odbc-1.4.2/odbc/man/figures/lifecycle-stable.svg |only odbc-1.4.2/odbc/man/figures/lifecycle-superseded.svg |only odbc-1.4.2/odbc/man/odbcConnectionActions.Rd | 2 odbc-1.4.2/odbc/man/odbcConnectionColumns.Rd | 30 odbc-1.4.2/odbc/man/odbcConnectionIcon.Rd | 1 odbc-1.4.2/odbc/man/odbcSetTransactionIsolationLevel.Rd | 2 odbc-1.4.2/odbc/man/quote_value.Rd |only odbc-1.4.2/odbc/src/odbc_connection.h | 1 odbc-1.4.2/odbc/src/odbc_result.cpp | 6 odbc-1.4.2/odbc/tests/testthat/_snaps/driver-sql-server.md | 21 odbc-1.4.2/odbc/tests/testthat/_snaps/odbc-connection.md | 26 odbc-1.4.2/odbc/tests/testthat/_snaps/utils.md |only odbc-1.4.2/odbc/tests/testthat/helper.R | 17 odbc-1.4.2/odbc/tests/testthat/test-driver-mysql.R | 57 - odbc-1.4.2/odbc/tests/testthat/test-driver-oracle.R |only odbc-1.4.2/odbc/tests/testthat/test-driver-postgres.R | 142 +-- odbc-1.4.2/odbc/tests/testthat/test-driver-sql-server.R | 479 ++++++------- odbc-1.4.2/odbc/tests/testthat/test-driver-sqlite.R | 33 odbc-1.4.2/odbc/tests/testthat/test-odbc-connection.R | 84 +- odbc-1.4.2/odbc/tests/testthat/test-utils.R | 36 odbc-1.4.2/odbc/vignettes/develop.Rmd | 35 59 files changed, 1156 insertions(+), 722 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Provides various features that help with creating publication-quality figures
with 'ggplot2', such as a set of themes, functions to align plots and arrange
them into complex compound figures, and functions that make it easy to annotate
plots and or mix plots with images. The package was originally written for
internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package).
It has also been used extensively in the book Fundamentals of Data
Visualization.
Author: Claus O. Wilke [aut, cre]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 1.1.2 dated 2023-12-15 and 1.1.3 dated 2024-01-22
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------- NEWS.md | 5 ++++ R/align_plots.R | 4 +-- inst/doc/introduction.html | 4 +-- tests/testthat/test_align_plots.R | 36 ++++++++++++++++++++-------------- tests/testthat/test_get_legend.R | 10 ++++++++- tests/testthat/test_plot_components.R | 7 ++++++ 8 files changed, 57 insertions(+), 29 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-29 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-22 1.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-22 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-16 0.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-24 1.0.1
2023-08-15 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-07 0.1-1
Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>
Diff between ecm versions 7.0.0 dated 2023-08-22 and 7.2.0 dated 2024-01-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/ecm.R | 14 ++++++++++++-- R/ecmpredict.r | 25 +++++++++---------------- README.md | 2 +- 5 files changed, 29 insertions(+), 26 deletions(-)
Title: Dynamic Estimator of Microbial Communities
Description: Multi-sample algorithm based on contigs and coverage values, to
infer the relative distances of contigs from the replication origin and to
accurately compare bacterial growth rates between samples. Yuan Gao and
Hongzhe Li (2018) <doi:10.1038/s41592-018-0182-0>.
Author: Yuan Gao [aut, cph],
Charlie Bushman [cre]
Maintainer: Charlie Bushman <ctbushman@gmail.com>
Diff between demic versions 1.0.3 dated 2024-01-11 and 2.0.0 dated 2024-01-22
demic-1.0.3/demic/man/combine_ests.Rd |only demic-1.0.3/demic/man/compare_x_y.Rd |only demic-1.0.3/demic/man/contigs_pipeline.Rd |only demic-1.0.3/demic/man/rand_ordered_contigs.Rd |only demic-1.0.3/demic/man/samples_pipeline.Rd |only demic-1.0.3/demic/tests/testthat/test-df_transfer.R |only demic-2.0.0/demic/DESCRIPTION | 6 demic-2.0.0/demic/MD5 | 40 + demic-2.0.0/demic/NAMESPACE | 5 demic-2.0.0/demic/NEWS.md |only demic-2.0.0/demic/R/est_PTR.R | 87 +++- demic-2.0.0/demic/R/est_ptr_stats.R |only demic-2.0.0/demic/R/pipeline_core.R | 16 demic-2.0.0/demic/R/pipeline_utils.R | 310 +++++++-------- demic-2.0.0/demic/R/pipelines.R | 244 ++++------- demic-2.0.0/demic/R/utils.R | 13 demic-2.0.0/demic/man/compare_contig_subsets.Rd |only demic-2.0.0/demic/man/compare_sample_subsets.Rd |only demic-2.0.0/demic/man/cor_diff.Rd | 4 demic-2.0.0/demic/man/est_ptr.Rd | 34 + demic-2.0.0/demic/man/est_ptr_on.Rd |only demic-2.0.0/demic/man/est_ptr_on_all.Rd |only demic-2.0.0/demic/man/get_eptr_stats.Rd |only demic-2.0.0/demic/man/lme4_model.Rd | 2 demic-2.0.0/demic/man/verify_input.Rd | 11 demic-2.0.0/demic/tests/testthat/test-est_ptr.R | 40 + demic-2.0.0/demic/tests/testthat/test-filter_sample.R |only demic-2.0.0/demic/tests/testthat/test-reshape_filtered.R |only demic-2.0.0/demic/tests/testthat/test-transfers.R |only 29 files changed, 413 insertions(+), 399 deletions(-)
Title: Handling an Inconsistently Coded Categorical Variable in a
Longitudinal Dataset
Description: Unifying an inconsistently coded categorical variable between two different time points in accordance with a mapping table.
The main rule is to replicate the observation if it could be assigned to a few categories.
Then using frequencies or statistical methods to approximate the probabilities of being assigned to each of them.
This procedure was invented and implemented in the paper by Nasinski, Majchrowska, and Broniatowska (2020) <doi:10.24425/cejeme.2020.134747>.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between cat2cat versions 0.4.6 dated 2023-02-01 and 0.4.7 dated 2024-01-22
cat2cat-0.4.6/cat2cat/tests/testthat/test-cat2cat-internal-utils.R |only cat2cat-0.4.6/cat2cat/tests/testthat/test-cat2cat-utils.R |only cat2cat-0.4.6/cat2cat/tests/testthat/test-multi-cat2cat.R |only cat2cat-0.4.7/cat2cat/DESCRIPTION | 12 cat2cat-0.4.7/cat2cat/MD5 | 46 cat2cat-0.4.7/cat2cat/NAMESPACE | 2 cat2cat-0.4.7/cat2cat/NEWS.md | 8 cat2cat-0.4.7/cat2cat/R/cat2cat.R | 267 --- cat2cat-0.4.7/cat2cat/R/cat2cat_agg.R | 4 cat2cat-0.4.7/cat2cat/R/cat2cat_ml.R |only cat2cat-0.4.7/cat2cat/R/cat2cat_utils.R | 6 cat2cat-0.4.7/cat2cat/build/vignette.rds |binary cat2cat-0.4.7/cat2cat/inst/CITATION |only cat2cat-0.4.7/cat2cat/inst/doc/cat2cat.R | 33 cat2cat-0.4.7/cat2cat/inst/doc/cat2cat.Rmd | 31 cat2cat-0.4.7/cat2cat/inst/doc/cat2cat.html | 799 ++++------ cat2cat-0.4.7/cat2cat/man/cat2cat.Rd | 31 cat2cat-0.4.7/cat2cat/man/cat2cat_agg.Rd | 4 cat2cat-0.4.7/cat2cat/man/cat2cat_ml.Rd | 2 cat2cat-0.4.7/cat2cat/man/cat2cat_ml_run.Rd |only cat2cat-0.4.7/cat2cat/man/prune_c2c.Rd | 6 cat2cat-0.4.7/cat2cat/man/validate_cover_cats.Rd | 4 cat2cat-0.4.7/cat2cat/tests/testthat/Rplots.pdf |binary cat2cat-0.4.7/cat2cat/tests/testthat/test-cat2cat_internal_utils.R |only cat2cat-0.4.7/cat2cat/tests/testthat/test-cat2cat_ml.R |only cat2cat-0.4.7/cat2cat/tests/testthat/test-cat2cat_utils.R |only cat2cat-0.4.7/cat2cat/tests/testthat/test-cat2cat_validate.R |only cat2cat-0.4.7/cat2cat/tests/testthat/test-multi_cat2cat.R |only cat2cat-0.4.7/cat2cat/tests/testthat/test-softwarex_paper.R |only cat2cat-0.4.7/cat2cat/vignettes/cat2cat.Rmd | 31 30 files changed, 577 insertions(+), 709 deletions(-)
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and
collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph]
,
Peter Danenberg [aut, cph],
Gabor Csardi [aut],
Manuel Eugster [aut, cph],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between roxygen2 versions 7.3.0 dated 2024-01-11 and 7.3.1 dated 2024-01-22
DESCRIPTION | 9 +-- MD5 | 34 +++++++------ NEWS.md | 17 ++++++ R/namespace.R | 25 +++++++-- R/rd-family.R | 7 +- R/util-locale.R | 8 ++- R/utils.R | 1 inst/doc/rd-other.Rmd | 2 inst/doc/rd-other.html | 2 man/tags-index-crossref.Rd | 2 man/tags-reuse.Rd | 4 - tests/testthat/_snaps/namespace.md | 23 ++++---- tests/testthat/_snaps/rd-family.md |only tests/testthat/test-namespace.R | 90 +++++++++++++++++++++++++++++------ tests/testthat/test-rd-describe-in.R | 9 ++- tests/testthat/test-rd-family.R | 24 +++++++++ tests/testthat/testRawNamespace |only vignettes/rd-other.Rmd | 2 18 files changed, 194 insertions(+), 65 deletions(-)
Title: Reads Mass Spectrometry Data in Bruker *flex Format
Description: Reads data files acquired by Bruker Daltonics' matrix-assisted
laser desorption/ionization-time-of-flight mass spectrometer of the *flex
series.
Author: Sebastian Gibb [aut, cre] ,
Samuel Granjeaud [ctb],
Alan Race [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readBrukerFlexData versions 1.9.1 dated 2023-04-01 and 1.9.2 dated 2024-01-22
DESCRIPTION | 13 +++++++------ MD5 | 24 ++++++++++++------------ NEWS | 5 +++++ R/hpc-functions.R | 6 +++--- R/package.R | 3 +-- R/readAcquFile-functions.R | 2 +- R/readBrukerFlexDir-functions.R | 6 +++--- R/readBrukerFlexFile-functions.R | 8 ++++---- man/extractHPCConstants.Rd | 6 +++--- man/readAcquFile.Rd | 6 +++--- man/readBrukerFlexData-package.Rd | 10 ++++++++++ man/readBrukerFlexDir.Rd | 6 +++--- man/readBrukerFlexFile.Rd | 8 ++++---- 13 files changed, 59 insertions(+), 44 deletions(-)
More information about readBrukerFlexData at CRAN
Permanent link
Title: Manipulation Testing Based on Density Discontinuity
Description: Density discontinuity testing (a.k.a. manipulation testing) is commonly employed in regression discontinuity designs and other program evaluation settings to detect perfect self-selection (manipulation) around a cutoff where treatment/policy assignment changes. This package implements manipulation testing procedures using the local polynomial density estimators: rddensity() to construct test statistics and p-values given a prespecified cutoff, rdbwdensity() to perform data-driven bandwidth selection, and rdplotdensity() to construct density plots.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between rddensity versions 2.4 dated 2023-01-21 and 2.5 dated 2024-01-22
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/rdbwdensity.R | 4 ++-- R/rddensity-package.R | 16 ++++++++-------- R/rddensity.R | 12 ++++++------ R/rddensity_fun.R | 4 +--- R/rddensity_senate.R | 2 +- R/rdplotdensity.R | 12 ++++++------ build/partial.rdb |binary man/h_opt_density_res.Rd | 8 ++------ man/rdbwdensity.Rd | 4 ++-- man/rddensity-package.Rd | 17 ++++++++--------- man/rddensity.Rd | 12 ++++++------ man/rddensity_senate.Rd | 2 +- man/rdplotdensity.Rd | 12 ++++++------ 15 files changed, 67 insertions(+), 74 deletions(-)
Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).
Author: Alexander Ilich [aut, cre] ,
Vincent Lecours [aut],
Benjamin Misiuk [aut],
Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between MultiscaleDTM versions 0.8.2 dated 2023-09-15 and 0.8.3 dated 2024-01-22
DESCRIPTION | 6 +- MD5 | 26 +++++----- R/AdjSD.R | 2 R/RcppExports.R | 8 +-- R/SAPA.R | 105 +++++++++++++++++++++++++++++++----------- R/SurfaceArea.R | 5 +- README.md | 4 - inst/doc/README.R | 2 inst/doc/README.html | 4 - man/SAPA.Rd | 10 +++- man/SurfaceArea.Rd | 10 +++- man/fragments/README_Frag.Rmd | 2 src/RcppExports.cpp | 18 +++---- src/cpp_code.cpp | 22 +++++++- 14 files changed, 153 insertions(+), 71 deletions(-)
Title: Core Functionality for Environmental Time Series
Description: Utility functions for working with environmental time series data from known
locations. The compact data model is structured as a list with two dataframes. A
'meta' dataframe contains spatial and measuring device metadata associated with
deployments at known locations. A 'data' dataframe contains a 'datetime' column
followed by columns of measurements associated with each "device-deployment".
Ephemerides calculations are based on code originally found in NOAA's
"Solar Calculator" <https://gml.noaa.gov/grad/solcalc/>.
