Title: Handle Data with Messy Header Rows and Broken Values
Description: Verb-like functions to work with messy data, often derived from
spreadsheets or parsed PDF tables. Includes functions for unwrapping
values broken up across rows, relocating embedded grouping values,
and to annotate meaningful formatting in spreadsheet files.
Author: Luis D. Verde Arregoitia [aut, cre]
(<https://orcid.org/0000-0001-9520-6543>)
Maintainer: Luis D. Verde Arregoitia <luis@liomys.mx>
Diff between unheadr versions 0.3.1 dated 2021-02-06 and 0.3.2 dated 2021-04-09
DESCRIPTION | 6 MD5 | 14 NEWS.md | 5 R/mash_colnames.R | 2 R/unbreak_fn.R | 2 build/partial.rdb |binary inst/doc/unheadr-vignette.html | 684 +++++++++++++++++++++++++---------------- man/unbreak_vals.Rd | 2 8 files changed, 451 insertions(+), 264 deletions(-)
Title: Robust Backfitting
Description: A robust backfitting algorithm for additive models based on (robust) local polynomial
kernel smoothers. It includes both bounded and re-descending (kernel) M-estimators, and
it computes predictions for points outside the training set if desired. See
Boente, Martinez and Salibian-Barrera (2017) <doi:10.1080/10485252.2017.1369077> and
Martinez and Salibian-Barrera (2021) <doi:10.21105/joss.02992> for details.
Author: Matias Salibian-Barrera [aut, cre],
Alejandra Martinez [aut]
Maintainer: Matias Salibian-Barrera <matias@stat.ubc.ca>
Diff between RBF versions 2.0.1 dated 2020-07-30 and 2.1.0 dated 2021-04-09
DESCRIPTION | 16 +++++---- MD5 | 39 ++++++++++++++++++++--- NAMESPACE | 3 + NEWS.md |only R/RBF-fn.R | 83 ++++++++++++++++++++++++++++++++++++++------------- build |only inst |only man/backf.cl.Rd | 13 ++++++- man/backf.rob.Rd | 18 +++++++++-- man/figures |only man/summary.backf.Rd | 5 +-- vignettes |only 12 files changed, 137 insertions(+), 40 deletions(-)
Title: Estimation of Hawkes Processes from Binned Observations
Description: Implements an estimation method for Hawkes processes when count data are only observed in discrete time, using a spectral approach derived from the Bartlett spectrum, see Cheysson and Lang (2020) <arXiv:2003.04314>. Some general use functions for Hawkes processes are also included: simulation of (in)homogeneous Hawkes process, maximum likelihood estimation, residual analysis, etc.
Author: Felix Cheysson [aut, cre] (<https://orcid.org/0000-0002-9095-2878>)
Maintainer: Felix Cheysson <felix@cheysson.fr>
Diff between hawkesbow versions 1.0.1 dated 2021-04-07 and 1.0.2 dated 2021-04-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/hawkesbow.pdf |binary src/utils.cpp | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Climate Indices
Description: Computes 138 standard climate indices at monthly, seasonal and annual resolution. These indices were selected, based on their direct and significant impacts on target sectors, after a thorough review of the literature in the field of extreme weather events and natural hazards. Overall, the selected indices characterize different aspects of the frequency, intensity and duration of extreme events, and are derived from a broad set of climatic variables, including surface air temperature, precipitation, relative humidity, wind speed, cloudiness, solar radiation, and snow cover. The 138 indices have been classified as follow: Temperature based indices (42), Precipitation based indices (22), Bioclimatic indices (21), Wind-based indices (5), Aridity/ continentality indices (10), Snow-based indices (13), Cloud/radiation based indices (6), Drought indices (8), Fire indices (5), Tourism indices (5).
Author: Fergus Reig-Gracia [aut, cre], Sergio M. Vicente-Serrano [aut], Fernando Dominguez-Castro [aut], Joaquin Bedia-Jiménez [ctb]
Maintainer: Fergus Reig-Gracia <fergusrg@gmail.com>
Diff between ClimInd versions 0.1-2 dated 2019-07-18 and 0.1-3 dated 2021-04-09
ClimInd-0.1-2/ClimInd/man/calcf_data_max_min_mean.Rd |only ClimInd-0.1-2/ClimInd/man/cd.Rd |only ClimInd-0.1-2/ClimInd/man/cn.Rd |only ClimInd-0.1-2/ClimInd/man/ffdi.Rd |only ClimInd-0.1-2/ClimInd/man/fffi.Rd |only ClimInd-0.1-2/ClimInd/man/fwi.Rd |only ClimInd-0.1-2/ClimInd/man/hciu.Rd |only ClimInd-0.1-2/ClimInd/man/kbdi.Rd |only ClimInd-0.1-2/ClimInd/man/ldp.Rd |only ClimInd-0.1-2/ClimInd/man/lwp.Rd |only ClimInd-0.1-2/ClimInd/man/mni.Rd |only ClimInd-0.1-2/ClimInd/man/ntn.Rd |only ClimInd-0.1-2/ClimInd/man/ntx.Rd |only ClimInd-0.1-2/ClimInd/man/rtwd.Rd |only ClimInd-0.1-2/ClimInd/man/rx.Rd |only ClimInd-0.1-2/ClimInd/man/sdd.Rd |only ClimInd-0.1-2/ClimInd/man/sud.Rd |only ClimInd-0.1-2/ClimInd/man/tci.Rd |only ClimInd-0.1-2/ClimInd/man/tci60.Rd |only ClimInd-0.1-2/ClimInd/man/tci80.Rd |only ClimInd-0.1-2/ClimInd/man/tn.Rd |only ClimInd-0.1-2/ClimInd/man/wd.Rd |only ClimInd-0.1-2/ClimInd/man/wn.Rd |only ClimInd-0.1-2/ClimInd/man/wsd.Rd |only ClimInd-0.1-2/ClimInd/man/xtn.Rd |only ClimInd-0.1-2/ClimInd/man/xtx.Rd |only ClimInd-0.1-3/ClimInd/DESCRIPTION | 10 ClimInd-0.1-3/ClimInd/MD5 | 307 +-- ClimInd-0.1-3/ClimInd/NAMESPACE | 40 ClimInd-0.1-3/ClimInd/NEWS.md | 6 ClimInd-0.1-3/ClimInd/R/indecis.R | 116 - ClimInd-0.1-3/ClimInd/R/indecis_indices.R | 1724 +++++++------------ ClimInd-0.1-3/ClimInd/R/indecis_indices_functions.R | 78 ClimInd-0.1-3/ClimInd/R/penman_fao_dia.R | 497 ++--- ClimInd-0.1-3/ClimInd/build |only ClimInd-0.1-3/ClimInd/man/Datasets.Rd | 4 ClimInd-0.1-3/ClimInd/man/aci.Rd | 6 ClimInd-0.1-3/ClimInd/man/asd.Rd | 6 ClimInd-0.1-3/ClimInd/man/at.Rd | 11 ClimInd-0.1-3/ClimInd/man/average_temp.Rd | 3 ClimInd-0.1-3/ClimInd/man/bi.Rd | 8 ClimInd-0.1-3/ClimInd/man/bio10.Rd | 8 ClimInd-0.1-3/ClimInd/man/bio11.Rd | 8 ClimInd-0.1-3/ClimInd/man/bio13.Rd | 8 ClimInd-0.1-3/ClimInd/man/bio14.Rd | 8 ClimInd-0.1-3/ClimInd/man/bio15.Rd | 10 ClimInd-0.1-3/ClimInd/man/bio16.Rd | 8 ClimInd-0.1-3/ClimInd/man/bio17.Rd | 8 ClimInd-0.1-3/ClimInd/man/bio18.Rd | 10 ClimInd-0.1-3/ClimInd/man/bio19.Rd | 10 ClimInd-0.1-3/ClimInd/man/bio20.Rd | 6 ClimInd-0.1-3/ClimInd/man/bio4.Rd | 10 ClimInd-0.1-3/ClimInd/man/bio5.Rd | 10 ClimInd-0.1-3/ClimInd/man/bio6.Rd | 10 ClimInd-0.1-3/ClimInd/man/bio7.Rd | 12 ClimInd-0.1-3/ClimInd/man/bio8.Rd | 10 ClimInd-0.1-3/ClimInd/man/bio9.Rd | 10 ClimInd-0.1-3/ClimInd/man/calc_eto.Rd | 17 ClimInd-0.1-3/ClimInd/man/calc_spi.Rd | 2 ClimInd-0.1-3/ClimInd/man/calcf_data.Rd | 12 ClimInd-0.1-3/ClimInd/man/calcf_data_.Rd | 4 ClimInd-0.1-3/ClimInd/man/calculate_all.Rd | 18 ClimInd-0.1-3/ClimInd/man/calculate_all_scales.Rd | 4 ClimInd-0.1-3/ClimInd/man/cc.Rd | 4 ClimInd-0.1-3/ClimInd/man/cdd.Rd | 13 ClimInd-0.1-3/ClimInd/man/cfd.Rd | 4 ClimInd-0.1-3/ClimInd/man/cmd.Rd | 21 ClimInd-0.1-3/ClimInd/man/csd.Rd | 4 ClimInd-0.1-3/ClimInd/man/csdi.Rd |only ClimInd-0.1-3/ClimInd/man/cwd.Rd |only ClimInd-0.1-3/ClimInd/man/d32.Rd | 10 ClimInd-0.1-3/ClimInd/man/d50mm.Rd | 4 ClimInd-0.1-3/ClimInd/man/d95p.Rd | 6 ClimInd-0.1-3/ClimInd/man/dd.Rd | 4 ClimInd-0.1-3/ClimInd/man/dd17.Rd | 4 ClimInd-0.1-3/ClimInd/man/dfx21.Rd | 6 ClimInd-0.1-3/ClimInd/man/dr1mm.Rd | 4 ClimInd-0.1-3/ClimInd/man/dr3mm.Rd | 4 ClimInd-0.1-3/ClimInd/man/dtr.Rd | 6 ClimInd-0.1-3/ClimInd/man/eai.Rd | 8 ClimInd-0.1-3/ClimInd/man/ep.Rd | 8 ClimInd-0.1-3/ClimInd/man/eto.Rd | 40 ClimInd-0.1-3/ClimInd/man/etr.Rd | 6 ClimInd-0.1-3/ClimInd/man/fd.Rd | 4 ClimInd-0.1-3/ClimInd/man/fg.Rd | 4 ClimInd-0.1-3/ClimInd/man/fg6bft.Rd | 4 ClimInd-0.1-3/ClimInd/man/fgcalm.Rd | 4 ClimInd-0.1-3/ClimInd/man/fod.Rd | 6 ClimInd-0.1-3/ClimInd/man/fpsc.Rd | 7 ClimInd-0.1-3/ClimInd/man/fsc.Rd | 6 ClimInd-0.1-3/ClimInd/man/fsd.Rd | 6 ClimInd-0.1-3/ClimInd/man/fwi1D.Rd | 13 ClimInd-0.1-3/ClimInd/man/fxx.Rd | 6 ClimInd-0.1-3/ClimInd/man/gd4.Rd | 4 ClimInd-0.1-3/ClimInd/man/gsl.Rd | 8 ClimInd-0.1-3/ClimInd/man/gsr.Rd | 6 ClimInd-0.1-3/ClimInd/man/gtg.Rd | 4 ClimInd-0.1-3/ClimInd/man/gtn.Rd | 4 ClimInd-0.1-3/ClimInd/man/gtx.Rd | 4 ClimInd-0.1-3/ClimInd/man/hd17.Rd | 6 ClimInd-0.1-3/ClimInd/man/hi.Rd | 8 ClimInd-0.1-3/ClimInd/man/hsd.Rd | 6 ClimInd-0.1-3/ClimInd/man/id.Rd | 4 ClimInd-0.1-3/ClimInd/man/jci.Rd | 6 ClimInd-0.1-3/ClimInd/man/koi.Rd | 8 ClimInd-0.1-3/ClimInd/man/lpsc.Rd | 6 ClimInd-0.1-3/ClimInd/man/mai.Rd | 8 ClimInd-0.1-3/ClimInd/man/maximum_temp.Rd | 3 ClimInd-0.1-3/ClimInd/man/mfi.Rd | 6 ClimInd-0.1-3/ClimInd/man/mi.Rd | 6 ClimInd-0.1-3/ClimInd/man/minimum_temp.Rd | 3 ClimInd-0.1-3/ClimInd/man/moi.Rd | 16 ClimInd-0.1-3/ClimInd/man/months_quarter.Rd | 3 ClimInd-0.1-3/ClimInd/man/ms.Rd | 6 ClimInd-0.1-3/ClimInd/man/msd.Rd | 8 