Author: Jonathan Callahan [aut, cre],
Hans Martin [ctb],
Eli Grosman [ctb],
Roger Bivand [ctb],
Sebastian Luque [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaTimeSeries versions 0.2.15 dated 2023-09-22 and 0.2.16 dated 2024-01-22
DESCRIPTION | 6 +++--- MD5 | 13 ++++++++----- NAMESPACE | 1 + NEWS.md | 4 ++++ R/mts_pull.R |only inst/doc/Developer_Style_Guide.html | 14 +++++++------- inst/doc/MazamaTimeSeries.html | 14 +++++++------- man/mts_pull.Rd |only tests/testthat/test-mts_pull.R |only 9 files changed, 30 insertions(+), 22 deletions(-)
More information about MazamaTimeSeries at CRAN
Permanent link
Title: Extra Methods for Sparse Matrices
Description: Extends sparse matrix and vector classes from the 'Matrix' package by providing:
(a) Methods and operators that work natively on CSR formats (compressed sparse row,
a.k.a. 'RsparseMatrix') such as slicing/sub-setting, assignment, rbind(),
mathematical operators for CSR and COO such as addition ("+") or sqrt(), and methods such as diag();
(b) Multi-threaded matrix multiplication and cross-product for many <sparse, dense> types,
including the 'float32' type from 'float';
(c) Coercion methods between pairs of classes which are not present in 'Matrix',
such as 'dgCMatrix' -> 'ngRMatrix', as well as convenience conversion functions;
(d) Utility functions for sparse matrices such as sorting the indices or removing
zero-valued entries;
(e) Fast transposes that work by outputting in the opposite storage format;
(f) Faster replacements for many 'Matrix' methods for all sparse types, such as
slicing and elementwise multiplication.
(g) Convenience functions for sparse objects, such as 'm [...truncated...]
Author: David Cortes [aut, cre, cph],
Dmitry Selivanov [cph],
Thibaut Goetghebuer-Planchon [cph] ,
Martin Maechler [cph] ,
Robert Gentleman [cph] ,
Ross Ihaka [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between MatrixExtra versions 0.1.14 dated 2023-08-20 and 0.1.15 dated 2024-01-22
MatrixExtra-0.1.14/MatrixExtra/vignettes/Introducing_MatrixExtra.R |only MatrixExtra-0.1.14/MatrixExtra/vignettes/Introducing_MatrixExtra.html |only MatrixExtra-0.1.15/MatrixExtra/DESCRIPTION | 6 +++--- MatrixExtra-0.1.15/MatrixExtra/MD5 | 8 ++++---- MatrixExtra-0.1.15/MatrixExtra/inst/doc/Introducing_MatrixExtra.R |only MatrixExtra-0.1.15/MatrixExtra/inst/doc/Introducing_MatrixExtra.Rmd |only MatrixExtra-0.1.15/MatrixExtra/vignettes/Introducing_MatrixExtra.Rmd | 5 ++++- 7 files changed, 11 insertions(+), 8 deletions(-)
Title: Import/Export Routines for 'MALDIquant'
Description: Functions for reading (tab, csv, Bruker fid, Ciphergen
XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and
writing (tab, csv, mMass MSD, mzML, imzML) different file
formats of mass spectrometry data into/from 'MALDIquant'
objects.
Author: Sebastian Gibb [aut, cre] ,
Pietro Franceschi [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquantForeign versions 0.14 dated 2023-08-11 and 0.14.1 dated 2024-01-22
DESCRIPTION | 13 +++++++------ MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/package.R | 3 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/MALDIquantForeign-intro.Rnw | 2 +- inst/doc/MALDIquantForeign-intro.pdf |binary man/MALDIquantForeign-package.Rd | 10 ++++++++++ vignettes/MALDIquantForeign-intro.Rnw | 2 +- 10 files changed, 37 insertions(+), 19 deletions(-)
More information about MALDIquantForeign at CRAN
Permanent link
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre] ,
Korbinian Strimmer [ths] ,
Sigurdur Smarason [ctb],
Laurent Gatto [ctb] ,
Paolo Inglese [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.22.1 dated 2023-03-20 and 1.22.2 dated 2024-01-22
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NEWS | 9 +++++++++ R/determineWarpingFunctions-functions.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/MALDIquant-intro.Rnw | 2 +- inst/doc/MALDIquant-intro.pdf |binary vignettes/MALDIquant-intro.Rnw | 2 +- 9 files changed, 28 insertions(+), 18 deletions(-)
Title: Simple Peak Alignment for Gas-Chromatography Data
Description: Aligns peak based on peak retention times and matches homologous peaks
across samples. The underlying alignment procedure comprises three sequential steps.
(1) Full alignment of samples by linear transformation of retention times to
maximise similarity among homologous peaks (2) Partial alignment of peaks within
a user-defined retention time window to cluster homologous peaks (3) Merging rows
that are likely representing homologous substances (i.e. no sample shows peaks in
both rows and the rows have similar retention time means). The algorithm is described in detail
in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Author: Meinolf Ottensmann [aut, cre] ,
Martin Stoffel [aut],
Hazel J. Nichols [aut],
Joseph I. Hoffman [aut]
Maintainer: Meinolf Ottensmann <meinolf.ottensmann@web.de>
Diff between GCalignR versions 1.0.5 dated 2023-01-26 and 1.0.6 dated 2024-01-22
DESCRIPTION | 10 MD5 | 22 NEWS.md | 161 - R/align_peaks.R | 4 README.md | 25 build/vignette.rds |binary inst/CITATION | 10 inst/doc/GCalignR_How_does_the_Algorithm_work.R | 38 inst/doc/GCalignR_How_does_the_Algorithm_work.html | 73 inst/doc/GCalignR_step_by_step.R | 22 inst/doc/GCalignR_step_by_step.html | 3062 ++++++++++----------- man/align_peaks.Rd | 4 12 files changed, 1723 insertions(+), 1708 deletions(-)
Title: Diverse Cluster Ensemble in R
Description: Performs cluster analysis using an ensemble clustering
framework, Chiu & Talhouk (2018) <doi:10.1186/s12859-017-1996-y>.
Results from a diverse set of algorithms are pooled together using
methods such as majority voting, K-Modes, LinkCluE, and CSPA. There
are options to compare cluster assignments across algorithms using
internal and external indices, visualizations such as heatmaps, and
significance testing for the existence of clusters.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between diceR versions 2.1.0 dated 2023-09-28 and 2.2.0 dated 2024-01-22
DESCRIPTION | 45 +++++++++--------------- MD5 | 20 +++++------ NEWS.md | 7 +++ R/algorithms.R | 16 ++------ R/consensus_cluster.R | 58 ++++++++++++++++++++++++-------- R/diceR-package.R | 4 +- R/pcn.R | 2 - build/partial.rdb |binary build/vignette.rds |binary man/consensus_cluster.Rd | 8 +++- tests/testthat/test-consensus_cluster.R | 15 +++++++- 11 files changed, 106 insertions(+), 69 deletions(-)
Title: Stability-enHanced Approaches using Resampling Procedures
Description: In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023a) <doi:10.1093/jrsssc/qlad058> and B Bodinier et al (2023b) <doi:10.1093/bioinformatics/btad635>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <barbara.bodinier@gmail.com>
Diff between sharp versions 1.4.4 dated 2023-10-21 and 1.4.5 dated 2024-01-22
DESCRIPTION | 17 +-- MD5 | 117 ++++++++++++---------- NEWS.md | 63 ++++++------ R/algorithms.R | 8 - R/bi_selection.R | 74 +++++++------- R/calibration.R | 38 +++---- R/check.R | 39 +++---- R/clustering.R | 135 ++++++++++++++++++++------ R/clustering_algorithms.R | 34 +++--- R/decision_trees.R | 2 R/dimensionality_reduction.R | 60 +++++------ R/ensemble.R | 6 - R/explanatory_performance.R | 30 +++-- R/graphical_model.R | 124 ++++++++++++++++++------ R/igraph_object.R | 4 R/lambda_grid.R | 19 +-- R/metrics.R | 8 - R/multi_block.R | 2 R/parallelisation.R | 16 +-- R/penalised_models.R | 24 ++-- R/resampling.R | 13 +- R/s3_coef.R | 12 +- R/s3_plot.R | 10 - R/s3_summary.R | 18 +-- R/selection_performance.R | 6 - R/sharp-package.R | 5 R/stability_output.R | 6 - R/stability_score.R | 2 R/structural_equation_modelling.R | 124 +++++++++++++++++++----- R/utils.R | 79 ++++++++++++++- R/variable_selection.R | 165 ++++++++++++++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/overview.pdf |binary man/AggregatedEffects.Rd | 2 man/BiSelection.Rd | 19 +-- man/CheckInputClustering.Rd | 3 man/Clustering.Rd | 25 +++- man/ClusteringPerformance.Rd | 2 man/Concatenate.Rd |only man/ExplanatoryPerformance.Rd | 2 man/GMMClustering.Rd | 2 man/Graph.Rd | 2 man/GraphicalModel.Rd | 24 +++- man/HierarchicalClustering.Rd | 4 man/Incremental.Rd | 2 man/KMeansClustering.Rd | 4 man/OpenMxModel.Rd | 4 man/PAMClustering.Rd | 4 man/PLS.Rd | 6 - man/Refit.Rd | 4 man/SerialClustering.Rd | 3 man/StructuralModel.Rd | 24 +++- man/VariableSelection.Rd | 32 ++++-- man/sharp-package.Rd | 5 tests/testthat/test-BiSelection.R |only tests/testthat/test-Clustering.R |only tests/testthat/test-GraphicalModel.R |only tests/testthat/test-StructuralModel.R |only tests/testthat/test-VariableSelection.R |only tests/testthat/test-nloptr.R |only vignettes/jss_submission.pdf |binary 63 files changed, 949 insertions(+), 485 deletions(-)
Title: Convert Colour Specification to Colour Name
Description: Functions to convert an R colour specification to a colour name. The user can select and create different lists of colour names and different colour metrics for the conversion.
Author: Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between roloc versions 0.1-1 dated 2018-07-30 and 0.1-2 dated 2024-01-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary man/roloc-package.Rd | 7 +++++-- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: GLCM Textures of Raster Layers
Description: Calculates grey level co-occurrence matrix (GLCM) based texture measures (Hall-Beyer (2017) <https://prism.ucalgary.ca/bitstream/handle/1880/51900/texture%20tutorial%20v%203_0%20180206.pdf>; Haralick et al. (1973) <doi:10.1109/TSMC.1973.4309314>) of raster layers using a sliding rectangular window. It also includes functions to quantize a raster into grey levels as well as tabulate a glcm and calculate glcm texture metrics for a matrix.
Author: Alexander Ilich [aut, cre]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between GLCMTextures versions 0.3.9 dated 2023-11-10 and 0.4.1 dated 2024-01-22
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- R/RcppExports.R | 8 ++++++-- R/glcm_metrics.R | 10 ++++++---- R/glcm_textures.R | 11 ++++++----- R/make_glcm.R | 2 +- R/quantize_raster.R | 7 +++++-- README.md | 28 ++++++++++++++++++++++++---- inst/doc/README.html | 28 ++++++++++++++++++++++------ man/figures/README-textures1-1.png |binary man/figures/README-textures3-1.png |binary man/fragments/README_Frag.Rmd | 10 +++++++++- man/glcm_metrics.Rd | 2 +- man/glcm_textures.Rd | 7 +++++-- man/quantize_raster.Rd | 3 +++ src/RcppExports.cpp | 23 +++++++++++++++++++---- src/glcm_cpp_functions.cpp | 29 +++++++++++++++++++++++++++-- 17 files changed, 153 insertions(+), 53 deletions(-)
Title: Drawing Gapped Cluster Heatmaps with 'ggplot2'
Description: The gap encodes the distance between clusters and improves
interpretation of cluster heatmaps. The gaps can be of the same
distance based on a height threshold to cut the dendrogram. Another
option is to vary the size of gaps based on the distance between
clusters.
Author: Ryo Sakai [aut],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between gapmap versions 0.1.0 dated 2021-04-19 and 1.0.0 dated 2024-01-22
DESCRIPTION | 10 MD5 | 14 - R/as.gapdata.R | 3 README.md | 11 build/vignette.rds |binary inst/doc/simple_example.html | 464 ++++++++++++++++++++++++++++------------ inst/doc/tcga_example.html | 491 +++++++++++++++++++++++++++++-------------- man/as.gapdata.Rd | 2 8 files changed, 689 insertions(+), 306 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' ('CTGOV', using the classic interface at
<https://classic.clinicaltrials.gov/>, and 'CTGOV2', using the
current interface at <https://www.clinicaltrials.gov/>), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Documents in registers associated with trials can also be downloaded.
Other functions identify deduplicated records,
easily find and extract variables (fields) of interest even
from complex nested data as used by the registers,
merge variables and update queries.
The pack [...truncated...]
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.16.0 dated 2023-11-24 and 1.17.0 dated 2024-01-22
ctrdata-1.16.0/ctrdata/R/ctrQueryHistoryInDb.R |only ctrdata-1.16.0/ctrdata/man/dfFindUniqueEuctrRecord.Rd |only ctrdata-1.17.0/ctrdata/DESCRIPTION | 14 ctrdata-1.17.0/ctrdata/MD5 | 95 - ctrdata-1.17.0/ctrdata/NAMESPACE | 6 ctrdata-1.17.0/ctrdata/NEWS.md | 26 ctrdata-1.17.0/ctrdata/R/ctrLoadQueryIntoDbCtgov.R | 20 ctrdata-1.17.0/ctrdata/R/ctrLoadQueryIntoDbCtgov2.R | 17 ctrdata-1.17.0/ctrdata/R/ctrLoadQueryIntoDbCtis.R | 68 ctrdata-1.17.0/ctrdata/R/ctrLoadQueryIntoDbEuctr.R | 91 - ctrdata-1.17.0/ctrdata/R/ctrLoadQueryIntoDbIsrctn.R | 16 ctrdata-1.17.0/ctrdata/R/ctrOpenSearchPagesInBrowser.R | 2 ctrdata-1.17.0/ctrdata/R/ctrdata-registers.R | 2 ctrdata-1.17.0/ctrdata/R/dbFindFields.R | 221 +-- ctrdata-1.17.0/ctrdata/R/dbFindIdsUniqueTrials.R | 30 ctrdata-1.17.0/ctrdata/R/dbGetFieldsIntoDf.R | 405 +---- ctrdata-1.17.0/ctrdata/R/dbQueryHistory.R |only ctrdata-1.17.0/ctrdata/R/utils.R | 698 +++++++--- ctrdata-1.17.0/ctrdata/R/zzz.R | 11 ctrdata-1.17.0/ctrdata/README.md | 190 +- ctrdata-1.17.0/ctrdata/inst/WORDLIST |only ctrdata-1.17.0/ctrdata/inst/doc/ctrdata_install.pdf |binary ctrdata-1.17.0/ctrdata/inst/doc/ctrdata_retrieve.pdf |binary ctrdata-1.17.0/ctrdata/inst/doc/ctrdata_summarise.pdf |binary ctrdata-1.17.0/ctrdata/inst/extdata/demo.sqlite |binary ctrdata-1.17.0/ctrdata/inst/tinytest/ctrdata_ctgov.R | 118 - ctrdata-1.17.0/ctrdata/inst/tinytest/ctrdata_ctgov2.R | 46 ctrdata-1.17.0/ctrdata/inst/tinytest/ctrdata_ctis.R | 77 - ctrdata-1.17.0/ctrdata/inst/tinytest/ctrdata_euctr.R | 167 -- ctrdata-1.17.0/ctrdata/inst/tinytest/ctrdata_isrctn.R | 108 - ctrdata-1.17.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_remote_ro.R | 23 ctrdata-1.17.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_ctgov2.R |only ctrdata-1.17.0/ctrdata/inst/tinytest/test_ctrdata_mongo_local_ctgov2.R | 2 ctrdata-1.17.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_ctgov2.R | 2 ctrdata-1.17.0/ctrdata/man/ctrdata-registers.Rd | 2 ctrdata-1.17.0/ctrdata/man/ctrdata.Rd | 2 ctrdata-1.17.0/ctrdata/man/dbFindFields.Rd | 57 ctrdata-1.17.0/ctrdata/man/dbFindIdsUniqueTrials.Rd | 4 ctrdata-1.17.0/ctrdata/man/dbGetFieldsIntoDf.Rd | 42 ctrdata-1.17.0/ctrdata/man/dbQueryHistory.Rd | 2 ctrdata-1.17.0/ctrdata/man/figures/README-ctrdata_across_registers.png |binary ctrdata-1.17.0/ctrdata/man/figures/README-ctrdata_results_neuroblastoma.png |binary ctrdata-1.17.0/ctrdata/vignettes/boxpep.png |binary ctrdata-1.17.0/ctrdata/vignettes/ctrdata_install.Rmd | 6 ctrdata-1.17.0/ctrdata/vignettes/ctrdata_retrieve.Rmd | 126 - ctrdata-1.17.0/ctrdata/vignettes/ctrdata_summarise.Rmd | 325 ++-- ctrdata-1.17.0/ctrdata/vignettes/nb1.png |binary ctrdata-1.17.0/ctrdata/vignettes/nb2.png |binary ctrdata-1.17.0/ctrdata/vignettes/nbtrials.png |binary ctrdata-1.17.0/ctrdata/vignettes/phase23_paed_p_values.png |binary ctrdata-1.17.0/ctrdata/vignettes/phase23_paed_p_values_participants.png |binary 51 files changed, 1658 insertions(+), 1363 deletions(-)
Title: Community Climate Statistics
Description: Computes community climate statistics for volume and mismatch using species' climate niches either unscaled or scaled relative to a regional species pool. These statistics can be used to describe biogeographic patterns and infer community assembly processes. Includes a vignette outlining usage.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between comclim versions 0.9.5 dated 2018-05-30 and 0.9.6 dated 2024-01-22
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/comclim.pdf |binary man/summary.CommunityClimateInput.Rd | 4 ++-- man/summary.CommunityClimateStatistics.Rd | 6 +++--- 6 files changed, 15 insertions(+), 15 deletions(-)
Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre] ,
Jennifer Bryan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between bigrquery versions 1.4.2 dated 2023-04-20 and 1.5.0 dated 2024-01-22
bigrquery-1.4.2/bigrquery/R/RcppExports.R |only bigrquery-1.4.2/bigrquery/R/old-auth.R |only bigrquery-1.4.2/bigrquery/R/old-dataset.R |only bigrquery-1.4.2/bigrquery/R/old-id.R |only bigrquery-1.4.2/bigrquery/R/old-job-extract.R |only bigrquery-1.4.2/bigrquery/R/old-job-query.R |only bigrquery-1.4.2/bigrquery/R/old-job-upload.R |only bigrquery-1.4.2/bigrquery/R/old-job.R |only bigrquery-1.4.2/bigrquery/R/old-project.R |only bigrquery-1.4.2/bigrquery/R/old-projects.R |only bigrquery-1.4.2/bigrquery/R/old-query.R |only bigrquery-1.4.2/bigrquery/R/old-table.R |only bigrquery-1.4.2/bigrquery/R/old-tabledata.R |only bigrquery-1.4.2/bigrquery/man/bigrquery-deprecated.Rd |only bigrquery-1.4.2/bigrquery/man/dataset-dep.Rd |only bigrquery-1.4.2/bigrquery/man/get_job.Rd |only bigrquery-1.4.2/bigrquery/man/id-dep.Rd |only bigrquery-1.4.2/bigrquery/man/insert_extract_job.Rd |only bigrquery-1.4.2/bigrquery/man/insert_query_job.Rd |only bigrquery-1.4.2/bigrquery/man/insert_upload_job.Rd |only bigrquery-1.4.2/bigrquery/man/list_datasets.Rd |only bigrquery-1.4.2/bigrquery/man/list_projects.Rd |only bigrquery-1.4.2/bigrquery/man/list_tabledata.Rd |only bigrquery-1.4.2/bigrquery/man/query_exec.Rd |only bigrquery-1.4.2/bigrquery/man/table-dep.Rd |only bigrquery-1.4.2/bigrquery/man/wait_for.Rd |only bigrquery-1.4.2/bigrquery/src/Makevars |only bigrquery-1.4.2/bigrquery/src/RcppExports.cpp |only bigrquery-1.4.2/bigrquery/src/gmtime.c |only bigrquery-1.4.2/bigrquery/src/null.c |only bigrquery-1.4.2/bigrquery/src/strptime.c |only bigrquery-1.4.2/bigrquery/tests/testthat/test-bq-project-api.R |only bigrquery-1.4.2/bigrquery/tests/testthat/test-request.R |only bigrquery-1.4.2/bigrquery/tests/testthat/test-test.R |only bigrquery-1.5.0/bigrquery/DESCRIPTION | 52 - bigrquery-1.5.0/bigrquery/LICENSE |only bigrquery-1.5.0/bigrquery/MD5 | 195 +++--- bigrquery-1.5.0/bigrquery/NAMESPACE | 46 - bigrquery-1.5.0/bigrquery/NEWS.md | 78 ++ bigrquery-1.5.0/bigrquery/R/bigrquery-package.R | 7 bigrquery-1.5.0/bigrquery/R/bq-auth.R | 45 - bigrquery-1.5.0/bigrquery/R/bq-dataset.R | 8 bigrquery-1.5.0/bigrquery/R/bq-download.R | 164 +++-- bigrquery-1.5.0/bigrquery/R/bq-field.R | 28 bigrquery-1.5.0/bigrquery/R/bq-job.R | 66 +- bigrquery-1.5.0/bigrquery/R/bq-param.R | 8 bigrquery-1.5.0/bigrquery/R/bq-perform.R | 73 +- bigrquery-1.5.0/bigrquery/R/bq-project.R | 16 bigrquery-1.5.0/bigrquery/R/bq-projects.R | 4 bigrquery-1.5.0/bigrquery/R/bq-query.R | 54 - bigrquery-1.5.0/bigrquery/R/bq-refs.R | 184 ++++-- bigrquery-1.5.0/bigrquery/R/bq-request.R | 58 + bigrquery-1.5.0/bigrquery/R/bq-table.R | 22 bigrquery-1.5.0/bigrquery/R/bq-test.R | 40 - bigrquery-1.5.0/bigrquery/R/connections-page.R |only bigrquery-1.5.0/bigrquery/R/cpp11.R |only bigrquery-1.5.0/bigrquery/R/dbi-connection.R | 297 +++++++--- bigrquery-1.5.0/bigrquery/R/dbi-driver.R | 21 bigrquery-1.5.0/bigrquery/R/dbi-result.R | 34 - bigrquery-1.5.0/bigrquery/R/dplyr.R | 119 ++-- bigrquery-1.5.0/bigrquery/R/gs-object.R | 14 bigrquery-1.5.0/bigrquery/R/import-standalone-obj-type.R |only bigrquery-1.5.0/bigrquery/R/import-standalone-s3-register.R |only bigrquery-1.5.0/bigrquery/R/import-standalone-types-check.R |only bigrquery-1.5.0/bigrquery/R/utils.R | 50 - bigrquery-1.5.0/bigrquery/R/zzz.R | 47 - bigrquery-1.5.0/bigrquery/README.md | 80 +- bigrquery-1.5.0/bigrquery/inst/icons |only bigrquery-1.5.0/bigrquery/inst/rstudio |only bigrquery-1.5.0/bigrquery/inst/secret/bigrquery-testing.json |binary bigrquery-1.5.0/bigrquery/man/DBI.Rd | 57 + bigrquery-1.5.0/bigrquery/man/api-dataset.Rd | 4 bigrquery-1.5.0/bigrquery/man/api-job.Rd | 18 bigrquery-1.5.0/bigrquery/man/api-perform.Rd | 4 bigrquery-1.5.0/bigrquery/man/api-project.Rd | 6 bigrquery-1.5.0/bigrquery/man/api-table.Rd | 24 bigrquery-1.5.0/bigrquery/man/bigquery.Rd | 7 bigrquery-1.5.0/bigrquery/man/bigrquery-package.Rd | 2 bigrquery-1.5.0/bigrquery/man/bq_auth.Rd | 102 ++- bigrquery-1.5.0/bigrquery/man/bq_field.Rd | 22 bigrquery-1.5.0/bigrquery/man/bq_projects.Rd | 4 bigrquery-1.5.0/bigrquery/man/bq_query.Rd | 6 bigrquery-1.5.0/bigrquery/man/bq_refs.Rd | 23 bigrquery-1.5.0/bigrquery/man/bq_table_download.Rd | 8 bigrquery-1.5.0/bigrquery/man/bq_test_project.Rd | 10 bigrquery-1.5.0/bigrquery/src/BqField.cpp | 217 ++----- bigrquery-1.5.0/bigrquery/src/base64.c | 8 bigrquery-1.5.0/bigrquery/src/base64.h | 3 bigrquery-1.5.0/bigrquery/src/cpp11.cpp |only bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-auth.md |only bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-dataset.md |only bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-download.md |only bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-field.md | 23 bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-job.md | 19 bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-param.md | 13 bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-perform.md | 12 bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-query.md |only bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-refs.md | 67 ++ bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-request.md |only bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/bq-test.md |only bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/dbi-connection.md | 61 ++ bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/dbi-result.md | 21 bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/dplyr.md |only bigrquery-1.5.0/bigrquery/tests/testthat/_snaps/utils.md |only bigrquery-1.5.0/bigrquery/tests/testthat/helper-auth.R | 5 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-auth.R | 15 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-dataset.R | 10 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-download.R | 20 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-field.R | 9 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-job.R | 24 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-param.R | 7 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-parse.R | 42 - bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-perform.R | 12 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-project.R |only bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-query.R |only bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-refs.R | 55 + bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-request.R | 27 bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-table.R | 49 - bigrquery-1.5.0/bigrquery/tests/testthat/test-bq-test.R | 17 bigrquery-1.5.0/bigrquery/tests/testthat/test-dbi-connection.R | 115 +++ bigrquery-1.5.0/bigrquery/tests/testthat/test-dbi-result.R | 25 bigrquery-1.5.0/bigrquery/tests/testthat/test-dplyr.R | 76 ++ bigrquery-1.5.0/bigrquery/tests/testthat/test-utils.R | 6 123 files changed, 1959 insertions(+), 1106 deletions(-)
Title: Export R Objects to Several Markup Languages
Description: Coerce R object to 'asciidoc', 'txt2tags',
'restructuredText', 'org', 'textile' or 'pandoc' syntax.
Package comes with a set of drivers for 'Sweave'.
Author: David Hajage [aut],
Mark Clements [cre, ctb],
Seth Falcon [ctb],
Terry Therneau [ctb],
Matti Pastell [ctb],
Friedrich Leisch [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between ascii versions 2.4 dated 2020-09-17 and 2.6 dated 2024-01-22
ascii-2.4/ascii/inst/examples/iris-boxplot.png |only ascii-2.4/ascii/inst/examples/iris.png |only ascii-2.4/ascii/man/rep.char.Rd |only ascii-2.6/ascii/DESCRIPTION | 10 ascii-2.6/ascii/MD5 | 65 +++-- ascii-2.6/ascii/NAMESPACE | 3 ascii-2.6/ascii/NEWS | 10 ascii-2.6/ascii/R/RweaveAscii.r | 27 +- ascii-2.6/ascii/R/asciiDescr.r | 186 ++++++++++++++++ ascii-2.6/ascii/R/export.r | 30 +- ascii-2.6/ascii/R/print.character.matrix.r | 6 ascii-2.6/ascii/R/show.asciidoc.r | 21 + ascii-2.6/ascii/R/show.org.r | 7 ascii-2.6/ascii/R/show.pandoc.r | 33 +- ascii-2.6/ascii/R/show.rest.r | 5 ascii-2.6/ascii/R/show.t2t.r | 7 ascii-2.6/ascii/R/show.textile.r | 6 ascii-2.6/ascii/inst/examples/Asciidoc-test-1.nw |only ascii-2.6/ascii/inst/examples/Org-test-1.nw | 24 +- ascii-2.6/ascii/inst/examples/Org-test-1.org | 115 +++++---- ascii-2.6/ascii/inst/examples/Pandoc-test-1.nw |only ascii-2.6/ascii/inst/examples/ReST-test-1.nw |only ascii-2.6/ascii/inst/examples/ReST-test-1.rst |only ascii-2.6/ascii/inst/examples/T2t-test-1.nw |only ascii-2.6/ascii/inst/examples/T2t-test-1.t2t |only ascii-2.6/ascii/inst/examples/Textile-test-1.nw |only ascii-2.6/ascii/inst/examples/test-1-ReST.Rrst |only ascii-2.6/ascii/inst/examples/test-1-Rmd.Rmd |only ascii-2.6/ascii/inst/examples/test-1-asciidoc.Rasciidoc |only ascii-2.6/ascii/inst/examples/test-1-org.org |only ascii-2.6/ascii/inst/examples/test.pdf |only ascii-2.6/ascii/man/RweaveAsciiSetup.Rd | 2 ascii-2.6/ascii/man/RweaveAsciidoc.Rd | 4 ascii-2.6/ascii/man/RweaveOrg.Rd | 5 ascii-2.6/ascii/man/RweavePandoc.Rd | 2 ascii-2.6/ascii/man/RweaveReST.Rd | 18 - ascii-2.6/ascii/man/RweaveT2t.Rd | 2 ascii-2.6/ascii/man/RweaveTextile.Rd | 2 ascii-2.6/ascii/man/ascii.microbenchmark.Rd |only ascii-2.6/ascii/man/asciiCoefmat.Rd |only ascii-2.6/ascii/man/createreport.Rd | 2 ascii-2.6/ascii/man/escape.pandoc.Rd |only ascii-2.6/ascii/man/repchar.Rd |only 43 files changed, 427 insertions(+), 165 deletions(-)
Title: Revealed Preference and Attention Analysis in Random Limited
Attention Models
Description: It is widely documented in psychology, economics and other disciplines that socio-economic agent may not pay full attention to all available alternatives, rendering standard revealed preference theory invalid. This package implements the estimation and inference procedures of Cattaneo, Ma, Masatlioglu and Suleymanov (2020) <arXiv:1712.03448> and Cattaneo, Cheung, Ma, and Masatlioglu (2022) <arXiv:2110.10650>, which utilizes standard choice data to partially identify and estimate a decision maker's preference and attention. For inference, several simulation-based critical values are provided.