ClimInd-0.1-3/ClimInd/man/ngsr.Rd | 6 ClimInd-0.1-3/ClimInd/man/no_null.Rd |only ClimInd-0.1-3/ClimInd/man/ntg.Rd | 2 ClimInd-0.1-3/ClimInd/man/ogs10.Rd | 4 ClimInd-0.1-3/ClimInd/man/ogs6.Rd | 4 ClimInd-0.1-3/ClimInd/man/pci.Rd | 6 ClimInd-0.1-3/ClimInd/man/penman_fao_diario.Rd | 26 ClimInd-0.1-3/ClimInd/man/pici.Rd | 8 ClimInd-0.1-3/ClimInd/man/prcptot.Rd |only ClimInd-0.1-3/ClimInd/man/ptg.Rd | 6 ClimInd-0.1-3/ClimInd/man/r10mm.Rd | 4 ClimInd-0.1-3/ClimInd/man/r20mm.Rd | 4 ClimInd-0.1-3/ClimInd/man/r95tot.Rd | 8 ClimInd-0.1-3/ClimInd/man/r99tot.Rd | 6 ClimInd-0.1-3/ClimInd/man/rti.Rd | 4 ClimInd-0.1-3/ClimInd/man/rx1day.Rd |only ClimInd-0.1-3/ClimInd/man/rx5d.Rd | 4 ClimInd-0.1-3/ClimInd/man/scd.Rd | 4 ClimInd-0.1-3/ClimInd/man/sd0_10.Rd | 6 ClimInd-0.1-3/ClimInd/man/sd10_20.Rd | 6 ClimInd-0.1-3/ClimInd/man/sdii.Rd | 4 ClimInd-0.1-3/ClimInd/man/snd.Rd | 4 ClimInd-0.1-3/ClimInd/man/spei1.Rd | 12 ClimInd-0.1-3/ClimInd/man/spei12.Rd | 12 ClimInd-0.1-3/ClimInd/man/spei3.Rd | 12 ClimInd-0.1-3/ClimInd/man/spei6.Rd | 12 ClimInd-0.1-3/ClimInd/man/spi1.Rd | 6 ClimInd-0.1-3/ClimInd/man/spi12.Rd | 6 ClimInd-0.1-3/ClimInd/man/spi3.Rd | 6 ClimInd-0.1-3/ClimInd/man/spi6.Rd | 6 ClimInd-0.1-3/ClimInd/man/ss.Rd | 4 ClimInd-0.1-3/ClimInd/man/ssd.Rd | 4 ClimInd-0.1-3/ClimInd/man/ssp.Rd | 4 ClimInd-0.1-3/ClimInd/man/stn10.Rd | 6 ClimInd-0.1-3/ClimInd/man/stn15.Rd | 6 ClimInd-0.1-3/ClimInd/man/stx32.Rd | 6 ClimInd-0.1-3/ClimInd/man/su.Rd |only ClimInd-0.1-3/ClimInd/man/ta_o.Rd | 6 ClimInd-0.1-3/ClimInd/man/td_to_rh.Rd | 2 ClimInd-0.1-3/ClimInd/man/tm_s.Rd | 6 ClimInd-0.1-3/ClimInd/man/tn10p.Rd |only ClimInd-0.1-3/ClimInd/man/tn90p.Rd |only ClimInd-0.1-3/ClimInd/man/tnn.Rd |only ClimInd-0.1-3/ClimInd/man/tnx.Rd |only ClimInd-0.1-3/ClimInd/man/tr.Rd |only ClimInd-0.1-3/ClimInd/man/tx10p.Rd |only ClimInd-0.1-3/ClimInd/man/tx90p.Rd |only ClimInd-0.1-3/ClimInd/man/txn.Rd |only ClimInd-0.1-3/ClimInd/man/txx.Rd |only ClimInd-0.1-3/ClimInd/man/uai.Rd | 10 ClimInd-0.1-3/ClimInd/man/utci.Rd | 32 ClimInd-0.1-3/ClimInd/man/vcd.Rd | 6 ClimInd-0.1-3/ClimInd/man/vdtr.Rd | 6 ClimInd-0.1-3/ClimInd/man/vwd.Rd | 6 ClimInd-0.1-3/ClimInd/man/wci.Rd | 6 ClimInd-0.1-3/ClimInd/man/wki.Rd | 6 ClimInd-0.1-3/ClimInd/man/ws.Rd | 6 ClimInd-0.1-3/ClimInd/man/wsdi.Rd |only ClimInd-0.1-3/ClimInd/man/xtg.Rd | 2 ClimInd-0.1-3/ClimInd/man/zcd.Rd | 6 ClimInd-0.1-3/ClimInd/tests/testthat/test-indices.R | 4 176 files changed, 1685 insertions(+), 2005 deletions(-)
Title: Metadata Processing for the German Modification of the ICD-10
Coding System
Description: Provides convenient access to the German modification of the International Classification of Diagnoses, 10th revision (ICD-10-GM). It provides functionality to aid in the identification, specification and historisation of ICD-10 codes. Its intended use is the analysis of routinely collected data in the context of epidemiology, medical research and health services research. The underlying metadata are released by the German Institute for Medical Documentation and Information <https://www.dimdi.de>, and are redistributed in accordance with their license.
Author: Ewan Donnachie [aut, cre] (<https://orcid.org/0000-0002-0668-0049>)
Maintainer: Ewan Donnachie <ewan@donnachie.net>
Diff between ICD10gm versions 1.1 dated 2020-04-14 and 1.2.2 dated 2021-04-09
DESCRIPTION | 15 +++--- MD5 | 42 +++++++++++------- NEWS.md | 10 ++++ R/data.R | 44 +++++++++++++++++++ README.md | 4 - build/partial.rdb |only build/vignette.rds |binary data/charlson_rcs.rda |only data/charlson_sundararajan.rda |only data/icd_meta_blocks.rda |binary data/icd_meta_chapters.rda |binary data/icd_meta_codes.rda |binary data/icd_meta_transition.rda |binary inst/doc/coding_covid-19.R |only inst/doc/coding_covid-19.Rmd |only inst/doc/coding_covid-19.html |only inst/doc/icd10gm_intro.Rmd | 6 +- inst/doc/icd10gm_intro.html | 94 +++++++++++++++++++++++++++++++++++------ inst/extdata |only man/charlson_rcs.Rd |only man/charlson_sundararajan.Rd |only man/icd_meta_blocks.Rd | 4 + man/icd_meta_chapters.Rd | 4 + man/icd_meta_codes.Rd | 6 +- man/icd_meta_transition.Rd | 4 + vignettes/coding_covid-19.Rmd |only vignettes/icd10gm_intro.Rmd | 6 +- 27 files changed, 191 insertions(+), 48 deletions(-)
Title: Differential Gene Expression (DGE) Analysis Results Data Object
Description: Provides a flexible container to manage and annotate Differential Gene
Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>).
The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows
by m-samples dimensions) and metadata (not keyed to row, col, or assays).
A set of accessory functions to deposit, query and retrieve subsets of a data
workflow has been provided. Attributes are used to capture metadata such as
species and gene model, including reproducibility information such that a 3rd
party can access a DGEobj history to see how each data object was created or
modified. Since the DGEobj is customizable and extensible it is not limited
to RNA-seq analysis types of workflows -- it can accommodate nearly any data
analysis workflow that starts from a matrix of assays (rows) by samples (columns).
Author: John Thompson [aut],
Connie Brett [aut, cre],
Isaac Neuhaus [aut],
Ryan Thompson [aut]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between DGEobj versions 1.0.1 dated 2020-12-07 and 1.0.3 dated 2021-04-09
DGEobj-1.0.1/DGEobj/inst/doc/DGEobj_Overview.R |only DGEobj-1.0.1/DGEobj/man/getAttribute.Rd |only DGEobj-1.0.1/DGEobj/man/rmItems.Rd |only DGEobj-1.0.1/DGEobj/man/setAttribute.Rd |only DGEobj-1.0.3/DGEobj/DESCRIPTION | 9 DGEobj-1.0.3/DGEobj/MD5 | 113 DGEobj-1.0.3/DGEobj/NAMESPACE | 4 DGEobj-1.0.3/DGEobj/NEWS.md | 6 DGEobj-1.0.3/DGEobj/R/DGEobj.R | 6 DGEobj-1.0.3/DGEobj/R/addItem.R | 33 DGEobj-1.0.3/DGEobj/R/annotate.R | 40 DGEobj-1.0.3/DGEobj/R/attributes.R | 88 DGEobj-1.0.3/DGEobj/R/get.R | 14 DGEobj-1.0.3/DGEobj/R/init.R | 223 + DGEobj-1.0.3/DGEobj/R/internal.R | 55 DGEobj-1.0.3/DGEobj/R/reset.R | 5 DGEobj-1.0.3/DGEobj/R/rmItem.R | 41 DGEobj-1.0.3/DGEobj/R/subset.R | 2 DGEobj-1.0.3/DGEobj/R/types.R | 22 DGEobj-1.0.3/DGEobj/R/utils.R | 20 DGEobj-1.0.3/DGEobj/README.md | 8 DGEobj-1.0.3/DGEobj/build/vignette.rds |binary DGEobj-1.0.3/DGEobj/inst/doc/DGEobj_Overview.Rmd | 1039 +++++++- DGEobj-1.0.3/DGEobj/inst/doc/DGEobj_Overview.html | 2200 ++++++++++++----- DGEobj-1.0.3/DGEobj/inst/exampleObj.RDS |binary DGEobj-1.0.3/DGEobj/man/DGEobj-package.Rd | 6 DGEobj-1.0.3/DGEobj/man/addItem.Rd | 2 DGEobj-1.0.3/DGEobj/man/addItems.Rd | 29 DGEobj-1.0.3/DGEobj/man/annotateDGEobj.Rd | 31 DGEobj-1.0.3/DGEobj/man/as.list.DGEobj.Rd | 4 DGEobj-1.0.3/DGEobj/man/baseType.Rd | 2 DGEobj-1.0.3/DGEobj/man/baseTypes.Rd | 2 DGEobj-1.0.3/DGEobj/man/dim.DGEobj.Rd | 2 DGEobj-1.0.3/DGEobj/man/getBaseType.Rd | 2 DGEobj-1.0.3/DGEobj/man/getItem.Rd | 2 DGEobj-1.0.3/DGEobj/man/getItems.Rd | 9 DGEobj-1.0.3/DGEobj/man/getType.Rd | 3 DGEobj-1.0.3/DGEobj/man/initDGEobj.Rd | 50 DGEobj-1.0.3/DGEobj/man/initDGEobjDef.Rd |only DGEobj-1.0.3/DGEobj/man/inventory.Rd | 4 DGEobj-1.0.3/DGEobj/man/newType.Rd | 2 DGEobj-1.0.3/DGEobj/man/print.DGEobj.Rd | 4 DGEobj-1.0.3/DGEobj/man/resetDGEobj.Rd | 3 DGEobj-1.0.3/DGEobj/man/rmItem.Rd | 2 DGEobj-1.0.3/DGEobj/man/showAttributes.Rd | 4 DGEobj-1.0.3/DGEobj/man/showMeta.Rd | 8 DGEobj-1.0.3/DGEobj/man/showTypes.Rd | 6 DGEobj-1.0.3/DGEobj/man/subset.DGEobj.Rd | 2 DGEobj-1.0.3/DGEobj/tests/testthat/setup.R | 2 DGEobj-1.0.3/DGEobj/tests/testthat/test_annotate.R | 20 DGEobj-1.0.3/DGEobj/tests/testthat/test_attributes.R | 13 DGEobj-1.0.3/DGEobj/tests/testthat/test_get.R | 6 DGEobj-1.0.3/DGEobj/tests/testthat/test_init.R | 54 DGEobj-1.0.3/DGEobj/tests/testthat/test_reset.R | 4 DGEobj-1.0.3/DGEobj/tests/testthat/test_rmItem.R | 19 DGEobj-1.0.3/DGEobj/tests/testthat/test_subset.R | 8 DGEobj-1.0.3/DGEobj/tests/testthat/test_types.R | 13 DGEobj-1.0.3/DGEobj/tests/testthat/test_utils.R | 4 DGEobj-1.0.3/DGEobj/vignettes/DGEobj_Overview.Rmd | 1039 +++++++- DGEobj-1.0.3/DGEobj/vignettes/DGEobj_Overview.Rmd.orig |only DGEobj-1.0.3/DGEobj/vignettes/precompiled_vignettes.R |only 61 files changed, 3990 insertions(+), 1299 deletions(-)
Title: PRO-CTCAE Data Management, Analysis, and Graphical Tools
Description: A collection of tools to facilitate standardized analysis
and graphical procedures when using the National Cancer Institute’s
Patient-Reported Outcomes version of the Common Terminology Criteria for
Adverse Events (PRO-CTCAE).