Author: Matias D. Cattaneo, Paul Cheung, Xinwei Ma, Yusufcan Masatlioglu, Elchin Suleymanov
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between ramchoice versions 2.1 dated 2022-05-23 and 2.2 dated 2024-01-22
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/auxiliaryFunctions.R | 2 +- R/ramchoice-package.R | 4 ++-- R/revealAtte.R | 6 +++--- R/revealPref.R | 6 +++--- R/revealPrefModel.R | 8 ++++---- build/partial.rdb |binary man/print.ramchoiceRevealAtte.Rd | 2 +- man/print.ramchoiceRevealPref.Rd | 2 +- man/print.ramchoiceRevealPrefModel.Rd | 2 +- man/ramchoice-package.Rd | 6 +++--- man/revealAtte.Rd | 4 ++-- man/revealPref.Rd | 4 ++-- man/revealPrefModel.Rd | 6 +++--- man/sumData.Rd | 2 +- 16 files changed, 46 insertions(+), 46 deletions(-)
Title: Implements the O'Connell-Dobson-Schouten Estimators of Agreement
for Multiple Observers
Description: Implements an interface to the legacy Fortran code from O'Connell and Dobson (1984) <DOI:10.2307/2531148>. Implements Fortran 77 code for the methods developed by Schouten (1982) <DOI:10.1111/j.1467-9574.1982.tb00774.x>. Includes estimates of average agreement for each observer and average agreement for each subject.
Author: Mark Clements, Dianne O'Connell
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between magree versions 1.1 dated 2020-09-03 and 1.2 dated 2024-01-22
magree-1.1/magree/data/landis.R |only magree-1.2/magree/DESCRIPTION | 8 ++++---- magree-1.2/magree/MD5 | 20 ++++++++++---------- magree-1.2/magree/NAMESPACE | 1 - magree-1.2/magree/R/oconnell.R | 7 +++---- magree-1.2/magree/build/vignette.rds |binary magree-1.2/magree/data/landis.rda |only magree-1.2/magree/inst/doc/landis.pdf |binary magree-1.2/magree/man/oconnell.Rd | 2 +- magree-1.2/magree/man/plot.magree.Rd | 8 ++++---- magree-1.2/magree/man/print.summary.magree.Rd | 5 +++-- magree-1.2/magree/man/summary.magree.Rd | 4 ++-- 12 files changed, 27 insertions(+), 28 deletions(-)
Title: Simplified Fetching and Processing of Microarray and RNA-Seq
Data
Description: Wrapper around various existing tools and command-line interfaces,
providing a standard interface, simple parallelization, and detailed logging.
For microarray data, maps probe sets to standard gene IDs, building on
'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>,
'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>,
Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>,
and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>.
For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology
Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and
quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>,
performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>,
quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197& [...truncated...]
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between seeker versions 1.1.4 dated 2023-12-04 and 1.1.5 dated 2024-01-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/introduction.html | 4 ++-- inst/doc/reproducibility.html | 4 ++-- inst/extdata/platform_cdf.csv | 1 + tests/testthat/setup.R | 2 +- 6 files changed, 14 insertions(+), 13 deletions(-)
Title: Interface to the arXiv API
Description: An interface to the API for 'arXiv',
a repository of electronic preprints for
computer science, mathematics, physics, quantitative biology,
quantitative finance, and statistics.
Author: Karthik Ram [aut] ,
Karl Broman [aut, cre]
Maintainer: Karl Broman <broman@wisc.edu>
Diff between aRxiv versions 0.6 dated 2021-12-06 and 0.8 dated 2024-01-22
aRxiv-0.6/aRxiv/NEWS |only aRxiv-0.6/aRxiv/inst/scripts/grab_api_manual_tables.R |only aRxiv-0.8/aRxiv/DESCRIPTION | 12 aRxiv-0.8/aRxiv/MD5 | 31 aRxiv-0.8/aRxiv/NEWS.md |only aRxiv-0.8/aRxiv/R/arxiv_cats-data.R | 9 aRxiv-0.8/aRxiv/R/query_terms-data.R | 2 aRxiv-0.8/aRxiv/README.md | 18 aRxiv-0.8/aRxiv/build/vignette.rds |binary aRxiv-0.8/aRxiv/data/arxiv_cats.RData |binary aRxiv-0.8/aRxiv/data/query_terms.RData |binary aRxiv-0.8/aRxiv/inst/doc/aRxiv.Rmd | 10 aRxiv-0.8/aRxiv/inst/doc/aRxiv.html | 656 +++++++++++++----- aRxiv-0.8/aRxiv/inst/scripts/README.md | 17 aRxiv-0.8/aRxiv/inst/scripts/grab_arxiv_cats.R |only aRxiv-0.8/aRxiv/inst/scripts/grab_query_terms.R |only aRxiv-0.8/aRxiv/man/arxiv_cats.Rd | 9 aRxiv-0.8/aRxiv/man/query_terms.Rd | 2 aRxiv-0.8/aRxiv/vignettes/aRxiv.Rmd | 10 19 files changed, 544 insertions(+), 232 deletions(-)
Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based
inventory data from the U.S. Department of Agriculture, Forest Service,
Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut],
Gretchen Moisen [aut],
Paul Patterson [aut],
Chris Toney [aut],
Grayson White [aut, cre] ,
Joshua Yamamoto [aut]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTA versions 3.6.0 dated 2023-11-21 and 3.6.1 dated 2024-01-22
DESCRIPTION | 10 MD5 | 104 - R/DBgetPlots.R | 66 - R/DBgetXY.R | 51 R/check.auxiliary.R | 145 +- R/check.estdata.R | 173 +- R/check.pltcnt.R | 4 R/check.popdataCHNG.R | 368 ++++- R/check.popdataPLT.R | 114 + R/check.popdataVOL.R | 6 R/check.rowcol.R | 548 ++++++-- R/check.tree.R | 11 R/datBarplot.R | 2 R/datLUTnm.R | 56 R/datLUTspp.R | 8 R/datSumTreeDom.R | 2 R/est.outtabs.R | 16 R/modGBarea.R | 67 - R/modGBchng.R | 129 +- R/modGBpop.R | 85 + R/modGBratio.R | 84 - R/modGBtree.R | 123 + R/modMAarea.R | 79 - R/modMApop.R | 45 R/modMAratio.R | 101 - R/modMAtree.R | 134 +- R/modSAarea.R | 44 R/modSApop.R | 51 R/modSAtree.R | 140 +- R/popTableIDs.R | 28 R/popTables.R | 57 R/spClassifyRast.R | 5 R/spExtractPoly.R | 56 R/spGetPlots.R | 66 - R/spGetStrata.R | 85 + R/spGetXY.R | 3 inst/doc/FIESTA_tutorial_GB.R | 3 inst/doc/FIESTA_tutorial_GB.Rmd | 3 inst/doc/FIESTA_tutorial_GB.html | 2364 +++++++++++++++++++------------------- inst/doc/FIESTA_tutorial_MA.html | 382 ++---- inst/doc/FIESTA_tutorial_PB.html | 30 inst/doc/FIESTA_tutorial_SA.R | 1 inst/doc/FIESTA_tutorial_SA.Rmd | 1 inst/doc/FIESTA_tutorial_SA.html | 2 inst/doc/FIESTA_tutorial_dat.html | 24 man/DBgetPlots.Rd | 8 man/popTableIDs.Rd | 34 man/popTables.Rd | 67 - man/ref_codes.Rd | 2 man/spExtractPoly.Rd | 5 man/spGetStrata.Rd | 7 vignettes/FIESTA_tutorial_GB.Rmd | 3 vignettes/FIESTA_tutorial_SA.Rmd | 1 53 files changed, 3491 insertions(+), 2512 deletions(-)
Title: Analyzing Categorical Time Series
Description: An implementation of several functions for feature extraction in
categorical time series datasets. Specifically, some features related to
marginal distributions and serial dependence patterns can be computed. These
features can be used to feed clustering and classification algorithms for
categorical time series, among others. The package also includes some
interesting datasets containing biological sequences. Practitioners from a
broad variety of fields could benefit from the general framework provided
by 'ctsfeatures'.
Author: Angel Lopez-Oriona [aut, cre],
Jose A. Vilar [aut]
Maintainer: Angel Lopez-Oriona <oriona38@hotmail.com>
Diff between ctsfeatures versions 1.1.0 dated 2023-10-24 and 1.2.0 dated 2024-01-22
DESCRIPTION | 6 - MD5 | 140 +++++++++++++++---------------- R/GeneticSequences.R | 13 +- R/ProteinSequences.R | 13 +- R/SleepStages.R | 20 ++-- R/SyntheticData1.R | 12 +- R/SyntheticData2.R | 12 +- R/SyntheticData3.R | 12 +- R/auxiliary_chebycheff_dispersion.R | 12 +- R/auxiliary_cohens_kappa.R | 9 - R/auxiliary_cohens_kappa_function.R | 14 +-- R/auxiliary_correlation_i_j_k_function.R | 6 - R/auxiliary_cramers_vi.R | 19 ++-- R/auxiliary_cramers_vi_function.R | 12 +- R/auxiliary_entropy.R | 12 +- R/auxiliary_gini_index.R | 12 +- R/auxiliary_gk_lambda.R | 12 +- R/auxiliary_gk_tau.R | 13 +- R/auxiliary_p_i_j_k_function.R | 6 - R/auxiliary_pearson_measure.R | 10 +- R/auxiliary_phi2_measure.R | 9 - R/auxiliary_sakoda_measure.R | 17 ++- R/auxiliary_total_correlation.R | 21 ++-- R/auxiliary_total_mixed_correlation_1.R | 25 ++--- R/auxiliary_total_mixed_correlation_2.R | 25 ++--- R/auxiliary_uncertainty_coefficient.R | 12 +- R/binarization.R | 26 +++-- R/calculate_features.R | 51 +++++------ R/calculate_motifs.R | 26 +++-- R/calculate_subfeatures.R | 47 +++++----- R/conditional_probabilities.R | 21 ++-- R/joint_probabilities.R | 18 ++- R/marginal_probabilities.R | 18 +-- R/plot_ccc.R | 26 ++--- R/plot_cohen.R | 22 ++-- R/plot_cramer.R | 24 ++--- R/plot_cts.R | 23 ++--- R/plot_ifsct.R | 28 +++--- R/plot_mcc.R | 32 +++---- R/plot_ph.R | 16 ++- R/plot_reg.R | 21 ++-- R/plot_se.R | 14 +-- build/partial.rdb |binary data/GeneticSequences.RData |binary data/ProteinSequences.RData |binary data/SleepStages.RData |binary data/SyntheticData1.RData |binary data/SyntheticData2.RData |binary data/SyntheticData3.RData |binary man/GeneticSequences.Rd | 13 +- man/ProteinSequences.Rd | 13 +- man/SleepStages.Rd | 20 ++-- man/SyntheticData1.Rd | 18 +-- man/SyntheticData2.Rd | 18 +-- man/SyntheticData3.Rd | 18 +-- man/binarization.Rd | 13 +- man/calculate_features.Rd | 16 +-- man/calculate_motifs.Rd | 13 +- man/calculate_subfeatures.Rd | 16 +-- man/conditional_probabilities.Rd | 13 +- man/joint_probabilities.Rd | 13 +- man/marginal_probabilities.Rd | 13 +- man/plot_ccc.Rd | 15 +-- man/plot_cohen.Rd | 15 +-- man/plot_cramer.Rd | 15 +-- man/plot_cts.Rd | 13 +- man/plot_ifsct.Rd | 21 +--- man/plot_mcc.Rd | 19 +--- man/plot_ph.Rd | 9 + man/plot_reg.Rd | 12 +- man/plot_se.Rd | 13 +- 71 files changed, 620 insertions(+), 596 deletions(-)
More information about ConconiAnaerobicThresholdTest at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-06 1.6.11
2022-12-15 1.6.10
2022-11-08 1.6.9
2022-09-21 1.6.8
2022-07-20 1.6.7
2021-12-10 1.6.6
2021-04-27 1.6.5
2020-06-02 1.6.4
2019-01-30 1.6.3
2018-08-22 1.6.1
2017-06-06 1.5.5
2017-03-14 1.5.4
2016-12-27 1.5.2
2016-12-19 1.5.1
2016-10-27 1.4.0
2016-04-06 1.3.0
2016-02-18 1.2.1
2016-02-11 1.2.0
2016-01-20 1.1.3
2015-10-04 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-09 0.4.4
2018-10-01 0.3.0
2018-08-17 0.2.0
2017-12-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-16 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-08 1.3.3
2021-09-20 1.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-29 0.2.0
2015-09-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-22 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-17 0.4.1
2017-04-30 0.4.0
2016-07-13 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-08 1.2
2020-07-02 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-21 0.1.5
2021-03-18 0.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-05 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-15 0.0.1
Title: Spatial Transfer of Statistics among Spanish Census Sections
Description: Transfers/imputes statistics among Spanish spatial polygons (census sections or postal code areas) from different moments in time (2001-202)3 without need of spatial files, just linking statistics to the ID codes of the spatial units.
The data available in the census sections of a partition/division (cartography) into force in a moment of time is transferred to the census sections of another partition/division employing the geometric approach (also known as areal weighting or polygon overlay).
References:
Goerlich (2022) <doi:10.12842/WPIVIE_0322>.