Author: Blake Langlais [aut, cre], Amylou Dueck [aut]
Maintainer: Blake Langlais <langlais.blake@mayo.edu>
Diff between ProAE versions 0.1.1 dated 2021-02-24 and 0.1.2 dated 2021-04-09
DESCRIPTION | 9 +- MD5 | 20 +++-- R/ProAE.R | 18 ++++ R/toxFigures.R | 66 ++++++++++-------- R/toxTables.R | 173 +++++++++++++++++++++++++++++++++++++++++++----- data/tox_acute.rda |binary data/tox_chronic.rda |binary data/tox_cumulative.rda |binary data/tox_cyclic.rda |only data/tox_late.rda |binary man/toxTables.Rd | 11 +++ man/tox_cyclic.Rd |only 12 files changed, 242 insertions(+), 55 deletions(-)
Title: Quality Control Metrics for Gene Signatures
Description: Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
Author: Andrew Dhawan [aut],
Alessandro Barberis [aut],
Wei-Chen Cheng [aut],
Francesca Buffa [aut, cre]
Maintainer: Francesca Buffa <francesca.buffa@oncology.ox.ac.uk>
Diff between sigQC versions 0.1.21 dated 2018-07-24 and 0.1.22 dated 2021-04-09
DESCRIPTION | 9 +--- MD5 | 17 ++++--- README.md | 6 ++ build/vignette.rds |binary inst/CITATION |only inst/doc/vignette.R | 6 +- inst/doc/vignette.Rmd | 11 ++++ inst/doc/vignette.html | 110 +++++++++++++++++++++++++++++++++++-------------- man/make_all_plots.Rd | 17 +++++-- vignettes/vignette.Rmd | 11 ++++ 10 files changed, 132 insertions(+), 55 deletions(-)
Title: Automatic Calculation of Effects for Piecewise Structural
Equation Models
Description: Provides functionality to automatically calculate direct, indirect,
and total effects for piecewise structural equation models, comprising lists
of fitted models representing structured equations (Lefcheck 2016
<doi:10/f8s8rb>). Confidence intervals are provided via bootstrapping.
Author: Mark Murphy [aut, cre]
Maintainer: Mark Murphy <murphymv@gmail.com>
Diff between semEff versions 0.4.0 dated 2020-10-01 and 0.5.0 dated 2021-04-09
semEff-0.4.0/semEff/man/stdCoeff.Rd |only semEff-0.5.0/semEff/DESCRIPTION | 7 semEff-0.5.0/semEff/MD5 | 72 +-- semEff-0.5.0/semEff/NAMESPACE | 2 semEff-0.5.0/semEff/NEWS.md | 131 ++---- semEff-0.5.0/semEff/R/bootEff-fun.R | 252 +++++++------ semEff-0.5.0/semEff/R/data.R | 11 semEff-0.5.0/semEff/R/helper-fun.R | 47 +- semEff-0.5.0/semEff/R/semEff-fun.R | 216 +++++------ semEff-0.5.0/semEff/R/stdEff-fun.R | 529 ++++++++++++++-------------- semEff-0.5.0/semEff/README.md | 67 +-- semEff-0.5.0/semEff/inst/WORDLIST | 55 +- semEff-0.5.0/semEff/man/Object.Type.Rd | 2 semEff-0.5.0/semEff/man/Param.Type.Rd | 4 semEff-0.5.0/semEff/man/R2.Rd | 251 +++++++------ semEff-0.5.0/semEff/man/RVIF.Rd |only semEff-0.5.0/semEff/man/Shipley.Growth.Rd | 12 semEff-0.5.0/semEff/man/Shipley.Rd | 4 semEff-0.5.0/semEff/man/Shipley.SEM.Boot.Rd | 13 semEff-0.5.0/semEff/man/Shipley.SEM.Eff.Rd | 10 semEff-0.5.0/semEff/man/Shipley.SEM.Rd | 8 semEff-0.5.0/semEff/man/VIF.Rd | 41 +- semEff-0.5.0/semEff/man/avgEst.Rd | 87 ++-- semEff-0.5.0/semEff/man/bootCI.Rd | 83 ++-- semEff-0.5.0/semEff/man/bootEff.Rd | 203 +++++----- semEff-0.5.0/semEff/man/getData.Rd | 29 - semEff-0.5.0/semEff/man/getEff.Rd | 6 semEff-0.5.0/semEff/man/getY.Rd | 27 - semEff-0.5.0/semEff/man/glt.Rd | 197 +++++----- semEff-0.5.0/semEff/man/pSapply.Rd | 28 - semEff-0.5.0/semEff/man/predEff.Rd | 394 ++++++++++---------- semEff-0.5.0/semEff/man/print.semEff.Rd | 34 - semEff-0.5.0/semEff/man/rMapply.Rd | 31 - semEff-0.5.0/semEff/man/sdW.Rd | 6 semEff-0.5.0/semEff/man/semEff.Rd | 162 ++++---- semEff-0.5.0/semEff/man/stdEff.Rd | 248 ++++++------- semEff-0.5.0/semEff/man/varW.Rd | 16 semEff-0.5.0/semEff/man/xNam.Rd | 10 38 files changed, 1660 insertions(+), 1635 deletions(-)
Title: Color Palettes Based on Fish Species
Description: Implementation of color palettes based on fish species.
Author: Nina M. D. Schiettekatte [cre, aut],
Simon J. Brandl [aut],
Jordan M. Casey [aut]
Maintainer: Nina M. D. Schiettekatte <nina.schiettekatte@gmail.com>
Diff between fishualize versions 0.2.1 dated 2021-03-12 and 0.2.2 dated 2021-04-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/fish_shapes.R | 4 ++++ inst/doc/contribute.html | 4 ++-- inst/doc/overview_colors.html | 4 ++-- 6 files changed, 24 insertions(+), 12 deletions(-)
Title: Visualisation Toolbox for 'easystats' and Extra Geoms, Themes
and Color Palettes for 'ggplot2'
Description: Provides plotting utilities supporting
easystats-packages (<https://github.com/easystats/easystats>) and some
extra themes, geoms, and scales for 'ggplot2'. Color scales are based
on <https://www.materialui.co/colors>.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, inv] (<https://orcid.org/0000-0001-5375-9967>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Brenton M. Wiernik [ctb] (<https://orcid.org/0000-0001-9560-6336>),
Jeffrey R. Stevens [ctb] (<https://orcid.org/0000-0003-2375-1360>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between see versions 0.6.2 dated 2021-02-04 and 0.6.3 dated 2021-04-09
DESCRIPTION | 109 +++++++------ MD5 | 247 ++++++++++++++++++------------ NAMESPACE | 5 NEWS.md | 240 +++++++++++++++++++++++------ R/coord_radar.R | 17 +- R/data_plot.R | 32 ++- R/geom_point2.R | 55 +++++- R/geom_poolpoint.R | 36 ++-- R/geom_violindot.R | 49 +++-- R/geom_violinhalf.R | 87 +++++----- R/golden_ratio.R | 4 R/plot.bayesfactor_models.R | 131 +++++++-------- R/plot.bayesfactor_parameters.R | 24 +- R/plot.check_collinearity.R | 10 - R/plot.check_distribution.R | 2 R/plot.check_heteroscedasticity.R | 51 +++++- R/plot.check_homogeneity.R | 13 - R/plot.check_normality.R | 12 - R/plot.check_outliers.R | 87 +++++++--- R/plot.check_outliers_new.R |only R/plot.cluster_analysis.R | 23 +- R/plot.compare_parameters.R |only R/plot.compare_performance.R | 2 R/plot.describe_distribution.R | 4 R/plot.easycormatrix.R | 14 + R/plot.effectsize_table.R | 24 +- R/plot.equivalence_test.R | 64 ++++--- R/plot.estimate_contrasts.R | 22 +- R/plot.estimate_density.R | 92 ++++++++--- R/plot.hdi.R | 32 ++- R/plot.n_factors.R | 16 - R/plot.p_direction.R | 36 ++-- R/plot.p_significance.R | 35 ++-- R/plot.parameters_brms_meta.R | 88 +++++++--- R/plot.parameters_model.R | 34 ++-- R/plot.parameters_pca.R | 24 ++ R/plot.parameters_sem.R | 64 ++++--- R/plot.parameters_simulate.R | 26 ++- R/plot.performance_pp_check.R | 76 +++++++-- R/plot.performance_roc.R | 43 ++--- R/plot.point_estimates.R | 16 + R/plot.rope.R | 22 +- R/plot.si.R | 39 ++-- R/plots.R | 22 +- R/print.binned_residuals.R | 16 + R/print.check_model.R | 255 ++++++++++++++++++++----------- R/print.data_plot.R | 4 R/reshape_to_long.R | 9 - R/scale_color_bluebrown.R | 2 R/scale_color_flat.R | 10 - R/scale_color_material.R | 12 - R/scale_color_metro.R | 10 - R/scale_color_pizza.R | 2 R/scale_color_see.R | 8 R/scale_color_social.R | 10 - R/theme_abyss.R | 57 +++--- R/theme_blackboard.R | 6 R/theme_lucid.R | 90 +++++----- R/theme_modern.R | 140 ++++++++--------- R/theme_radar.R | 80 ++++----- R/utils.R | 12 - R/utils_add_prior_layer.R | 8 inst/CITATION | 4 inst/WORDLIST |only man/add_plot_attributes.Rd | 75 ++++----- man/coord_radar.Rd | 69 ++++---- man/data_plot.Rd | 2 man/flat_colors.Rd | 45 ++--- man/geom_point2.Rd | 123 ++++++++------ man/geom_poolpoint.Rd | 111 ++++++------- man/geom_violindot.Rd | 186 +++++++++++----------- man/geom_violinhalf.Rd | 167 ++++++++++---------- man/material_colors.Rd | 45 ++--- man/metro_colors.Rd | 45 ++--- man/plot.see_check_collinearity.Rd | 5 man/plot.see_check_heteroscedasticity.Rd | 59 +++---- man/plot.see_check_normality.Rd | 96 ++++++----- man/plot.see_check_outliers.Rd | 87 ++++++---- man/plot.see_cluster_analysis.Rd | 64 ++++--- man/plot.see_compare_parameters.Rd |only man/plot.see_equivalence_test.Rd | 122 +++++++------- man/plot.see_estimate_density.Rd | 137 ++++++++-------- man/plot.see_hdi.Rd | 106 ++++++------ man/plot.see_p_direction.Rd | 106 ++++++------ man/plot.see_p_significance.Rd | 106 ++++++------ man/plot.see_parameters_brms_meta.Rd | 173 ++++++++++----------- man/plot.see_parameters_model.Rd | 166 ++++++++++---------- man/plot.see_parameters_simulate.Rd | 131 ++++++++------- man/plot.see_performance_roc.Rd | 70 ++++---- man/plot.see_point_estimate.Rd | 132 ++++++++-------- man/plot.see_rope.Rd | 106 ++++++------ man/plot.see_si.Rd | 98 ++++++----- man/plots.Rd | 64 ++++--- man/scale_color_flat.Rd | 165 +++++++++----------- man/scale_color_material.Rd | 221 +++++++++++++------------- man/scale_color_metro.Rd | 211 ++++++++++++------------- man/scale_color_pizza.Rd | 203 ++++++++++++------------ man/scale_color_social.Rd | 221 +++++++++++++------------- man/social_colors.Rd | 45 ++--- man/theme_blackboard.Rd | 2 tests |only 101 files changed, 3656 insertions(+), 2872 deletions(-)
Title: Mass Spectrometry Tools
Description: Common mass spectrometry tools described in John Roboz (2013) <doi:10.1201/b15436>. It allows checking element
isotopes, calculating (isotope labelled) exact monoisitopic mass, m/z values and mass accuracy, and inspecting possible contaminant mass peaks,
examining possible adducts in electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI)
ion sources.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>
Diff between MSbox versions 1.3.8 dated 2021-02-10 and 1.3.9 dated 2021-04-09
MSbox-1.3.8/MSbox/R/getOPLSDA.R |only MSbox-1.3.8/MSbox/man/getOPLSDA.Rd |only MSbox-1.3.9/MSbox/DESCRIPTION | 11 +- MSbox-1.3.9/MSbox/MD5 | 16 +-- MSbox-1.3.9/MSbox/NAMESPACE | 2 MSbox-1.3.9/MSbox/R/doStat.R | 3 MSbox-1.3.9/MSbox/R/sysdata.rda |binary MSbox-1.3.9/MSbox/R/what.R | 63 ++++++--------- MSbox-1.3.9/MSbox/README.md | 150 ++++++++++++++++++++++++++++++------- MSbox-1.3.9/MSbox/man/what.Rd | 7 - 10 files changed, 165 insertions(+), 87 deletions(-)
Title: Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and
other environmental samples. Supported features include reading spectral
data files (.asp, .csv, .jdx, .spc, .spa, .0), Savitzky-Golay smoothing of
spectral intensities with smooth_intens(), correcting background noise with
subtr_bg() in accordance with Zhao et al. (2007)
<doi:10.1366/000370207782597003>, and identifying spectra using an onboard
reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>).
Analyzed spectra can be shared with the Open Specy community. A Shiny app is
available via run_app() or online at
<https://wincowger.shinyapps.io/OpenSpecy/>.
Author: Win Cowger [cre, aut] (<https://orcid.org/0000-0001-9226-3104>),
Zacharias Steinmetz [aut] (<https://orcid.org/0000-0001-6675-5033>),
Andrew Gray [ctb] (<https://orcid.org/0000-0003-2252-7367>),
Hannah Hapich [ctb] (<https://orcid.org/0000-0003-0000-6632>),
Jennifer Lynch [ctb, dtc] (<https://orcid.org/0000-0003-3572-8782>),
Hannah De Frond [ctb, dtc] (<https://orcid.org/0000-0003-1199-0727>),
Keenan Munno [ctb, dtc] (<https://orcid.org/0000-0003-2916-5944>),
Chelsea Rochman [ctb, dtc] (<https://orcid.org/0000-0002-7624-711X>),
Sebastian Primpke [ctb, dtc] (<https://orcid.org/0000-0001-7633-8524>),
Orestis Herodotou [ctb, dtc]
Maintainer: Win Cowger <wincowger@gmail.com>
Diff between OpenSpecy versions 0.8.2 dated 2021-03-31 and 0.9.0 dated 2021-04-09
OpenSpecy-0.8.2/OpenSpecy/inst/extdata/fitr_ps.1 |only OpenSpecy-0.8.2/OpenSpecy/inst/extdata/ftir_ps.2 |only OpenSpecy-0.8.2/OpenSpecy/inst/shiny/www/graphical_abstract.png |only OpenSpecy-0.9.0/OpenSpecy/DESCRIPTION | 10 OpenSpecy-0.9.0/OpenSpecy/MD5 | 54 OpenSpecy-0.9.0/OpenSpecy/NAMESPACE | 2 OpenSpecy-0.9.0/OpenSpecy/NEWS.md | 19 OpenSpecy-0.9.0/OpenSpecy/R/adj_intens.R | 6 OpenSpecy-0.9.0/OpenSpecy/R/manage_lib.R | 39 OpenSpecy-0.9.0/OpenSpecy/R/read_spec.R | 46 OpenSpecy-0.9.0/OpenSpecy/R/run_app.R | 33 OpenSpecy-0.9.0/OpenSpecy/R/share_spec.R | 86 + OpenSpecy-0.9.0/OpenSpecy/README.md | 16 OpenSpecy-0.9.0/OpenSpecy/build/partial.rdb |binary OpenSpecy-0.9.0/OpenSpecy/inst/doc/sop.html | 4 OpenSpecy-0.9.0/OpenSpecy/inst/shiny/config.yml | 11 OpenSpecy-0.9.0/OpenSpecy/inst/shiny/data/namekey.RData |binary OpenSpecy-0.9.0/OpenSpecy/inst/shiny/server.R | 271 +++- OpenSpecy-0.9.0/OpenSpecy/inst/shiny/ui.R | 575 ++++------ OpenSpecy-0.9.0/OpenSpecy/inst/shiny/www/js |only OpenSpecy-0.9.0/OpenSpecy/inst/shiny/www/jumbotron.png |only OpenSpecy-0.9.0/OpenSpecy/inst/shiny/www/logo.png |only OpenSpecy-0.9.0/OpenSpecy/man/adj_intens.Rd | 4 OpenSpecy-0.9.0/OpenSpecy/man/manage_lib.Rd | 10 OpenSpecy-0.9.0/OpenSpecy/man/read_spec.Rd | 59 - OpenSpecy-0.9.0/OpenSpecy/man/run_app.Rd | 10 OpenSpecy-0.9.0/OpenSpecy/man/share_spec.Rd | 36 OpenSpecy-0.9.0/OpenSpecy/tests/testthat/test-manage_lib.R | 19 OpenSpecy-0.9.0/OpenSpecy/tests/testthat/test-read_spec.R | 13 OpenSpecy-0.9.0/OpenSpecy/tests/testthat/test-share_spec.R | 16 30 files changed, 787 insertions(+), 552 deletions(-)
Title: Data Only Package to 'healthyR'
Description: Provides data for functions typically used in the 'healthyR' package.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.data versions 1.0.0 dated 2020-11-23 and 1.0.1 dated 2021-04-09
DESCRIPTION | 7 ++-- LICENSE | 4 +- MD5 | 12 +++---- NEWS.md | 6 +++ R/data_files.R | 64 ++++++++++++++++++++--------------------- README.md | 70 +++++++++++++++++++++++++++++++++++++++++---- man/healthyR_data.Rd | 78 +++++++++++++++++++++++++-------------------------- 7 files changed, 152 insertions(+), 89 deletions(-)
Title: Automatic Generation of Exams in R for 'Sakai'
Description: Automatic Generation of Exams in R for 'Sakai'.
Question templates in the form of the 'exams' package (see <http://www.r-exams.org/>)
are transformed into XML format required by 'Sakai'.