Pavía and Cantarino (2017a, b) <doi:10.1111/gean.12112>, <doi:10.1016/j.apgeog.2017.06.021>.
Acknowledgements:
The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257) and Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) for supporting this research.
Author: Virgilio Perez [aut] ,
Jose M. Pavia [aut, cre]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between sc2sc versions 0.0.1-7 dated 2023-03-21 and 0.0.1-9 dated 2024-01-22
DESCRIPTION | 18 +++++++------ MD5 | 21 ++++++++------- NEWS.md |only R/auxiliary_functions.R | 65 +++++++++++++++++++++++++++++++----------------- R/cp2sc.R | 12 ++++++-- R/sc2cp.R | 16 ++++++++--- R/sc2sc.R | 14 +++++++--- R/sysdata.rda |binary build/partial.rdb |binary man/cp2sc.Rd | 2 - man/sc2cp.Rd | 2 - man/sc2sc.Rd | 8 ++--- 12 files changed, 100 insertions(+), 58 deletions(-)
Title: Provide the 'x13ashtml' Seasonal Adjustment Binary
Description: The US Census Bureau provides a seasonal adjustment program now
called 'X-13ARIMA-SEATS' building on both earlier programs called X-11 and
X-12 as well as the SEATS program by the Bank of Spain. The US Census Bureau
offers both source and binary versions -- which this package integrates for
use by other R packages.
Author: Dirk Eddelbuettel [aut, cre] ,
Christoph Sax [aut] ,
Kirill Mueller [ctb] ,
Jeroen Ooms [ctb] ,
Michael Antonov [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between x13binary versions 1.1.57-4 dated 2023-09-07 and 1.1.60 dated 2024-01-22
x13binary-1.1.57-4/x13binary/configure |only x13binary-1.1.57-4/x13binary/configure.win |only x13binary-1.1.60/x13binary/ChangeLog | 43 x13binary-1.1.60/x13binary/DESCRIPTION | 29 x13binary-1.1.60/x13binary/LICENSE | 23 x13binary-1.1.60/x13binary/MD5 | 989 +++++++++++++++++- x13binary-1.1.60/x13binary/R/checkX13binary.R | 6 x13binary-1.1.60/x13binary/R/supportedPlatform.R | 42 x13binary-1.1.60/x13binary/README.md | 62 - x13binary-1.1.60/x13binary/cleanup |only x13binary-1.1.60/x13binary/inst/AUTHORS |only x13binary-1.1.60/x13binary/inst/COPYRIGHT | 10 x13binary-1.1.60/x13binary/man/supportedPlatform.Rd | 2 x13binary-1.1.60/x13binary/src |only x13binary-1.1.60/x13binary/tests/simpleTest.R | 10 x13binary-1.1.60/x13binary/tests/simpleTest.Rout.save |only x13binary-1.1.60/x13binary/tools |only 17 files changed, 1114 insertions(+), 102 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.6 dated 2023-10-20 and 1.3.7 dated 2024-01-22
DESCRIPTION | 6 +- MD5 | 14 ++--- R/vioplotW.R | 10 +-- build/vignette.rds |binary inst/doc/wrGraphVignette1.R | 2 inst/doc/wrGraphVignette1.Rmd | 13 ++--- inst/doc/wrGraphVignette1.html | 105 ++++++++++++++++++++--------------------- vignettes/wrGraphVignette1.Rmd | 13 ++--- 8 files changed, 83 insertions(+), 80 deletions(-)
Title: Exploratory Graph Analysis – a Framework for Estimating the
Number of Dimensions in Multivariate Data using Network
Psychometrics
Description: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality
and psychometric assessment. EGA estimates the number of dimensions in
psychological data using network estimation methods and community detection
algorithms. A bootstrap method is provided to assess the stability of dimensions
and items. Fit is evaluated using the Entropy Fit family of indices. Unique
Variable Analysis evaluates the extent to which items are locally dependent (or
redundant). Network loadings provide similar information to factor loadings and
can be used to compute network scores. A bootstrap and permutation approach are
available to assess configural and metric invariance. Hierarchical structures
can be detected using Hierarchical EGA. Time series and intensive longitudinal
data can be analyzed using Dynamic EGA, supporting individual, group, and
population level assessments.
Author: Hudson Golino [aut, cre] ,
Alexander Christensen [aut] ,
Robert Moulder [ctb] ,
Luis E. Garrido [ctb] ,
Laura Jamison [ctb] ,
Dingjing Shi [ctb]
Maintainer: Hudson Golino <hfg9s@virginia.edu>
Diff between EGAnet versions 2.0.3 dated 2023-11-17 and 2.0.4 dated 2024-01-22
DESCRIPTION | 10 MD5 | 234 - NAMESPACE | 301 - NEWS | 1001 ++--- R/CFA.R | 378 +- R/EBICglasso.qgraph.R | 1044 +++--- R/EGA.R | 1138 +++--- R/EGA.estimate.R | 922 ++--- R/EGA.fit.R | 1505 ++++---- R/EGAnet.R | 246 - R/Embed.R | 198 - R/S3plots.R | 302 - R/TMFG.R | 894 ++--- R/UVA.R | 2164 ++++++------ R/auto.correlate.R | 836 ++-- R/boot.ergoInfo.R | 868 ++--- R/bootEGA.R | 3344 +++++++++---------- R/color_palette_EGA.R | 632 +-- R/community.compare.R |only R/community.consensus.R | 1482 ++++---- R/community.detection.R | 1026 ++---- R/community.homogenize.R | 438 +- R/community.unidimensional.R | 948 ++--- R/compare.EGA.plots.R | 664 +-- R/convert2igraph.R | 140 R/convert2tidygraph.R | 98 R/development.R | 90 R/dimensionStability.R | 446 +- R/dynEGA.R | 3142 +++++++++--------- R/dynEGA.ind.pop.R | 494 +- R/entropyFit.R | 424 +- R/ergoInfo.R | 632 +-- R/genTEFI.R | 196 - R/glla.R | 336 - R/helpers.R | 6834 ++++++++++++++++++++-------------------- R/hierEGA.R | 2228 ++++++------- R/igraph2matrix.R | 136 R/infoCluster.R | 524 +-- R/invariance.R | 1928 +++++------ R/itemStability.R | 1636 ++++----- R/jsd.R | 564 +-- R/jsd.ergodicity.R | 464 +- R/mctest.ergoInfo.R | 746 ++-- R/modularity.R | 346 +- R/net.loads.R | 1676 ++++----- R/net.scores.R | 670 +-- R/network.estimation.R | 1280 +++---- R/oldUVA.R | 1586 ++++----- R/optimism.R | 50 R/polychoric.matrix.R | 466 +- R/prime.num.R | 40 R/riEGA.R | 994 ++--- R/rng_test.R | 184 - R/sim.dynEGA.R | 96 R/simDFM.R | 392 +- R/tefi.R | 906 ++--- R/totalCor.R | 212 - R/totalCorMat.R | 150 R/utils-EGAnet.R | 4486 +++++++++++++------------- R/vn.entropy.R | 456 +- R/wto.R | 224 - R/zzz.R | 26 inst/CITATION | 34 man/CFA.Rd | 164 man/EBICglasso.qgraph.Rd | 344 +- man/EGA.Rd | 500 +- man/EGA.estimate.Rd | 358 +- man/EGA.fit.Rd | 438 +- man/EGAnet-package.Rd | 256 - man/EGAnet-plot.Rd | 320 - man/Embed.Rd | 98 man/LCT.Rd | 392 +- man/TMFG.Rd | 322 - man/UVA.Rd | 312 - man/auto.correlate.Rd | 230 - man/boot.ergoInfo.Rd | 356 +- man/boot.wmt.Rd | 38 man/bootEGA.Rd | 704 ++-- man/color_palette_EGA.Rd | 146 man/community.compare.Rd |only man/community.consensus.Rd | 348 +- man/community.detection.Rd | 288 - man/community.homogenize.Rd | 124 man/community.unidimensional.Rd | 348 +- man/compare.EGA.plots.Rd | 202 - man/convert2igraph.Rd | 58 man/convert2tidygraph.Rd | 50 man/depression.Rd | 42 man/dimensionStability.Rd | 156 man/dnn.weights.Rd | 48 man/dynEGA.Rd | 720 ++-- man/dynEGA.ind.pop.Rd | 488 +- man/ega.wmt.Rd | 40 man/entropyFit.Rd | 108 man/ergoInfo.Rd | 158 man/genTEFI.Rd | 114 man/glla.Rd | 138 man/hierEGA.Rd | 596 +-- man/igraph2matrix.Rd | 64 man/infoCluster.Rd | 114 man/intelligenceBattery.Rd | 42 man/invariance.Rd | 638 +-- man/itemStability.Rd | 258 - man/jsd.Rd | 144 man/modularity.Rd | 146 man/net.loads.Rd | 184 - man/net.scores.Rd | 268 - man/network.estimation.Rd | 292 - man/optimism.Rd | 52 man/polychoric.matrix.Rd | 262 - man/prime.num.Rd | 42 man/riEGA.Rd | 442 +- man/sim.dynEGA.Rd | 100 man/simDFM.Rd | 174 - man/tefi.Rd | 144 man/totalCor.Rd | 86 man/totalCorMat.Rd | 76 man/vn.entropy.Rd | 100 man/wto.Rd | 88 119 files changed, 34326 insertions(+), 34301 deletions(-)
Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut],
Egill Fridgeirsson [aut],
Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between Andromeda versions 0.6.4 dated 2023-11-24 and 0.6.5 dated 2024-01-22
DESCRIPTION | 18 +++++++++--------- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/Andromeda.R | 2 +- R/Indices.R | 4 ++-- R/LoadingSaving.R | 2 +- R/Object.R | 2 +- R/Operations.R | 2 +- build/vignette.rds |binary inst/doc/UsingAndromeda.pdf |binary man/Andromeda-package.Rd | 5 +++-- tests/testthat/test-object.R | 11 +++++++---- 12 files changed, 41 insertions(+), 32 deletions(-)
Title: Formats Spatial Data for Use in Htmlwidgets
Description: Many packages use 'htmlwidgets' <https://CRAN.R-project.org/package=htmlwidgets>
for interactive plotting of spatial data.
This package provides functions for converting R objects, such as simple features,
into structures suitable for use in 'htmlwidgets' mapping libraries.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between spatialwidget versions 0.2.3 dated 2020-08-31 and 0.2.5 dated 2024-01-22
spatialwidget-0.2.3/spatialwidget/inst/include/spatialwidget/utils/where |only spatialwidget-0.2.5/spatialwidget/DESCRIPTION | 20 spatialwidget-0.2.5/spatialwidget/LICENSE |only spatialwidget-0.2.5/spatialwidget/MD5 | 64 - spatialwidget-0.2.5/spatialwidget/NEWS.md | 10 spatialwidget-0.2.5/spatialwidget/R/RcppExports.R | 12 spatialwidget-0.2.5/spatialwidget/R/data.R | 2 spatialwidget-0.2.5/spatialwidget/README.md | 60 - spatialwidget-0.2.5/spatialwidget/build/vignette.rds |binary spatialwidget-0.2.5/spatialwidget/inst/doc/spatialwidget.Rmd | 2 spatialwidget-0.2.5/spatialwidget/inst/doc/spatialwidget.html | 460 +++++----- spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/colour/colour.hpp | 55 - spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/data_construction/data_construction.hpp | 18 spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/geojson/geojson.hpp | 14 spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/legend/legend.hpp | 3 spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/palette/palette.hpp | 75 + spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/parameters/parameters.hpp | 40 spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/spatialwidget.hpp | 232 ++++- spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/utils/colour/colour.hpp | 34 spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/utils/dates/dates.hpp | 4 spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/utils/factors/factors.hpp | 4 spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/utils/fill/fill.hpp | 67 - spatialwidget-0.2.5/spatialwidget/inst/include/spatialwidget/utils/utils.hpp | 1 spatialwidget-0.2.5/spatialwidget/man/widget_melbourne.Rd | 2 spatialwidget-0.2.5/spatialwidget/src/Makevars | 2 spatialwidget-0.2.5/spatialwidget/src/Makevars.win | 2 spatialwidget-0.2.5/spatialwidget/src/RcppExports.cpp | 37 spatialwidget-0.2.5/spatialwidget/src/colour.cpp | 26 spatialwidget-0.2.5/spatialwidget/src/data_construction.cpp | 3 spatialwidget-0.2.5/spatialwidget/src/palette.cpp | 17 spatialwidget-0.2.5/spatialwidget/src/parameters.cpp | 5 spatialwidget-0.2.5/spatialwidget/src/utils.cpp | 3 spatialwidget-0.2.5/spatialwidget/tests/testthat/test-colours.R | 25 spatialwidget-0.2.5/spatialwidget/vignettes/spatialwidget.Rmd | 2 34 files changed, 872 insertions(+), 429 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 ML framework with spatio-temporal resampling
methods to account for the presence of spatiotemporal autocorrelation
(STAC) in predictor variables. STAC may cause highly biased
performance estimates in cross-validation if ignored.