Author: Fuensanta Arnaldos García [aut],
María Victoria Caballero Pintado [aut],
Úrsula Faura Martínez [aut],
María Teresa Díaz Delfa [aut],
Jesús María Méndez Pérez [aut, cre],
Lourdes Molera Peris [aut],
José Antonio Palazón Ferrando [aut],
Juan José Pérez Castejón [aut],
Isabel Parra Frutos [aut],
Raúl Sánchez Sánchez [aut],
Nicolás Andrés Ubero Pascal [aut],
Nikolaus Umlauf [ctb],
Achim Zeileis [ctb] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Jesús María Méndez Pérez <jesus.mendez@ticarum.es>
Diff between exams2sakai versions 0.1 dated 2021-03-20 and 0.2 dated 2021-04-09
DESCRIPTION | 7 ++--- MD5 | 10 +++---- NEWS.md | 8 ++++++ R/exams2sakai.R | 70 +++++++++++++++++++++++++++++++---------------------- README.md | 3 +- man/exams2sakai.Rd | 7 ++--- 6 files changed, 62 insertions(+), 43 deletions(-)
Title: Representation of Archaeological Data
Description: A collection of classes that represent
archaeological data. This package provides a set of S4 classes that
represent different special types of matrix (absolute/relative
frequency, presence/absence data, co-occurrence matrix, etc.) upon
which package developers can build subclasses. It also provides a set
of generic methods (mutators and coercion mechanisms) and functions
(e.g. summary statistics, predicates). In addition, a few classes of
general interest (e.g. that represent stratigraphic relationships)
are implemented.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>),
Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>)
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between arkhe versions 0.2.2 dated 2020-03-23 and 0.3.0 dated 2021-04-09
arkhe-0.2.2/arkhe/R/chronology.R |only arkhe-0.2.2/arkhe/R/deprecate.R |only arkhe-0.2.2/arkhe/R/extract.R |only arkhe-0.2.2/arkhe/R/geography.R |only arkhe-0.2.2/arkhe/R/initialize.R |only arkhe-0.2.2/arkhe/inst/examples/ex-chronology.R |only arkhe-0.2.2/arkhe/inst/examples/ex-geography.R |only arkhe-0.2.2/arkhe/inst/examples/ex-logical-class.R |only arkhe-0.2.2/arkhe/inst/examples/ex-numeric-class.R |only arkhe-0.2.2/arkhe/man/LogicalMatrix-class.Rd |only arkhe-0.2.2/arkhe/man/Matrix-class.Rd |only arkhe-0.2.2/arkhe/man/NumericMatrix-class.Rd |only arkhe-0.2.2/arkhe/man/SimilarityMatrix-class.Rd |only arkhe-0.2.2/arkhe/man/chronology.Rd |only arkhe-0.2.2/arkhe/man/deprecated.Rd |only arkhe-0.2.2/arkhe/man/geography.Rd |only arkhe-0.2.2/arkhe/tests/testthat/test-chronology.R |only arkhe-0.2.2/arkhe/tests/testthat/test-geography.R |only arkhe-0.2.2/arkhe/tests/testthat/test-replacement.R |only arkhe-0.2.2/arkhe/tests/testthat/test-uuid.R |only arkhe-0.3.0/arkhe/DESCRIPTION | 60 +- arkhe-0.3.0/arkhe/MD5 | 148 ++--- arkhe-0.3.0/arkhe/NAMESPACE | 59 +- arkhe-0.3.0/arkhe/NEWS.md | 28 - arkhe-0.3.0/arkhe/R/AllClasses.R | 307 +++++------ arkhe-0.3.0/arkhe/R/AllGenerics.R | 360 ++++++------- arkhe-0.3.0/arkhe/R/arkhe-package.R | 60 +- arkhe-0.3.0/arkhe/R/check.R | 151 +++-- arkhe-0.3.0/arkhe/R/clean.R |only arkhe-0.3.0/arkhe/R/coerce.R | 506 ++++++++++--------- arkhe-0.3.0/arkhe/R/conditions.R | 49 + arkhe-0.3.0/arkhe/R/mutators.R |only arkhe-0.3.0/arkhe/R/predicates.R | 152 ++--- arkhe-0.3.0/arkhe/R/show.R | 86 --- arkhe-0.3.0/arkhe/R/subset.R |only arkhe-0.3.0/arkhe/R/utilities.R | 149 ++--- arkhe-0.3.0/arkhe/R/validate.R | 260 ++------- arkhe-0.3.0/arkhe/R/zzz.R |only arkhe-0.3.0/arkhe/README.md | 139 ++--- arkhe-0.3.0/arkhe/build/partial.rdb |only arkhe-0.3.0/arkhe/build/vignette.rds |binary arkhe-0.3.0/arkhe/inst/CITATION | 16 arkhe-0.3.0/arkhe/inst/doc/arkhe.R | 36 - arkhe-0.3.0/arkhe/inst/doc/arkhe.Rmd | 53 - arkhe-0.3.0/arkhe/inst/doc/arkhe.html | 419 ++++----------- arkhe-0.3.0/arkhe/inst/examples/ex-clean.R |only arkhe-0.3.0/arkhe/inst/examples/ex-coerce.R | 21 arkhe-0.3.0/arkhe/inst/examples/ex-matrix.R |only arkhe-0.3.0/arkhe/inst/examples/ex-operators.R |only arkhe-0.3.0/arkhe/inst/examples/ex-statistics.R |only arkhe-0.3.0/arkhe/inst/examples/ex-stratigraphy.R | 1 arkhe-0.3.0/arkhe/inst/examples/ex-summary.R |only arkhe-0.3.0/arkhe/man/AbundanceMatrix-class.Rd | 112 ---- arkhe-0.3.0/arkhe/man/CompositionMatrix-class.Rd |only arkhe-0.3.0/arkhe/man/CountMatrix-class.Rd | 113 ---- arkhe-0.3.0/arkhe/man/DataMatrix.Rd |only arkhe-0.3.0/arkhe/man/IncidenceMatrix-class.Rd | 98 --- arkhe-0.3.0/arkhe/man/OccurrenceMatrix-class.Rd | 113 +--- arkhe-0.3.0/arkhe/man/StratigraphicMatrix-class.Rd | 79 -- arkhe-0.3.0/arkhe/man/arkhe-package.Rd | 47 + arkhe-0.3.0/arkhe/man/check-attribute.Rd | 10 arkhe-0.3.0/arkhe/man/check-missing.Rd | 4 arkhe-0.3.0/arkhe/man/check-numeric.Rd | 5 arkhe-0.3.0/arkhe/man/check-type.Rd | 8 arkhe-0.3.0/arkhe/man/coerce.Rd | 116 ++-- arkhe-0.3.0/arkhe/man/conditions.Rd | 8 arkhe-0.3.0/arkhe/man/figures |only arkhe-0.3.0/arkhe/man/generate_uuid.Rd | 12 arkhe-0.3.0/arkhe/man/mutator.Rd | 117 ++-- arkhe-0.3.0/arkhe/man/predicate-graph.Rd | 9 arkhe-0.3.0/arkhe/man/predicate-matrix.Rd | 7 arkhe-0.3.0/arkhe/man/predicate-numeric.Rd | 47 - arkhe-0.3.0/arkhe/man/predicate-scalar.Rd | 1 arkhe-0.3.0/arkhe/man/predicate-trend.Rd | 29 - arkhe-0.3.0/arkhe/man/predicate-type.Rd | 1 arkhe-0.3.0/arkhe/man/predicate-utils.Rd | 16 arkhe-0.3.0/arkhe/man/remove.Rd |only arkhe-0.3.0/arkhe/man/replace.Rd |only arkhe-0.3.0/arkhe/man/subset.Rd | 81 +-- arkhe-0.3.0/arkhe/tests/testthat.R | 1 arkhe-0.3.0/arkhe/tests/testthat/test-check.R | 26 arkhe-0.3.0/arkhe/tests/testthat/test-class.R | 273 +--------- arkhe-0.3.0/arkhe/tests/testthat/test-clean.R |only arkhe-0.3.0/arkhe/tests/testthat/test-coerce.R | 207 +++---- arkhe-0.3.0/arkhe/tests/testthat/test-conditions.R | 8 arkhe-0.3.0/arkhe/tests/testthat/test-getters.R | 69 +- arkhe-0.3.0/arkhe/tests/testthat/test-predicates.R | 51 - arkhe-0.3.0/arkhe/tests/testthat/test-show.R | 36 - arkhe-0.3.0/arkhe/tests/testthat/test-stratigraphy.R | 17 arkhe-0.3.0/arkhe/tests/testthat/test-subset.R |only arkhe-0.3.0/arkhe/tests/testthat/test-utilities.R | 44 - arkhe-0.3.0/arkhe/vignettes/arkhe.Rmd | 53 - arkhe-0.3.0/arkhe/vignettes/uml-1.png |binary arkhe-0.3.0/arkhe/vignettes/uml.R |only 94 files changed, 2044 insertions(+), 2834 deletions(-)
Title: Sign-Simplicity-Regression-Solver
Description: Implementation of the SSR-Algorithm. The Sign-Simplicity-Regression model is a nonparametric statistical model which is based on residual signs and simplicity assumptions on the regression function. Goal is to calculate the most parsimonious regression function satisfying the statistical adequacy requirements. Theory and functions are specified in Metzner (2020, ISBN: 979-8-68239-420-3, "Trendbasierte Prognostik") and Metzner (2021, ISBN: 979-8-59347-027-0, "Adäquates Maschinelles Lernen").
Author: Lars Metzner [aut, cre]
Maintainer: Lars Metzner <lars.metzner@ppi.de>
Diff between sisireg versions 0.9.0 dated 2021-04-01 and 0.9.1 dated 2021-04-09
DESCRIPTION | 6 ++--- MD5 | 8 +++---- R/ssrMLP.R | 57 +++++++++++++++++++++++++++++++++++--------------- man/ssrmlp_predict.Rd | 5 ---- man/ssrmlp_train.Rd | 10 ++------ 5 files changed, 51 insertions(+), 35 deletions(-)
Title: Computationally Efficient Queue Simulation
Description: Implementation of a computationally efficient method for
simulating queues with arbitrary arrival and service times.
Please see Ebert, Wu, Mengersen & Ruggeri (2020, <doi:10.18637/jss.v095.i05>)
for further details.
Author: Anthony Ebert [aut, cre] (<https://orcid.org/0000-0003-3002-6300>),
Kerrie Mengersen [ths],
Paul Wu [ths],
Fabrizio Ruggeri [ths]
Maintainer: Anthony Ebert <anthonyebert+CRAN@gmail.com>
Diff between queuecomputer versions 1.0.0 dated 2020-10-06 and 1.1.0 dated 2021-04-09
DESCRIPTION | 11 MD5 | 16 - NEWS.md | 7 R/core_queuefunctions.R | 13 README.md | 1 build/vignette.rds |binary inst/doc/Howto.html | 344 ++++++------------------ inst/doc/MMk_queues.html | 514 ++++++++++++------------------------ tests/testthat/test_deterministic.R | 37 ++ 9 files changed, 328 insertions(+), 615 deletions(-)
Title: Spatial Seemingly Unrelated Regression Models
Description: A collection of functions to test and estimate Seemingly
Unrelated Regression (usually called SUR) models, with spatial structure, by maximum
likelihood and three-stage least squares. The package estimates the
most common spatial specifications, that is, SUR with Spatial Lag of
X regressors (called SUR-SLX), SUR with Spatial Lag Model (called SUR-SLM),
SUR with Spatial Error Model (called SUR-SEM), SUR with Spatial Durbin Model (called SUR-SDM),
SUR with Spatial Durbin Error Model (called SUR-SDEM),
SUR with Spatial Autoregressive terms and Spatial Autoregressive
Disturbances (called SUR-SARAR), SUR-SARAR with Spatial Lag of X
regressors (called SUR-GNM) and SUR with Spatially Independent Model (called SUR-SIM).
The methodology of these models can be found in next references
Mur, J., Lopez, F., and Herrera, M. (2010) <doi:10.1080/17421772.2010.516443>
Lopez, F.A., Mur, J., and Angulo, A. (2014) <doi:10.1007/s00168-014-0624-2>.