Author: Patrick Schratz [aut, cre] ,
Marc Becker [aut] ,
Jannes Muenchow [ctb] ,
Michel Lang [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3spatiotempcv versions 2.2.0 dated 2023-10-24 and 2.3.0 dated 2024-01-22
mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/R/ResamplingSpCVknndm.R |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/custom-cv-fold-1-2-sample-fold-n.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/custom-cv-fold-1-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/cv-fold-1-2-groups-col-role.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/cv-fold-1-2-sample-fold-n.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/cv-fold-1-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/repcv-fold-1-2-rep-1.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/repspcvblock-fold-1-2-rep-1.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/repspcvcoords-fold-1-2-rep-1.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/repspcvcoords-fold-1-2-sample-fold-n.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/repspcvenv-fold-1-2-rep-1.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/spcvblock-fold-1-2-sample-fold-n.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/spcvblock-fold-1-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/spcvcoords-fold-1-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/spcvenv-fold-1-2-sample-fold-n.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/1-autoplot/spcvenv-fold-1-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/2-autoplot/repspcvdisc-fold-1-2-sample-fold-n.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/2-autoplot/repspcvknndm-fold-1-2-sample-fold-n.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2-rep-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2-sample-fold-n.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/2-autoplot/spcvdisc-fold-1-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/2-autoplot/spcvknndm-fold-1-2.new.svg |only mlr3spatiotempcv-2.2.0/mlr3spatiotempcv/tests/testthat/_snaps/autoplot_buffer/spcvbuffer-fold-1-2.new.svg |only mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/DESCRIPTION | 24 +- mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/MD5 | 111 ++++------ mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/NEWS.md | 14 + mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingRepeatedSpCVBlock.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingRepeatedSpCVCoords.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingRepeatedSpCVDisc.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingRepeatedSpCVEnv.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingRepeatedSpCVTiles.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingRepeatedSpCVknndm.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingRepeatedSptCVCstf.R | 5 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingSpCVBlock.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingSpCVBuffer.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingSpCVCoords.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingSpCVDisc.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingSpCVEnv.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingSpCVKnndm.R |only mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingSpCVTiles.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/ResamplingSptCVCstf.R | 5 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/aaa.R |only mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/as_task_regr_st.R | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/autoplot.R | 30 +- mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/R/zzz.R | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/build/partial.rdb |binary mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/build/vignette.rds |binary mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/inst/doc/mlr3spatiotempcv.R | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/inst/doc/mlr3spatiotempcv.html | 13 - mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/inst/doc/spatiotemp-viz.R | 9 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/inst/doc/spatiotemp-viz.Rmd | 3 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/inst/doc/spatiotemp-viz.html | 4 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/inst/references.bib | 13 + mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/as_task_regr_st.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingCV.Rd | 4 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingCustomCV.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingSpCVBlock.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingSpCVBuffer.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingSpCVCoords.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingSpCVDisc.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingSpCVEnv.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingSpCVKnndm.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/autoplot.ResamplingSpCVTiles.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/mlr_resamplings_repeated_sptcv_cstf.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/mlr_resamplings_spcv_knndm.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/man/mlr_resamplings_sptcv_cstf.Rd | 2 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/tests/testthat.R | 5 mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/tests/testthat/test-unload.R |only mlr3spatiotempcv-2.3.0/mlr3spatiotempcv/vignettes/spatiotemp-viz.Rmd | 3 70 files changed, 189 insertions(+), 121 deletions(-)
More information about mlr3spatiotempcv at CRAN
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Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust
results, without the need of repetitive coding or extensive R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.4 dated 2023-12-07 and 5.2.5 dated 2024-01-22
lares-5.2.4/lares/build |only lares-5.2.4/lares/inst/doc |only lares-5.2.4/lares/vignettes |only lares-5.2.5/lares/DESCRIPTION | 14 +++--- lares-5.2.5/lares/MD5 | 67 +++++++++++++------------------ lares-5.2.5/lares/NAMESPACE | 27 +++--------- lares-5.2.5/lares/R/cache.R | 17 +++++++ lares-5.2.5/lares/R/chatgpt.R | 10 +++- lares-5.2.5/lares/R/gemini.R |only lares-5.2.5/lares/R/lares.R | 18 ++++++-- lares-5.2.5/lares/R/maze.R |only lares-5.2.5/lares/R/model_functions.R | 1 lares-5.2.5/lares/R/other_functions.R | 28 +++++++++++- lares-5.2.5/lares/R/robyn.R | 24 ++++++++--- lares-5.2.5/lares/R/zzz.R | 5 ++ lares-5.2.5/lares/man/bring_api.Rd | 1 lares-5.2.5/lares/man/cache_write.Rd | 7 +++ lares-5.2.5/lares/man/fb_accounts.Rd | 1 lares-5.2.5/lares/man/fb_ads.Rd | 1 lares-5.2.5/lares/man/fb_creatives.Rd | 1 lares-5.2.5/lares/man/fb_insights.Rd | 1 lares-5.2.5/lares/man/fb_process.Rd | 1 lares-5.2.5/lares/man/fb_report_check.Rd | 1 lares-5.2.5/lares/man/fb_rf.Rd | 1 lares-5.2.5/lares/man/fb_token.Rd | 1 lares-5.2.5/lares/man/gemini_ask.Rd |only lares-5.2.5/lares/man/gpt_ask.Rd | 14 +++++- lares-5.2.5/lares/man/gpt_prompter.Rd | 5 ++ lares-5.2.5/lares/man/li_auth.Rd | 1 lares-5.2.5/lares/man/li_profile.Rd | 1 lares-5.2.5/lares/man/maze_solve.Rd |only lares-5.2.5/lares/man/queryGA.Rd | 1 lares-5.2.5/lares/man/slackSend.Rd | 1 lares-5.2.5/lares/man/what_size.Rd | 16 ++++++- 34 files changed, 180 insertions(+), 86 deletions(-)
Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive
Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2022) <arXiv:2007.04713>,
Savi Virolainen (2022) <arXiv:2109.13648>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 2.1.0 dated 2023-11-14 and 2.1.1 dated 2024-01-22
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 7 +++++++ R/MAINest.R | 6 +++--- R/generateParams.R | 10 ++++++++-- R/geneticAlgorithm.R | 30 +++++++++++++++++++++++------- R/linearIRF.R | 9 +++++---- inst/doc/gmvarkit-vignette.pdf |binary man/GAfit.Rd | 17 +++++++++++++---- man/linear_IRF.Rd | 8 ++++---- man/random_coefmats2.Rd | 8 +++++++- man/random_ind2.Rd | 8 +++++--- man/smart_ind.Rd | 8 +++++--- 13 files changed, 95 insertions(+), 46 deletions(-)
Title: R Functions for Generalized Simulated Annealing
Description: Performs search for global minimum of a very complex non-linear
objective function with a very large number of optima.
Author: Sylvain Gubian, Yang Xiang, Brian Suomela, Julia Hoeng, PMP SA.
Maintainer: Sylvain Gubian <DL.RSupport@pmi.com>
Diff between GenSA versions 1.1.12 dated 2023-12-12 and 1.1.14 dated 2024-01-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 +++++++- src/Caller.cpp | 11 ++++++++--- src/Caller.h | 3 +++ src/Engine.cpp | 5 ++++- src/Engine.h | 1 - 7 files changed, 32 insertions(+), 16 deletions(-)
Title: GCxGC Preprocessing and Analysis
Description: Provides complete detailed preprocessing of two-dimensional gas chromatogram (GCxGC) samples. Baseline correction, smoothing, peak detection, and peak alignment. Also provided are some analysis functions, such as finding extracted ion chromatograms, finding mass spectral data, targeted analysis, and nontargeted analysis with either the 'National Institute of Standards and Technology Mass Spectral Library' or with the mass data. There are also several visualization methods provided for each step of the preprocessing and analysis.
Author: Stephanie Gamble [aut, cre] ,
Mannion Joseph [ctb],
Granger Caroline [ctb],
Battelle Savannah River Alliance [cph],
NNSA, US DOE [fnd]
Maintainer: Stephanie Gamble <stephanie.gamble@srnl.doe.gov>
Diff between gcxgclab versions 1.0.0 dated 2024-01-17 and 1.0.1 dated 2024-01-22
gcxgclab-1.0.0/gcxgclab/inst/README.html |only gcxgclab-1.0.1/gcxgclab/DESCRIPTION | 12 +++++--- gcxgclab-1.0.1/gcxgclab/MD5 | 43 ++++++++++++++++++++++++++--- gcxgclab-1.0.1/gcxgclab/build/partial.rdb |binary gcxgclab-1.0.1/gcxgclab/build/vignette.rds |only gcxgclab-1.0.1/gcxgclab/inst/doc |only gcxgclab-1.0.1/gcxgclab/man/figures |only gcxgclab-1.0.1/gcxgclab/vignettes |only 8 files changed, 48 insertions(+), 7 deletions(-)
Title: Fast JSON Parser and Generator
Description: A fast JSON parser, generator and validator which converts JSON
data to/from R objects. The standard R data types are supported
(e.g. logical, numeric, integer) with configurable handling of NULL and NA
values. Data frames, atomic vectors and lists are all supported as data
containers translated to/from JSON.
This implementation is a wrapper around the 'yyjson' 'C' library which
is available from <https://github.com/ibireme/yyjson>.
Author: Mike Cheng [aut, cre, cph],
Yao Yuan [cph]
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Diff between yyjsonr versions 0.1.16 dated 2024-01-17 and 0.1.18 dated 2024-01-22
DESCRIPTION | 6 - MD5 | 10 +-- NEWS.md | 20 +++++- src/R-yyjson-parse.c | 151 +++++++++++++++++++++++------------------------ src/R-yyjson-parse.h | 2 src/R-yyjson-serialize.c | 74 +++++++++++------------ 6 files changed, 138 insertions(+), 125 deletions(-)
Title: Non-Smooth Regularization for Structural Equation Models
Description: Provides regularized structural equation modeling
(regularized SEM) with non-smooth penalty functions (e.g., lasso) building
on 'lavaan'. The package is heavily inspired by the
['regsem'](<https://github.com/Rjacobucci/regsem>) and
['lslx'](<https://github.com/psyphh/lslx>) packages.
Author: Jannik H. Orzek [aut, cre, cph]
Maintainer: Jannik H. Orzek <jannik.orzek@mailbox.org>
Diff between lessSEM versions 1.5.4 dated 2024-01-09 and 1.5.5 dated 2024-01-22