Author: Ana Angulo [aut],
Fernando A Lopez [aut],
Roman Minguez [aut, cre],
Jesus Mur [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between spsur versions 1.0.1.6 dated 2020-09-17 and 1.0.1.7 dated 2021-04-09
DESCRIPTION | 10 MD5 | 61 - R/datasets.R | 1 R/dgp_spSUR.R | 270 ++++-- R/fit_spsur_3sls.R | 197 ++-- R/impactspsur.R | 3 R/lmtestspsur.R | 7 R/spsur3sls.R | 54 - R/spsurml.R | 41 R/spsurtime.R | 58 + R/summary.spsur.R | 2 R/wald_betas.R | 8 R/wald_deltas.R | 2 build/vignette.rds |binary data/spc.RData |binary inst/CITATION |only inst/doc/Vignette_User_Guide.Rmd | 6 inst/doc/Vignette_User_Guide.html | 1500 ++---------------------------------- inst/doc/spsur-vs-spatialreg.Rmd | 2 inst/doc/spsur-vs-spatialreg.html | 1563 +++----------------------------------- man/dgp_spsur.Rd | 168 ++-- man/impactspsur.Rd | 3 man/lmtestspsur.Rd | 7 man/spc.Rd | 1 man/spsur3sls.Rd | 52 - man/spsurml.Rd | 40 man/spsurtime.Rd | 19 man/wald_betas.Rd | 8 man/wald_deltas.Rd | 2 vignettes/Vignette_User_Guide.Rmd | 6 vignettes/bibliosure.bib | 488 ++++++++--- vignettes/spsur-vs-spatialreg.Rmd | 2 32 files changed, 1267 insertions(+), 3314 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between performance versions 0.7.0 dated 2021-02-03 and 0.7.1 dated 2021-04-09
performance-0.7.0/performance/man/figures/unnamed-chunk-13-1.png |only performance-0.7.0/performance/man/figures/unnamed-chunk-19-1.png |only performance-0.7.0/performance/man/figures/unnamed-chunk-22-1.png |only performance-0.7.1/performance/DESCRIPTION | 109 +- performance-0.7.1/performance/MD5 | 179 ++-- performance-0.7.1/performance/NAMESPACE | 14 performance-0.7.1/performance/NEWS.md | 417 ++++++++-- performance-0.7.1/performance/R/binned_residuals.R | 50 - performance-0.7.1/performance/R/check_autocorrelation.R | 4 performance-0.7.1/performance/R/check_collinearity.R | 15 performance-0.7.1/performance/R/check_heteroscedasticity.R | 38 performance-0.7.1/performance/R/check_homogeneity.R | 19 performance-0.7.1/performance/R/check_model.R | 63 + performance-0.7.1/performance/R/check_model_diagnostics.R | 61 + performance-0.7.1/performance/R/check_normality.R | 21 performance-0.7.1/performance/R/check_outliers.R | 82 + performance-0.7.1/performance/R/check_overdispersion.R | 62 - performance-0.7.1/performance/R/check_zeroinflation.R | 4 performance-0.7.1/performance/R/compare_performance.R | 5 performance-0.7.1/performance/R/cronbachs_alpha.R | 10 performance-0.7.1/performance/R/get_gradients.R | 14 performance-0.7.1/performance/R/helpers.R | 15 performance-0.7.1/performance/R/icc.R | 120 +- performance-0.7.1/performance/R/model_performance.bayesian.R | 85 +- performance-0.7.1/performance/R/model_performance.ivreg.R | 16 performance-0.7.1/performance/R/model_performance.kmeans.R |only performance-0.7.1/performance/R/model_performance.lm.R | 148 ++- performance-0.7.1/performance/R/model_performance.mixed.R | 29 performance-0.7.1/performance/R/model_performance_default.R | 22 performance-0.7.1/performance/R/performance_accuracy.R | 31 performance-0.7.1/performance/R/performance_aicc.R | 9 performance-0.7.1/performance/R/performance_logloss.R | 4 performance-0.7.1/performance/R/performance_mse.R | 14 performance-0.7.1/performance/R/performance_roc.R | 26 performance-0.7.1/performance/R/performance_score.R | 6 performance-0.7.1/performance/R/pp_check.R | 21 performance-0.7.1/performance/R/print-methods.R | 39 performance-0.7.1/performance/R/print_md.R | 8 performance-0.7.1/performance/R/r2.R | 143 ++- performance-0.7.1/performance/R/r2_bayes.R | 35 performance-0.7.1/performance/R/r2_mckelvey.R | 6 performance-0.7.1/performance/R/r2_somers.R | 1 performance-0.7.1/performance/R/test_bf.R | 12 performance-0.7.1/performance/R/test_likelihoodratio.R | 33 performance-0.7.1/performance/R/test_performance.R | 6 performance-0.7.1/performance/R/test_vuong.R | 5 performance-0.7.1/performance/R/test_wald.R | 7 performance-0.7.1/performance/README.md | 216 +++-- performance-0.7.1/performance/build/partial.rdb |binary performance-0.7.1/performance/inst/CITATION | 28 performance-0.7.1/performance/inst/WORDLIST | 221 +++-- performance-0.7.1/performance/man/binned_residuals.Rd | 136 +-- performance-0.7.1/performance/man/check_collinearity.Rd | 220 ++--- performance-0.7.1/performance/man/check_heteroscedasticity.Rd | 76 + performance-0.7.1/performance/man/check_homogeneity.Rd | 14 performance-0.7.1/performance/man/check_model.Rd | 177 ++-- performance-0.7.1/performance/man/check_normality.Rd | 8 performance-0.7.1/performance/man/check_outliers.Rd | 58 - performance-0.7.1/performance/man/check_overdispersion.Rd | 150 +-- performance-0.7.1/performance/man/check_zeroinflation.Rd | 76 - performance-0.7.1/performance/man/compare_performance.Rd | 1 performance-0.7.1/performance/man/cronbachs_alpha.Rd | 73 - performance-0.7.1/performance/man/figures/figure_workflow.png |only performance-0.7.1/performance/man/figures/unnamed-chunk-15-1.png |only performance-0.7.1/performance/man/figures/unnamed-chunk-21-1.png |only performance-0.7.1/performance/man/icc.Rd | 112 +- performance-0.7.1/performance/man/model_performance.ivreg.Rd | 2 performance-0.7.1/performance/man/model_performance.kmeans.Rd |only performance-0.7.1/performance/man/model_performance.lm.Rd | 3 performance-0.7.1/performance/man/model_performance.merMod.Rd | 2 performance-0.7.1/performance/man/model_performance.stanreg.Rd | 7 performance-0.7.1/performance/man/performance_accuracy.Rd | 22 performance-0.7.1/performance/man/performance_aicc.Rd | 73 - performance-0.7.1/performance/man/performance_roc.Rd | 114 +- performance-0.7.1/performance/man/pp_check.Rd | 182 ++-- performance-0.7.1/performance/man/r2.Rd | 114 +- performance-0.7.1/performance/man/r2_bayes.Rd | 9 performance-0.7.1/performance/man/r2_somers.Rd | 55 - performance-0.7.1/performance/man/test_performance.Rd | 21 performance-0.7.1/performance/tests/testthat.R | 17 performance-0.7.1/performance/tests/testthat/test-backticks.R | 4 performance-0.7.1/performance/tests/testthat/test-coxph.R | 5 performance-0.7.1/performance/tests/testthat/test-icc.R | 4 performance-0.7.1/performance/tests/testthat/test-model_performance-various.R | 8 performance-0.7.1/performance/tests/testthat/test-model_performance.bayesian.R | 108 +- performance-0.7.1/performance/tests/testthat/test-model_performance.gam.R |only performance-0.7.1/performance/tests/testthat/test-model_performance.kmeans.R |only performance-0.7.1/performance/tests/testthat/test-model_performance.lm.R | 6 performance-0.7.1/performance/tests/testthat/test-performance_roc.R | 16 performance-0.7.1/performance/tests/testthat/test-r2_mcfadden.R | 3 performance-0.7.1/performance/tests/testthat/test-r2_nagelkerke.R | 2 performance-0.7.1/performance/tests/testthat/test-roc.R |only performance-0.7.1/performance/tests/testthat/test-test_likelihoodratio.R | 7 performance-0.7.1/performance/tests/testthat/test-test_performance.R | 1 performance-0.7.1/performance/tests/testthat/test-test_vuong.R | 5 performance-0.7.1/performance/tests/testthat/test-test_wald.R | 8 96 files changed, 2716 insertions(+), 1656 deletions(-)
Title: Detecting Changes in Autocorrelated and Fluctuating Signals
Description: Detect abrupt changes in time series with local fluctuations as a random walk process and autocorrelated noise as an AR(1) process. See Romano, G., Rigaill, G., Runge, V., Fearnhead, P. (2021) <doi:10.1080/01621459.2021.1909598>.
Author: Gaetano Romano [aut, cre],
Guillem Rigaill [aut],
Vincent Runge [aut],
Paul Fearnhead [aut]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between DeCAFS versions 3.1.5 dated 2020-05-18 and 3.2.3 dated 2021-04-09
DESCRIPTION | 14 ++++---- MD5 | 50 ++++++++++++++++------------- NAMESPACE | 3 + R/DeCAFS.R | 12 +++--- R/additional-estimators.R |only R/data.R | 2 - R/estimateParameters.R | 79 +++++++++++++++++++++++++++------------------- R/generateRWAR.R | 22 ++++++------ R/generateSinusoidal.R | 22 ++++++------ R/plot.R | 2 - R/scenarioGenerator.R |only build |only man/DeCAFS.Rd | 7 ++-- man/bestParameters.Rd |only man/cost.Rd |only man/dataRWAR.Rd | 21 ++++++------ man/dataSinusoidal.Rd | 27 ++++++++------- man/estimVar.Rd |only man/estimateParameters.Rd | 7 ++-- man/evalEtaNu.Rd |only man/oilWell.Rd | 2 - man/plot.DeCAFSout.Rd | 2 - man/scenarioGenerator.Rd |only src/algorithms.cpp | 46 +++++++++++++++++++++++--- src/algorithms.h | 12 +++++- src/fpop.cpp | 6 +++ src/fpopmain.cpp | 53 ++++++++++++++++++------------ src/fpopmain.h | 6 +++ src/quadratic.cpp | 6 +++ src/quadratic.h | 5 ++ 30 files changed, 257 insertions(+), 149 deletions(-)
More information about TensorClustering at CRAN
Permanent link
Title: Estimation and Plotting of IDF Curves
Description: Intensity-duration-frequency (IDF) curves are a widely used analysis-tool
in hydrology to assess extreme values of precipitation
[e.g. Mailhot et al., 2007, <doi:10.1016/j.jhydrol.2007.09.019>].
The package 'IDF' provides functions to estimate IDF parameters for given
precipitation time series on the basis of a duration-dependent
generalized extreme value distribution
[Koutsoyiannis et al., 1998, <doi:10.1016/S0022-1694(98)00097-3>].
Author: Jana Ulrich [aut, cre],
Laura Mack [ctb],
Oscar E. Jurado [ctb],
Felix S. Fauer [ctb],
Christoph Ritschel [aut],
Carola Detring [ctb],
Sarah Joedicke [ctb]
Maintainer: Jana Ulrich <jana.ulrich@met.fu-berlin.de>
Diff between IDF versions 2.0.0 dated 2021-01-15 and 2.1.0 dated 2021-04-09
DESCRIPTION | 10 - MD5 | 42 ++-- NEWS.md | 14 + R/IDF.R | 21 +- R/d-gev.R | 78 ++++++-- R/gevdfit.R | 307 ++++++++++++++++++++++++---------- README.md | 123 ++++++++++++- inst |only man/IDF-package.Rd | 5 man/dgev.d.Rd | 8 man/example.Rd | 4 man/figures/README-annualmax-1.png |binary man/figures/README-fit-1.png |binary man/figures/README-fit-2.png |binary man/figures/README-idf-1.png |binary man/figures/README-idf_features-1.png |only man/gev.d.fit.Rd | 28 ++- man/gev.d.init.Rd | 2 man/gev.d.lik.Rd | 15 + man/gev.d.params.Rd | 6 man/pgev.d.Rd | 6 man/qgev.d.Rd | 10 - man/rgev.d.Rd | 6 23 files changed, 519 insertions(+), 166 deletions(-)
Title: Composite Indicators Functions
Description: Contains functions to enhance approaches to the Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps.