DESCRIPTION | 8 MD5 | 730 +- NAMESPACE | 192 NEWS.md | 26 R/0-generics.R | 38 R/RcppExports.R | 1012 +- R/SEMData.R | 190 R/analyticDerivatives.R | 140 R/class-Rcpp_SEMCpp.R | 154 R/class-Rcpp_mgSEM.R | 156 R/class-coef.R | 266 R/class-cvRegularizedSEM.R | 368 - R/class-gpRegularized.R | 488 - R/class-logLikelihood.R | 42 R/class-misc.R | 302 R/class-regularizedSEM.R | 688 +- R/class-regularizedSEMMixedPenalty.R | 642 - R/class-regularizedSEMWithCustomPenalty.R | 256 R/class-stabSel.R | 262 R/computeFit.R | 206 R/controlOptimizer.R | 440 - R/createSubsets.R | 88 R/cvRegularizeSEMInterface.R | 2354 +++--- R/cvRegularizeSEMInternal.R | 778 +- R/cvRegularizeSmoothSEMInterface.R | 932 +- R/cvRegularizeSmoothSEMInternal.R | 602 - R/getMaxLambda.R | 234 R/gpOptimizationInterface.R | 3016 ++++---- R/gpOptimizationInterfaceCpp.R | 3370 ++++----- R/gpOptimizationInternal.R | 906 +- R/initializeSEM.R | 1454 ++-- R/lavaanHelperFunctions.R | 760 +- R/mixedPenalty.R | 3392 +++++----- R/modifyModel.R | 54 R/optimize.R | 124 R/parameters.R | 204 R/penaltyFunctions.R | 768 +- R/regularizationHelper.R | 352 - R/regularizeSEMInterface.R | 2450 +++---- R/regularizeSEMInternal.R | 1156 +-- R/regularizeSEMWithCustomPenalty.R | 400 - R/regularizeSmoothSEMInterface.R | 826 +- R/regularizedSmoothSEMInternal.R | 788 +- R/setupRegularizedSEM.R | 964 +- R/stabilitySelection.R | 366 - R/transformations.R | 674 - R/utils.R | 346 - R/zzz.R | 936 +- README.md | 1048 +-- build/vignette.rds |binary inst/CITATION | 132 inst/doc/Definition-Variables-and-Multi-Group-SEM.Rmd | 1068 +-- inst/doc/Definition-Variables-and-Multi-Group-SEM.html | 1678 ++-- inst/doc/Estimator-Settings.Rmd | 352 - inst/doc/Estimator-Settings.html | 1032 +-- inst/doc/General-Purpose-Optimization.Rmd | 1322 +-- inst/doc/General-Purpose-Optimization.html | 1784 ++--- inst/doc/Mixed-Penalties.Rmd | 552 - inst/doc/Mixed-Penalties.html | 1238 +-- inst/doc/Parameter-transformations.Rmd | 2726 ++++---- inst/doc/Parameter-transformations.html | 3090 ++++----- inst/doc/SCAD-and-MCP.Rmd | 368 - inst/doc/SCAD-and-MCP.html | 880 +- inst/doc/The-Structural-Equation-Model.Rmd | 1102 +-- inst/doc/The-Structural-Equation-Model.html | 1614 ++-- inst/doc/The-optimizer-interface.Rmd | 36 inst/doc/The-optimizer-interface.html | 530 - inst/doc/lessSEM.Rmd | 1584 ++-- inst/doc/lessSEM.html | 2114 +++--- inst/doc/log-likelihood-gradients.Rmd | 278 inst/doc/log-likelihood-gradients.html | 994 +- inst/include/lesstimate/Readme.md | 344 - inst/include/lesstimate/include/lesstimate/glmnet_mixedPenalty.h | 2 inst/include/lesstimate/include/lesstimate/ista_mixedPenalty.h | 3 inst/include/lesstimate/include/lesstimate/model.h | 3 inst/include/lesstimate/include/lesstimate/penalty.h | 3 inst/include/lesstimate/include/lesstimate/proximalOperator.h | 1 inst/include/lesstimate/include/lesstimate/smoothPenalty.h | 2 man/AIC-Rcpp_SEMCpp-method.Rd | 42 man/AIC-Rcpp_mgSEM-method.Rd | 42 man/AIC-gpRegularized-method.Rd | 42 man/AIC-regularizedSEM-method.Rd | 42 man/AIC-regularizedSEMMixedPenalty-method.Rd | 42 man/AIC-regularizedSEMWithCustomPenalty-method.Rd | 48 man/BIC-Rcpp_SEMCpp-method.Rd | 38 man/BIC-Rcpp_mgSEM-method.Rd | 38 man/BIC-gpRegularized-method.Rd | 38 man/BIC-regularizedSEM-method.Rd | 38 man/BIC-regularizedSEMMixedPenalty-method.Rd | 38 man/BIC-regularizedSEMWithCustomPenalty-method.Rd | 44 man/Rcpp_SEMCpp-class.Rd | 20 man/Rcpp_bfgsEnetMgSEM-class.Rd | 20 man/Rcpp_bfgsEnetSEM-class.Rd | 20 man/Rcpp_glmnetCappedL1MgSEM-class.Rd | 20 man/Rcpp_glmnetCappedL1SEM-class.Rd | 20 man/Rcpp_glmnetEnetGeneralPurpose-class.Rd | 20 man/Rcpp_glmnetEnetGeneralPurposeCpp-class.Rd | 20 man/Rcpp_glmnetEnetMgSEM-class.Rd | 20 man/Rcpp_glmnetEnetSEM-class.Rd | 20 man/Rcpp_glmnetLspMgSEM-class.Rd | 20 man/Rcpp_glmnetLspSEM-class.Rd | 20 man/Rcpp_glmnetMcpMgSEM-class.Rd | 20 man/Rcpp_glmnetMcpSEM-class.Rd | 20 man/Rcpp_glmnetScadMgSEM-class.Rd | 20 man/Rcpp_glmnetScadSEM-class.Rd | 20 man/Rcpp_istaCappedL1GeneralPurpose-class.Rd | 20 man/Rcpp_istaCappedL1GeneralPurposeCpp-class.Rd | 20 man/Rcpp_istaCappedL1SEM-class.Rd | 20 man/Rcpp_istaCappedL1mgSEM-class.Rd | 20 man/Rcpp_istaEnetGeneralPurpose-class.Rd | 20 man/Rcpp_istaEnetGeneralPurposeCpp-class.Rd | 20 man/Rcpp_istaEnetMgSEM-class.Rd | 24 man/Rcpp_istaEnetSEM-class.Rd | 24 man/Rcpp_istaLSPMgSEM-class.Rd | 20 man/Rcpp_istaLSPSEM-class.Rd | 20 man/Rcpp_istaLspGeneralPurpose-class.Rd | 20 man/Rcpp_istaLspGeneralPurposeCpp-class.Rd | 20 man/Rcpp_istaMcpGeneralPurpose-class.Rd | 20 man/Rcpp_istaMcpGeneralPurposeCpp-class.Rd | 20 man/Rcpp_istaMcpMgSEM-class.Rd | 20 man/Rcpp_istaMcpSEM-class.Rd | 20 man/Rcpp_istaMixedPenaltySEM-class.Rd | 20 man/Rcpp_istaMixedPenaltymgSEM-class.Rd | 20 man/Rcpp_istaScadGeneralPurpose-class.Rd | 20 man/Rcpp_istaScadGeneralPurposeCpp-class.Rd | 20 man/Rcpp_istaScadMgSEM-class.Rd | 20 man/Rcpp_istaScadSEM-class.Rd | 20 man/Rcpp_mgSEM-class.Rd | 20 man/SEMCpp.Rd | 80 man/adaptiveLasso.Rd | 364 - man/addCappedL1.Rd | 198 man/addElasticNet.Rd | 228 man/addLasso.Rd | 214 man/addLsp.Rd | 220 man/addMcp.Rd | 198 man/addScad.Rd | 210 man/bfgs.Rd | 120 man/bfgsEnet.Rd | 48 man/bfgsEnetMgSEM.Rd | 48 man/bfgsEnetSEM.Rd | 48 man/callFitFunction.Rd | 42 man/cappedL1.Rd | 294 man/coef-Rcpp_SEMCpp-method.Rd | 38 man/coef-Rcpp_mgSEM-method.Rd | 38 man/coef-cvRegularizedSEM-method.Rd | 38 man/coef-gpRegularized-method.Rd | 38 man/coef-regularizedSEM-method.Rd | 38 man/coef-regularizedSEMMixedPenalty-method.Rd | 38 man/coef-regularizedSEMWithCustomPenalty-method.Rd | 40 man/controlBFGS.Rd | 148 man/controlGlmnet.Rd | 170 man/controlIsta.Rd | 148 man/covariances.Rd | 84 man/createSubsets.Rd | 44 man/curveLambda.Rd | 58 man/cvAdaptiveLasso.Rd | 310 man/cvCappedL1.Rd | 304 man/cvElasticNet.Rd | 304 man/cvLasso.Rd | 298 man/cvLsp.Rd | 298 man/cvMcp.Rd | 302 man/cvRegularizedSEM-class.Rd | 72 man/cvRidge.Rd | 294 man/cvRidgeBfgs.Rd | 226 man/cvScad.Rd | 314 man/cvScaler.Rd | 60 man/cvSmoothAdaptiveLasso.Rd | 244 man/cvSmoothElasticNet.Rd | 244 man/cvSmoothLasso.Rd | 234 man/dot-SEMFromLavaan.Rd | 86 man/dot-SEMdata.Rd | 36 man/dot-SEMdataWLS.Rd | 40 man/dot-adaptBreakingForWls.Rd | 42 man/dot-addMeanStructure.Rd | 44 man/dot-checkLavaanModel.Rd | 36 man/dot-checkPenalties.Rd | 32 man/dot-compileTransformations.Rd | 56 man/dot-computeInitialHessian.Rd | 102 man/dot-createMultiGroupTransformations.Rd | 40 man/dot-createParameterTable.Rd | 60 man/dot-createRcppTransformationFunction.Rd | 40 man/dot-createTransformations.Rd | 44 man/dot-cvRegularizeSEMInternal.Rd | 116 man/dot-cvRegularizeSmoothSEMInternal.Rd | 118 man/dot-cvregsem2LavaanParameters.Rd | 42 man/dot-defineDerivatives.Rd | 46 man/dot-extractParametersFromSyntax.Rd | 42 man/dot-extractSEMFromLavaan.Rd | 82 man/dot-fit.Rd | 36 man/dot-fitElasticNetMix.Rd | 40 man/dot-fitFunction.Rd | 44 man/dot-fitMix.Rd | 40 man/dot-getGradients.Rd | 52 man/dot-getHessian.Rd | 60 man/dot-getMaxLambda_C.Rd | 70 man/dot-getParameters.Rd | 44 man/dot-getRawData.Rd | 46 man/dot-getScores.Rd | 52 man/dot-gpGetMaxLambda.Rd | 70 man/dot-gpOptimizationInternal.Rd | 114 man/dot-gradientFunction.Rd | 44 man/dot-initializeMultiGroupSEMForRegularization.Rd | 52 man/dot-initializeSEMForRegularization.Rd | 44 man/dot-initializeWeights.Rd | 84 man/dot-labelLavaanParameters.Rd | 36 man/dot-lavaan2regsemLabels.Rd | 38 man/dot-likelihoodRatioFit.Rd | 44 man/dot-makeSingleLine.Rd | 42 man/dot-multiGroupSEMFromLavaan.Rd | 84 man/dot-noDotDotDot.Rd | 46 man/dot-penaltyTypes.Rd | 38 man/dot-reduceSyntax.Rd | 36 man/dot-regularizeSEMInternal.Rd | 98 man/dot-regularizeSEMWithCustomPenaltyRsolnp.Rd | 86 man/dot-regularizeSmoothSEMInternal.Rd | 106 man/dot-ridgeGradient.Rd | 44 man/dot-ridgeHessian.Rd | 44 man/dot-ridgeValue.Rd | 44 man/dot-setAMatrix.Rd | 64 man/dot-setFmatrix.Rd | 48 man/dot-setMVector.Rd | 70 man/dot-setParameters.Rd | 48 man/dot-setSMatrix.Rd | 64 man/dot-setupMulticore.Rd | 36 man/dot-smoothAdaptiveLASSOGradient.Rd | 52 man/dot-smoothAdaptiveLASSOHessian.Rd | 52 man/dot-smoothAdaptiveLASSOValue.Rd | 52 man/dot-smoothCappedL1Value.Rd | 44 man/dot-smoothElasticNetGradient.Rd | 52 man/dot-smoothElasticNetHessian.Rd | 52 man/dot-smoothElasticNetValue.Rd | 44 man/dot-smoothLASSOGradient.Rd | 44 man/dot-smoothLASSOHessian.Rd | 44 man/dot-smoothLASSOValue.Rd | 44 man/dot-smoothLspValue.Rd | 44 man/dot-smoothMcpValue.Rd | 44 man/dot-smoothScadValue.Rd | 44 man/dot-standardErrors.Rd | 48 man/dot-updateLavaan.Rd | 46 man/dot-useElasticNet.Rd | 38 man/elasticNet.Rd | 302 man/estimates-cvRegularizedSEM-method.Rd | 42 man/estimates-regularizedSEM-method.Rd | 42 man/estimates-regularizedSEMMixedPenalty-method.Rd | 42 man/estimates.Rd | 42 man/figures/lessSEM.svg | 400 - man/figures/logo.svg | 230 man/figures/penaltyFunctions.tex | 58 man/fit.Rd | 104 man/fitIndices-cvRegularizedSEM-method.Rd | 34 man/fitIndices-regularizedSEM-method.Rd | 34 man/fitIndices-regularizedSEMMixedPenalty-method.Rd | 34 man/fitIndices.Rd | 34 man/getLavaanParameters.Rd | 74 man/getTuningParameterConfiguration.Rd | 122 man/glmnetCappedL1MgSEM.Rd | 46 man/glmnetCappedL1SEM.Rd | 46 man/glmnetEnetGeneralPurpose.Rd | 50 man/glmnetEnetGeneralPurposeCpp.Rd | 50 man/glmnetEnetMgSEM.Rd | 48 man/glmnetEnetSEM.Rd | 48 man/glmnetLspMgSEM.Rd | 46 man/glmnetLspSEM.Rd | 46 man/glmnetMcpMgSEM.Rd | 46 man/glmnetMcpSEM.Rd | 46 man/glmnetMixedMgSEM.Rd | 46 man/glmnetMixedPenaltyGeneralPurpose.Rd | 46 man/glmnetMixedPenaltyGeneralPurposeCpp.Rd | 46 man/glmnetMixedSEM.Rd | 46 man/glmnetScadMgSEM.Rd | 46 man/glmnetScadSEM.Rd | 46 man/gpAdaptiveLasso.Rd | 372 - man/gpAdaptiveLassoCpp.Rd | 412 - man/gpCappedL1.Rd | 372 - man/gpCappedL1Cpp.Rd | 404 - man/gpElasticNet.Rd | 352 - man/gpElasticNetCpp.Rd | 402 - man/gpLasso.Rd | 336 man/gpLassoCpp.Rd | 406 - man/gpLsp.Rd | 334 man/gpLspCpp.Rd | 400 - man/gpMcp.Rd | 320 man/gpMcpCpp.Rd | 404 - man/gpRegularized-class.Rd | 60 man/gpRidge.Rd | 330 man/gpRidgeCpp.Rd | 388 - man/gpScad.Rd | 350 - man/gpScadCpp.Rd | 416 - man/istaCappedL1SEM.Rd | 44 man/istaCappedL1mgSEM.Rd | 44 man/istaEnetGeneralPurpose.Rd | 46 man/istaEnetGeneralPurposeCpp.Rd | 46 man/istaEnetMgSEM.Rd | 44 man/istaEnetSEM.Rd | 44 man/istaLSPMgSEM.Rd | 44 man/istaLSPSEM.Rd | 44 man/istaMcpMgSEM.Rd | 44 man/istaMcpSEM.Rd | 44 man/istaMixedPenaltyGeneralPurpose.Rd | 40 man/istaMixedPenaltyGeneralPurposeCpp.Rd | 42 man/istaMixedPenaltySEM.Rd | 44 man/istaMixedPenaltymgSEM.Rd | 44 man/istaScadMgSEM.Rd | 44 man/istaScadSEM.Rd | 44 man/lasso.Rd | 348 - man/lavaan2lslxLabels.Rd | 82 man/lessSEM.Rd | 876 +- man/lessSEM2Lavaan.Rd | 138 man/lessSEMCoef-class.Rd | 38 man/loadings.Rd | 84 man/logLik-Rcpp_SEMCpp-method.Rd | 38 man/logLik-Rcpp_mgSEM-method.Rd | 38 man/logLikelihood-class.Rd | 42 man/logicalMatch.Rd | 40 man/lsp.Rd | 290 man/makePtrs.Rd | 48 man/mcp.Rd | 304 man/mcpPenalty_C.Rd | 42 man/mgSEM.Rd | 80 man/mixedPenalty.Rd | 298 man/modifyModel.Rd | 78 man/newTau.Rd | 106 man/plot-cvRegularizedSEM-missing-method.Rd | 42 man/plot-gpRegularized-missing-method.Rd | 42 man/plot-regularizedSEM-missing-method.Rd | 42 man/plot-stabSel-missing-method.Rd | 42 man/regressions.Rd | 84 man/regsem2LavaanParameters.Rd | 82 man/regularizedSEM-class.Rd | 68 man/regularizedSEMMixedPenalty-class.Rd | 74 man/regularizedSEMWithCustomPenalty-class.Rd | 52 man/ridge.Rd | 292 man/ridgeBfgs.Rd | 174 man/scad.Rd | 310 man/scadPenalty_C.Rd | 42 man/show-Rcpp_SEMCpp-method.Rd | 34 man/show-Rcpp_mgSEM-method.Rd | 34 man/show-cvRegularizedSEM-method.Rd | 34 man/show-gpRegularized-method.Rd | 34 man/show-lessSEMCoef-method.Rd | 34 man/show-logLikelihood-method.Rd | 34 man/show-regularizedSEM-method.Rd | 34 man/show-regularizedSEMMixedPenalty-method.Rd | 34 man/show-stabSel-method.Rd | 34 man/simulateExampleData.Rd | 56 man/smoothAdaptiveLasso.Rd | 244 man/smoothElasticNet.Rd | 214 man/smoothLasso.Rd | 206 man/stabSel-class.Rd | 54 man/stabilitySelection.Rd | 204 man/summary-cvRegularizedSEM-method.Rd | 38 man/summary-gpRegularized-method.Rd | 38 man/summary-regularizedSEM-method.Rd | 38 man/summary-regularizedSEMMixedPenalty-method.Rd | 38 man/summary-regularizedSEMWithCustomPenalty-method.Rd | 40 man/variances.Rd | 84 vignettes/Definition-Variables-and-Multi-Group-SEM.Rmd | 1068 +-- vignettes/Estimator-Settings.Rmd | 352 - vignettes/General-Purpose-Optimization.Rmd | 1322 +-- vignettes/Mixed-Penalties.Rmd | 552 - vignettes/Parameter-transformations.Rmd | 2726 ++++---- vignettes/SCAD-and-MCP.Rmd | 368 - vignettes/The-Structural-Equation-Model.Rmd | 1102 +-- vignettes/The-optimizer-interface.Rmd | 36 vignettes/lessSEM.Rmd | 1584 ++-- vignettes/log-likelihood-gradients.Rmd | 278 366 files changed, 48506 insertions(+), 48492 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: CRAN Team [ctb, cre] ,
Duncan Temple Lang [aut] ,
Tomas Kalibera [ctb]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between XML versions 3.99-0.16 dated 2023-11-29 and 3.99-0.16.1 dated 2024-01-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/DocParse.c | 8 +++++++- src/XMLEventParse.c | 11 +++++++++-- 4 files changed, 22 insertions(+), 9 deletions(-)
Title: Correction Factors for Tree Plot Areas Intersected by Stand
Boundaries
Description: The German national forest inventory uses angle count sampling,
a sampling method first published as `Bitterlich, W.: Die Winkelzählmessung.