Author: Francesco Vidoli, Elisa Fusco
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between Compind versions 2.1 dated 2019-03-12 and 2.2 dated 2021-04-09
Compind-2.1/Compind/R/bandwidth_CI_bad.R |only Compind-2.1/Compind/R/ci_bod_constr_mpi.R |only Compind-2.1/Compind/R/ci_rbod_constr_Q.R |only Compind-2.1/Compind/man/bandwidth_CI_bad.Rd |only Compind-2.1/Compind/man/ci_bod_constr_mpi.Rd |only Compind-2.1/Compind/man/ci_rbod_constr_Q.Rd |only Compind-2.2/Compind/DESCRIPTION | 8 - Compind-2.2/Compind/MD5 | 28 ++---- Compind-2.2/Compind/NEWS | 10 +- Compind-2.2/Compind/R/bandwidth_CI.R | 9 - Compind-2.2/Compind/R/ci_ampi.R | 102 +++++++--------------- Compind-2.2/Compind/build/vignette.rds |binary Compind-2.2/Compind/inst/doc/Compind_vignette.pdf |binary Compind-2.2/Compind/man/EU_2020.Rd | 4 Compind-2.2/Compind/man/bandwidth_CI.Rd | 12 +- Compind-2.2/Compind/man/ci_ampi.Rd | 10 +- Compind-2.2/Compind/man/ci_rbod_constr_bad.Rd | 6 - Compind-2.2/Compind/man/ci_rbod_constr_bad_Q.Rd | 2 18 files changed, 78 insertions(+), 113 deletions(-)
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface
Database (ISD, see <https://www.ncdc.noaa.gov/isd>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.9.3 dated 2021-03-29 and 0.9.4 dated 2021-04-09
worldmet-0.9.3/worldmet/R/sysdata.rda |only worldmet-0.9.3/worldmet/inst |only worldmet-0.9.4/worldmet/DESCRIPTION | 14 ++- worldmet-0.9.4/worldmet/MD5 | 20 ++--- worldmet-0.9.4/worldmet/NAMESPACE | 3 worldmet-0.9.4/worldmet/R/exportADMS.R | 50 ++++++++---- worldmet-0.9.4/worldmet/R/getMeta.R | 7 - worldmet-0.9.4/worldmet/R/metNOAA.R | 75 +++++++++--------- worldmet-0.9.4/worldmet/R/zzz.R | 2 worldmet-0.9.4/worldmet/README.md | 119 +++++++++++++++++++++--------- worldmet-0.9.4/worldmet/man/figures |only worldmet-0.9.4/worldmet/man/importNOAA.Rd | 14 ++- 12 files changed, 187 insertions(+), 117 deletions(-)
Title: Conditional Graphical LASSO for Gaussian Graphical Models with
Censored and Missing Values
Description: Conditional graphical lasso estimator is an extension of the graphical lasso proposed to estimate the conditional dependence structure of a set of p response variables given q predictors. This package provides suitable extensions developed to study datasets with censored and/or missing values. Standard conditional graphical lasso is available as a special case. Furthermore, the package provides an integrated set of core routines for visualization, analysis, and simulation of datasets with censored and/or missing values drawn from a Gaussian graphical model. Details about the implemented models can be found in Augugliaro et al. (2020b) <doi: 10.1007/s11222-020-09945-7>, Augugliaro et al. (2020a) <doi: 10.1093/biostatistics/kxy043>, Yin et al. (2001) <doi: 10.1214/11-AOAS494> and Stadler et al. (2012) <doi: 10.1007/s11222-010-9219-7>.
Author: Luigi Augugliaro [aut, cre] (<https://orcid.org/0000-0002-4603-7541>),
Gianluca Sottile [aut] (<https://orcid.org/0000-0001-9347-7251>),
Ernst C. Wit [aut] (<https://orcid.org/0000-0002-3671-9610>),
Veronica Vinciotti [aut] (<https://orcid.org/0000-0002-2625-7977>)
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between cglasso versions 2.0.3 dated 2021-04-06 and 2.0.4 dated 2021-04-09
ChangeLog | 9 +++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/cglasso.R | 14 ++++++++++---- build/partial.rdb |binary man/cglasso-package.Rd | 4 ++-- 6 files changed, 30 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-09 0.1.0
Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams
based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between yorkr versions 0.0.19 dated 2021-02-03 and 0.0.20 dated 2021-04-09
DESCRIPTION | 9 +++----- MD5 | 28 +++++++++++++------------- R/bowlerDeliveryWickets.R | 7 ++++-- R/convertAllYaml2RDataframesT20.R | 6 +++++ R/convertYaml2RDataframeT20.R | 9 +++++--- R/getDeliveryWickets.R | 9 +++++--- R/getIPLBattingDetails.R | 2 - R/getIPLBowlingDetails.R | 2 - R/saveAllMatchesAllOppositionIPLT20.R | 2 - R/saveAllMatchesBetween2IPLTeams.R | 2 - R/teamBowlingWicketKindAllOppnAllMatches.R | 1 R/teamBowlingWicketRunsAllOppnAllMatches.R | 1 R/teamBowlingWicketRunsMatch.R | 7 +++--- man/teamBowlingWicketKindAllOppnAllMatches.Rd | 1 man/teamBowlingWicketRunsAllOppnAllMatches.Rd | 1 15 files changed, 49 insertions(+), 38 deletions(-)
Title: Simple Visualisation with 'ggplot2' and 'leaflet' Wrappers
Description: Wrapper functions to make 'ggplot2' and 'leaflet' visualisation easier and prettier.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 2.4.0 dated 2021-03-12 and 2.6.0 dated 2021-04-09
simplevis-2.4.0/simplevis/R/ggplot_box_fun.R |only simplevis-2.4.0/simplevis/R/ggplot_hbar_fun.R |only simplevis-2.4.0/simplevis/R/ggplot_line_fun.R |only simplevis-2.4.0/simplevis/R/ggplot_point_fun.R |only simplevis-2.4.0/simplevis/R/ggplot_sf_fun.R |only simplevis-2.4.0/simplevis/R/ggplot_stars_fun.R |only simplevis-2.4.0/simplevis/R/ggplot_vbar_fun.R |only simplevis-2.4.0/simplevis/R/leaflet_basemap_fun.R |only simplevis-2.4.0/simplevis/R/leaflet_sf_fun.R |only simplevis-2.4.0/simplevis/R/leaflet_stars_fun.R |only simplevis-2.4.0/simplevis/R/run_app_fun.R |only simplevis-2.4.0/simplevis/data/nz_region.rda |only simplevis-2.4.0/simplevis/man/add_tip.Rd |only simplevis-2.4.0/simplevis/man/ggplot_box.Rd |only simplevis-2.4.0/simplevis/man/ggplot_box_facet.Rd |only simplevis-2.4.0/simplevis/man/ggplot_stars.Rd |only simplevis-2.4.0/simplevis/man/ggplot_stars_col.Rd |only simplevis-2.4.0/simplevis/man/ggplot_stars_col_facet.Rd |only simplevis-2.4.0/simplevis/man/ggplot_stars_facet.Rd |only simplevis-2.4.0/simplevis/man/leaflet_basemap_nz.Rd |only simplevis-2.4.0/simplevis/man/leaflet_stars.Rd |only simplevis-2.4.0/simplevis/man/leaflet_stars_col.Rd |only simplevis-2.4.0/simplevis/man/numeric_legend_labels.Rd |only simplevis-2.4.0/simplevis/man/nz_region.Rd |only simplevis-2.4.0/simplevis/man/pal_point_set1.Rd |only simplevis-2.4.0/simplevis/man/pal_snz.Rd |only simplevis-2.4.0/simplevis/man/sentence_spaced_colnames.Rd |only simplevis-2.4.0/simplevis/man/theme_box.Rd |only simplevis-2.4.0/simplevis/man/theme_stars.Rd |only simplevis-2.6.0/simplevis/DESCRIPTION | 10 simplevis-2.6.0/simplevis/MD5 | 162 ++--- simplevis-2.6.0/simplevis/NAMESPACE | 16 simplevis-2.6.0/simplevis/NEWS.md | 116 +++ simplevis-2.6.0/simplevis/R/data.R | 11 simplevis-2.6.0/simplevis/R/ggplot_boxplot.R |only simplevis-2.6.0/simplevis/R/ggplot_hbar.R |only simplevis-2.6.0/simplevis/R/ggplot_line.R |only simplevis-2.6.0/simplevis/R/ggplot_point.R |only simplevis-2.6.0/simplevis/R/ggplot_sf.R |only simplevis-2.6.0/simplevis/R/ggplot_vbar.R |only simplevis-2.6.0/simplevis/R/internal.R |only simplevis-2.6.0/simplevis/R/leaflet_basemap.R |only simplevis-2.6.0/simplevis/R/leaflet_sf.R |only simplevis-2.6.0/simplevis/R/logo.R | 34 - 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Title: Sean 'Lahman' Baseball Database
Description: Provides the tables from the 'Sean Lahman Baseball Database' as
a set of R data.frames. It uses the data on pitching, hitting and fielding
performance and other tables from 1871 through 2019, as recorded in the 2020
version of the database. Documentation examples show how many baseball
questions can be investigated.
Author: Michael Friendly [aut],
Chris Dalzell [cre, aut],
Martin Monkman [aut],
Dennis Murphy [aut],
Vanessa Foot [ctb],
Justeena Zaki-Azat [ctb]
Maintainer: Chris Dalzell <cdalzell@gmail.com>
Diff between Lahman versions 8.0-1 dated 2021-01-21 and 9.0-0 dated 2021-04-09
DESCRIPTION | 9 MD5 | 146 ++++---- NEWS | 4 build/vignette.rds |binary data/AllstarFull.RData |binary data/Appearances.RData |binary data/AwardsManagers.RData |binary data/AwardsPlayers.RData |binary data/AwardsShareManagers.RData |binary data/AwardsSharePlayers.RData |binary data/Batting.RData |binary data/BattingPost.RData |binary data/CollegePlaying.RData |binary data/Fielding.RData |binary data/FieldingOF.RData |binary data/FieldingOFsplit.RData |binary data/FieldingPost.RData |binary data/HallOfFame.RData |binary data/HomeGames.RData |binary data/LahmanData.RData |binary data/Managers.RData |binary data/ManagersHalf.RData |binary data/Master.RData |binary data/Parks.RData |binary data/People.RData |binary data/Pitching.RData |binary data/PitchingPost.RData |binary data/Salaries.RData |binary data/Schools.RData |binary data/SeriesPost.RData |binary data/Teams.RData |binary data/TeamsFranchises.RData |binary data/TeamsHalf.RData |binary data/battingLabels.RData |binary data/fieldingLabels.RData |binary data/pitchingLabels.RData |binary inst/doc/hits-by-type.html | 410 +++++------------------- inst/doc/payroll.html | 659 ++++++++++++--------------------------- inst/doc/run-scoring-trends.html | 330 +++---------------- inst/doc/strikeoutsandhr.Rmd | 2 inst/doc/strikeoutsandhr.html | 472 +++++++-------------------- inst/doc/vignette-intro.Rmd | 4 inst/doc/vignette-intro.html | 247 -------------- inst/scripts/readLahman.R | 6 man/AllstarFull.Rd | 2 man/Appearances.Rd | 4 man/AwardsManagers.Rd | 2 man/AwardsPlayers.Rd | 2 man/AwardsShareManagers.Rd | 2 man/AwardsSharePlayers.Rd | 2 man/Batting.Rd | 4 man/BattingPost.Rd | 4 man/CollegePlaying.Rd | 2 man/Fielding.Rd | 4 man/FieldingOF.Rd | 2 man/FieldingOFsplit.Rd | 4 man/FieldingPost.Rd | 4 man/HallOfFame.Rd | 2 man/HomeGames.Rd | 2 man/Managers.Rd | 4 man/ManagersHalf.Rd | 2 man/Master.Rd | 4 man/Parks.Rd | 2 man/People.Rd | 4 man/Pitching.Rd | 4 man/PitchingPost.Rd | 4 man/Salaries.Rd | 2 man/Schools.Rd | 2 man/SeriesPost.Rd | 4 man/Teams.Rd | 4 man/TeamsFranchises.Rd | 2 man/TeamsHalf.Rd | 2 vignettes/strikeoutsandhr.Rmd | 2 vignettes/vignette-intro.Rmd | 4 74 files changed, 625 insertions(+), 1752 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds
of correlations, such as partial correlations, Bayesian correlations,
multilevel correlations, polychoric correlations, biweight
correlations, distance correlations and more. Part of the 'easystats'
ecosystem.