Allgemeine Forst- und Holzwirtschaftliche Zeitung, 58. Jahrg., Folge 11/12
vom Juni 1947` and extended by Grosenbaugh
(<https://academic.oup.com/jof/article-abstract/50/1/32/4684174>)
as probability proportional to size sampling.
When plots are located near stand boundaries, their sizes and hence
their probabilities need to be corrected.
Author: Andreas Dominik Cullmann [aut, cre],
Bernhard Boesch [ctb],
Christoph Fischer [ctb],
Gerald Kaendler [ctb]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between treePlotArea versions 1.4.1 dated 2023-06-13 and 1.5.0 dated 2024-01-22
DESCRIPTION | 6 - MD5 | 34 +++--- NEWS.md | 8 + R/check_boundaries.R | 3 R/get_boundary_radius.R | 2 R/get_correction_factors.R | 15 +-- R/options.R | 21 ++-- R/plot_tree_plot_area.R | 127 ++++++++++++++++---------- R/split_coord.R | 3 R/validate_data.R | 8 - inst/NEWS.rd | 10 ++ inst/doc/An_Introduction_to_treePlotArea.Rnw | 4 inst/doc/An_Introduction_to_treePlotArea.pdf |binary inst/tinytest/test_plot.R | 15 ++- man/check_boundaries.Rd | 3 man/get_correction_factors.Rd | 4 man/plot_tree_plot_area.Rd | 20 ++-- vignettes/An_Introduction_to_treePlotArea.Rnw | 4 18 files changed, 176 insertions(+), 111 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Umer Zeeshan Ijaz [ctb],
Chenhao Li [ctb],
Yang Cao [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 1.3.0 dated 2023-12-11 and 1.4.0 dated 2024-01-22
DESCRIPTION | 6 MD5 | 34 +-- R/microtable.R | 37 ++- R/trans_alpha.R | 525 +++++++++++++++++++++++++++------------------------ R/trans_beta.R | 66 +++--- R/trans_diff.R | 90 ++++---- R/trans_env.R | 4 R/trans_func.R | 7 R/trans_venn.R | 6 R/utility.R | 38 ++- data/dataset.RData |binary man/microtable.Rd | 30 +- man/tidy_taxonomy.Rd | 15 - man/trans_alpha.Rd | 28 ++ man/trans_beta.Rd | 24 +- man/trans_diff.Rd | 31 +-- man/trans_func.Rd | 4 man/trans_venn.Rd | 6 18 files changed, 534 insertions(+), 417 deletions(-)
Title: HDX Theme, Scales, and Other Conveniences for 'ggplot2'
Description: A Humanitarian Data Exchange (HDX) theme, color palettes, and
scales for 'ggplot2' to allow users to easily follow the HDX visual design
guide, including convenience functions for for loading and using the
Source Sans 3 font.
Author: Seth Caldwell [aut, cre, cph]
Maintainer: Seth Caldwell <caldwellst@gmail.com>
Diff between gghdx versions 0.1.1 dated 2023-08-18 and 0.1.2 dated 2024-01-22
gghdx-0.1.1/gghdx/R/display_hdx_pal.R |only gghdx-0.1.2/gghdx/DESCRIPTION | 6 - gghdx-0.1.2/gghdx/MD5 | 29 +++---- gghdx-0.1.2/gghdx/NAMESPACE | 2 gghdx-0.1.2/gghdx/NEWS.md | 9 ++ gghdx-0.1.2/gghdx/R/gghdx.R | 62 +++++++++++++-- gghdx-0.1.2/gghdx/R/hdx_display_pal.R |only gghdx-0.1.2/gghdx/R/hdx_geom_defaults.R | 89 ++++++++++++++++++++-- gghdx-0.1.2/gghdx/R/load_source_sans_3.R | 70 ++++++++++++++++- gghdx-0.1.2/gghdx/build/vignette.rds |binary gghdx-0.1.2/gghdx/inst/doc/gghdx.html | 3 gghdx-0.1.2/gghdx/man/gghdx.Rd | 23 ++++- gghdx-0.1.2/gghdx/man/ggplot2_geom_defaults.Rd |only gghdx-0.1.2/gghdx/man/hdx_display_pal.Rd | 2 gghdx-0.1.2/gghdx/man/hdx_geom_defaults.Rd | 30 ++++++- gghdx-0.1.2/gghdx/man/load_source_sans_3.Rd | 22 +++++ gghdx-0.1.2/gghdx/tests/testthat/test-scale_hdx.R | 28 ++++-- 17 files changed, 320 insertions(+), 55 deletions(-)
Title: Download Online Imagery Tiles
Description: Download imagery tiles to a standard cache and load the data into raster objects.
Facilities for 'AWS' terrain <https://registry.opendata.aws/terrain-tiles/> terrain and 'Mapbox'
<https://www.mapbox.com/> servers are provided.
Author: Michael Sumner [aut, cre] ,
Miles McBain [ctb] ,
Ben Raymond [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between ceramic versions 0.8.0 dated 2023-04-21 and 0.9.0 dated 2024-01-22
ceramic-0.8.0/ceramic/man/figures/README-elevation-1.png |only ceramic-0.8.0/ceramic/man/figures/README-example-1.png |only ceramic-0.8.0/ceramic/man/figures/README-tasmania-1.png |only ceramic-0.8.0/ceramic/man/figures/README-tile-add-plot.png |only ceramic-0.8.0/ceramic/man/figures/README-tile-plot.png |only ceramic-0.8.0/ceramic/man/figures/README-unnamed-chunk-1-2.png |only ceramic-0.8.0/ceramic/man/figures/README-unnamed-chunk-2-1.png |only ceramic-0.8.0/ceramic/man/figures/README-unnamed-chunk-3-1.png |only ceramic-0.8.0/ceramic/man/figures/README-unnamed-chunk-4-1.png |only ceramic-0.8.0/ceramic/man/figures/README-unnamed-chunk-4-2.png |only ceramic-0.9.0/ceramic/DESCRIPTION | 10 - ceramic-0.9.0/ceramic/MD5 | 50 +++---- ceramic-0.9.0/ceramic/NAMESPACE | 1 ceramic-0.9.0/ceramic/NEWS.md | 5 ceramic-0.9.0/ceramic/R/ceramic-package.R | 2 ceramic-0.9.0/ceramic/R/gdal.R | 39 +++++ ceramic-0.9.0/ceramic/R/locale.R | 16 +- ceramic-0.9.0/ceramic/R/spatial.R | 17 +- ceramic-0.9.0/ceramic/R/tasmap.R |only ceramic-0.9.0/ceramic/README.md | 69 +++++++++- ceramic-0.9.0/ceramic/man/cc_location.Rd | 6 ceramic-0.9.0/ceramic/man/ceramic-package.Rd | 18 ++ ceramic-0.9.0/ceramic/man/cities.Rd | 2 ceramic-0.9.0/ceramic/man/figures/README-example01-1.png |binary ceramic-0.9.0/ceramic/man/figures/README-extent1-1.png |only ceramic-0.9.0/ceramic/man/figures/README-extent2-1.png |binary ceramic-0.9.0/ceramic/man/figures/README-nz-spData-1.png |binary ceramic-0.9.0/ceramic/man/figures/README-tasmap-1.png |only ceramic-0.9.0/ceramic/man/figures/README-tasmap-2.png |only ceramic-0.9.0/ceramic/man/figures/README-tasmap-3.png |only ceramic-0.9.0/ceramic/man/figures/README-tasmap-4.png |only ceramic-0.9.0/ceramic/man/figures/README-tasmap-5.png |only ceramic-0.9.0/ceramic/man/figures/README-tasmap-6.png |only ceramic-0.9.0/ceramic/man/figures/README-tasmap-7.png |only ceramic-0.9.0/ceramic/man/figures/README-tasmap-8.png |only ceramic-0.9.0/ceramic/man/figures/README-unnamed-chunk-1-1.png |binary 36 files changed, 184 insertions(+), 51 deletions(-)
Title: Expression Data Analysis and Visualization
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas(TCGA) are common bioinformatics public databases. We integrate the regular analysis and charts for expression data, to analyze and display the data concisely and intuitively.
Author: Xiaojie Sun [aut, cre]
Maintainer: Xiaojie Sun <18763899370@163.com>
Diff between tinyarray versions 2.3.1 dated 2023-08-18 and 2.3.2 dated 2024-01-22
DESCRIPTION | 6 ++-- MD5 | 13 ++++++---- NAMESPACE | 3 ++ NEWS.md | 11 ++++++++ R/2_geo_id.R | 57 +++++++++++++++++++++++++++++++++++++++++++++ R/8_tcga_group_trans_exp.R | 49 ++++++++++++++++++++++++++++++++++++++ man/get_count_txt.Rd |only man/get_gpl_txt.Rd |only man/trans_entrezexp.Rd |only 9 files changed, 131 insertions(+), 8 deletions(-)
Title: A Parametric Model for Estimating the Mean Number of Events
Description: Implementation of a parametric joint model for modelling recurrent
and competing event processes using generalised survival models. The joint
model can subsequently be used to predict the mean number of events in the
presence of competing risks at different time points. Comparisons of the mean
number of event functions, e.g. the differences in mean number of events
between two exposure groups, are also available.
Author: Joshua P. Entrop [aut, cre, cph]
,
Alessandro Gasparini [ctb],
Mark Clements [ctb]
Maintainer: Joshua P. Entrop <joshuaentrop@posteo.de>
Diff between JointFPM versions 1.1.0 dated 2023-11-27 and 1.2.0 dated 2024-01-22
DESCRIPTION | 13 - MD5 | 28 +- NAMESPACE | 2 NEWS.md | 4 R/JointFPM.R | 2 R/calc_N.R | 51 ++++- R/predict.JointFPM.R | 75 ++++++- README.md | 290 ++++++++++++++--------------- man/JointFPM-package.Rd | 1 man/predict.JointFPM.Rd | 11 + tests/testthat/_snaps/JointFPM.md | 200 ++++++++++---------- tests/testthat/_snaps/mean_no.md | 38 +-- tests/testthat/_snaps/predict.JointFPM.md | 149 ++++++++------ tests/testthat/_snaps/test_dfs_JointFPM.md | 34 +-- tests/testthat/test-predict.JointFPM.R | 75 +++++++ 15 files changed, 586 insertions(+), 387 deletions(-)
Title: Deal with Check Outputs
Description: Deal with packages 'check' outputs and reduce the risk of
rejection by 'CRAN' by following policies.
Author: Sebastien Rochette [aut, cre] ,
Vincent Guyader [aut] ,
Arthur Breant [aut] ,
Murielle Delmotte [aut] ,
ThinkR [cph]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Diff between checkhelper versions 0.1.0 dated 2023-06-21 and 0.1.1 dated 2024-01-22
DESCRIPTION | 11 +++- MD5 | 17 +++---- NEWS.md | 6 ++ README.md | 48 +++++++++++++-------- build/vignette.rds |binary inst/doc/check-with-real-cran-settings.R | 2 inst/doc/no-files-left-after-check.R | 2 man/checkhelper-package.Rd | 1 tests/testthat/helpers.R |only tests/testthat/test-find_missing_values.R | 68 +++++++++++++++++++----------- 10 files changed, 100 insertions(+), 55 deletions(-)
Title: Deal with Dependencies
Description: Manage dependencies during package development. This can
retrieve all dependencies that are used in ".R" files in the "R/"
directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2'
documentation of functions. There is a function to update the
"DESCRIPTION" file of your package with 'CRAN' packages or any other
remote package. All functions to retrieve dependencies of ".R"
scripts and ".Rmd" or ".qmd" files can be used independently of a
package development.
Author: Sebastien Rochette [cre, aut] ,
Vincent Guyader [aut] ,
Murielle Delmotte [aut] ,
Swann Floc'hlay [aut] ,
ThinkR [cph, fnd]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Diff between attachment versions 0.4.0 dated 2023-05-31 and 0.4.1 dated 2024-01-22
DESCRIPTION | 9 - MD5 | 35 +++--- NEWS.md | 6 + R/att_from_rmds.R | 2 R/create_renv.R | 4 build/vignette.rds |binary inst/doc/a-fill-pkg-description.R | 24 ++-- inst/doc/a-fill-pkg-description.html | 172 +++++++++++++++---------------- inst/doc/b-bookdown-and-scripts.R | 14 +- inst/doc/b-bookdown-and-scripts.html | 56 +++++----- inst/doc/create-dependencies-file.R | 2 inst/doc/create-dependencies-file.html | 78 +++++++------- inst/doc/use_renv.R | 8 - inst/doc/use_renv.html | 10 - man/att_from_rmds.Rd | 2 man/attachment-package.Rd | 4 man/create_renv_for_dev.Rd | 4 tests/testthat/helpers.R |only tests/testthat/test-att_from_namespace.R | 31 +++-- 19 files changed, 239 insertions(+), 222 deletions(-)
Title: Explore Temporal and Other Phylogenetic Signals
Description: Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.
Author: Guangchuang Yu [aut, cre, cph]
,
Xiao Luo [ctb],
Li Zhan [ctb],
Xuanan Zhu [ctb],
Jianfeng Lin [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between shinyTempSignal versions 0.0.5 dated 2023-12-12 and 0.0.6 dated 2024-01-22
shinyTempSignal-0.0.5/shinyTempSignal/data |only shinyTempSignal-0.0.6/shinyTempSignal/DESCRIPTION | 27 +- shinyTempSignal-0.0.6/shinyTempSignal/MD5 | 18 + shinyTempSignal-0.0.6/shinyTempSignal/NEWS.md | 6 shinyTempSignal-0.0.6/shinyTempSignal/R/app_server.R | 178 ++++++++++++------- shinyTempSignal-0.0.6/shinyTempSignal/R/app_ui.R | 11 - shinyTempSignal-0.0.6/shinyTempSignal/build |only shinyTempSignal-0.0.6/shinyTempSignal/inst/doc |only shinyTempSignal-0.0.6/shinyTempSignal/vignettes |only 9 files changed, 148 insertions(+), 92 deletions(-)
More information about shinyTempSignal at CRAN
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