Author: Dominique Makowski [aut, inv] (<https://orcid.org/0000-0001-5375-9967>),
Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between correlation versions 0.6.0 dated 2021-02-12 and 0.6.1 dated 2021-04-09
correlation-0.6.0/correlation/R/print.easycormatrix.R |only correlation-0.6.0/correlation/R/print.easycorrelation.R |only correlation-0.6.0/correlation/R/print_md.R |only correlation-0.6.0/correlation/vignettes/multilevel_files |only correlation-0.6.0/correlation/vignettes/types_files |only correlation-0.6.1/correlation/DESCRIPTION | 38 correlation-0.6.1/correlation/MD5 | 173 - correlation-0.6.1/correlation/NAMESPACE | 155 - correlation-0.6.1/correlation/NEWS.md | 235 + correlation-0.6.1/correlation/R/backports.R | 16 correlation-0.6.1/correlation/R/cor_test.R | 609 ++--- correlation-0.6.1/correlation/R/cor_test_bayes.R | 226 - correlation-0.6.1/correlation/R/cor_test_biserial.R | 152 - correlation-0.6.1/correlation/R/cor_test_biweight.R | 84 correlation-0.6.1/correlation/R/cor_test_blomqvist.R | 56 correlation-0.6.1/correlation/R/cor_test_distance.R | 288 +- correlation-0.6.1/correlation/R/cor_test_freq.R | 162 - correlation-0.6.1/correlation/R/cor_test_gamma.R | 58 correlation-0.6.1/correlation/R/cor_test_gaussian.R | 24 correlation-0.6.1/correlation/R/cor_test_hoeffding.R | 54 correlation-0.6.1/correlation/R/cor_test_percentage.R | 102 correlation-0.6.1/correlation/R/cor_test_polychoric.R | 102 correlation-0.6.1/correlation/R/cor_test_shepherd.R | 38 correlation-0.6.1/correlation/R/cor_test_somers.R | 50 correlation-0.6.1/correlation/R/cor_test_tetrachoric.R | 76 correlation-0.6.1/correlation/R/cor_to_ci.R | 180 - 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correlation-0.6.1/correlation/tests/testthat/test-correlation.R | 345 +- correlation-0.6.1/correlation/tests/testthat/test-display_print_dataframe.R | 78 correlation-0.6.1/correlation/tests/testthat/test-display_print_matrix.R | 97 correlation-0.6.1/correlation/tests/testthat/test-grouped_data2.R | 36 correlation-0.6.1/correlation/tests/testthat/test-methods.R | 10 correlation-0.6.1/correlation/tests/testthat/test-misc.R | 76 correlation-0.6.1/correlation/tests/testthat/test-selecting_variables.R |only correlation-0.6.1/correlation/tests/testthat/test-winsorization.R | 97 correlation-0.6.1/correlation/vignettes/bibliography.bib | 316 +- correlation-0.6.1/correlation/vignettes/multilevel.Rmd | 240 +- correlation-0.6.1/correlation/vignettes/types.Rmd | 427 ++- 92 files changed, 7353 insertions(+), 6376 deletions(-)
Title: Interval Mapping for Quantitative Trait Loci Underlying Neighbor
Effects
Description: To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1093/g3journal/jkab017>.
Author: Yasuhiro Sato [aut, cre] (<https://orcid.org/0000-0002-6466-723X>),
Kazuya Takeda [aut],
Atsushi J. Nagano [aut] (<https://orcid.org/0000-0001-7891-5049>)
Maintainer: Yasuhiro Sato <sato.yasuhiro.36c@kyoto-u.jp>
Diff between rNeighborQTL versions 1.1.1 dated 2020-11-12 and 1.1.2 dated 2021-04-09
rNeighborQTL-1.1.1/rNeighborQTL/inst/rNeighborQTL.Rmd |only rNeighborQTL-1.1.2/rNeighborQTL/DESCRIPTION | 16 rNeighborQTL-1.1.2/rNeighborQTL/MD5 | 47 rNeighborQTL-1.1.2/rNeighborQTL/R/calc_pve.R | 244 +- rNeighborQTL-1.1.2/rNeighborQTL/R/eff_neighbor.R | 366 ++-- rNeighborQTL-1.1.2/rNeighborQTL/R/rNeighborQTL-package.R | 51 rNeighborQTL-1.1.2/rNeighborQTL/R/scan_neighbor.R | 210 +- rNeighborQTL-1.1.2/rNeighborQTL/build/vignette.rds |binary rNeighborQTL-1.1.2/rNeighborQTL/inst/CITATION | 14 rNeighborQTL-1.1.2/rNeighborQTL/inst/doc/rNeighborQTL.R | 310 +-- rNeighborQTL-1.1.2/rNeighborQTL/inst/doc/rNeighborQTL.Rmd | 422 ++--- rNeighborQTL-1.1.2/rNeighborQTL/inst/doc/rNeighborQTL.html | 994 ++++-------- rNeighborQTL-1.1.2/rNeighborQTL/man/calc_neiprob.Rd | 86 - rNeighborQTL-1.1.2/rNeighborQTL/man/calc_pve.Rd | 154 - rNeighborQTL-1.1.2/rNeighborQTL/man/decompose_genoprobs.Rd | 54 rNeighborQTL-1.1.2/rNeighborQTL/man/eff_neighbor.Rd | 164 - rNeighborQTL-1.1.2/rNeighborQTL/man/get_markers.Rd | 40 rNeighborQTL-1.1.2/rNeighborQTL/man/int_neighbor.Rd | 152 - rNeighborQTL-1.1.2/rNeighborQTL/man/min_dist.Rd | 44 rNeighborQTL-1.1.2/rNeighborQTL/man/perm_neighbor.Rd | 154 - rNeighborQTL-1.1.2/rNeighborQTL/man/plot_eff.Rd | 44 rNeighborQTL-1.1.2/rNeighborQTL/man/plot_nei.Rd | 64 rNeighborQTL-1.1.2/rNeighborQTL/man/rNeighborQTL-package.Rd | 58 rNeighborQTL-1.1.2/rNeighborQTL/man/scan_neighbor.Rd | 158 - rNeighborQTL-1.1.2/rNeighborQTL/vignettes/rNeighborQTL.Rmd | 422 ++--- 25 files changed, 2036 insertions(+), 2232 deletions(-)
Title: Multiple Indicator Cluster Survey (MICS) 2014 Women
Questionnaire Data for Punjab, Pakistan
Description: Provides data set and function for exploration of Multiple Indicator Cluster Survey 2014 Women (age 15-49 years) questionnaire data for Punjab, Pakistan.
Author: Muhammad Yaseen [aut, cre],
Muhammad Usman [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakPMICS2014Wm versions 0.1.0 dated 2017-09-07 and 0.1.1 dated 2021-04-09
PakPMICS2014Wm-0.1.0/PakPMICS2014Wm/data/datalist |only PakPMICS2014Wm-0.1.1/PakPMICS2014Wm/DESCRIPTION | 13 +++++++------ PakPMICS2014Wm-0.1.1/PakPMICS2014Wm/MD5 | 11 +++++------ PakPMICS2014Wm-0.1.1/PakPMICS2014Wm/NEWS.md | 6 ++++++ PakPMICS2014Wm-0.1.1/PakPMICS2014Wm/R/MICS2014Wm.R | 2 +- PakPMICS2014Wm-0.1.1/PakPMICS2014Wm/README.md | 6 +++--- PakPMICS2014Wm-0.1.1/PakPMICS2014Wm/man/MICS2014Wm.Rd | 8 +++++--- 7 files changed, 27 insertions(+), 19 deletions(-)
More information about PakPMICS2014Wm at CRAN
Permanent link
Title: Multiple Indicator Cluster Survey (MICS) 2014 Household Listing
Questionnaire Data for Punjab, Pakistan
Description: Provides data set and function for exploration of Multiple Indicator Cluster Survey 2014 Household Listing questionnaire data for Punjab, Pakistan.
Author: Muhammad Yaseen [aut, cre],
Muhammad Usman [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakPMICS2014HL versions 0.1.0 dated 2017-09-07 and 0.1.1 dated 2021-04-09
PakPMICS2014HL-0.1.0/PakPMICS2014HL/data/datalist |only PakPMICS2014HL-0.1.1/PakPMICS2014HL/DESCRIPTION | 13 +++++++------ PakPMICS2014HL-0.1.1/PakPMICS2014HL/MD5 | 11 +++++------ PakPMICS2014HL-0.1.1/PakPMICS2014HL/NEWS.md | 5 +++++ PakPMICS2014HL-0.1.1/PakPMICS2014HL/R/MICS2014HL.R | 2 +- PakPMICS2014HL-0.1.1/PakPMICS2014HL/README.md | 6 +++--- PakPMICS2014HL-0.1.1/PakPMICS2014HL/man/MICS2014HL.Rd | 8 +++++--- 7 files changed, 26 insertions(+), 19 deletions(-)
More information about PakPMICS2014HL at CRAN
Permanent link
Title: Create Simple Yet Powerful HTML Documents with Light Weight CSS
Frameworks
Description: Create minimal, responsive, and style-agnostic HTML documents with
the lightweight CSS frameworks such as 'sakura', 'Water.css', and 'spcss'.
Powerful features include table of contents floating as a sidebar,
folding codes and results, and more.
Author: Atsushi Yasumoto [aut, cph, cre]
(<https://orcid.org/0000-0002-8335-495X>),
Angelos Chalaris [aut] (mini.css),
Susam Pal [aut] (spcss),
Mitesh Shah [aut] (sakura),
Kognise [aut] (Water.css)
Maintainer: Atsushi Yasumoto <atusy.rpkg@gmail.com>
Diff between minidown versions 0.1.0 dated 2021-04-04 and 0.1.1 dated 2021-04-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/spec-post-processor.R | 1 - tests/testthat/test-mini-document.R | 12 +++++++----- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Binary Expansion Testing
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921> and Zhigen Zhao, Michael Baiocchi, Kai Zhang. SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables.
Author: Wan Zhang [aut, cre],
Zhigen Zhao [aut],
Michael Baiocchi [aut],
Kai Zhang [aut]
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Diff between BET versions 0.3.5 dated 2021-04-02 and 0.3.6 dated 2021-04-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/RcppExports.R | 4 ++-- R/plot.R | 27 ++++++++++++++++++--------- build/partial.rdb |binary src/BET.h | 11 +++++++---- src/BET3.cpp | 47 +++++++++++++++++++++++++++++------------------ src/RcppExports.cpp | 9 ++++----- 8 files changed, 70 insertions(+), 48 deletions(-)
Title: Deployment Interface for R Markdown Documents and Shiny
Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and
'RStudio Connect'. Supported content types include R Markdown documents,
Shiny applications, Plumber APIs, plots, and static web content.
Author: JJ Allaire
Maintainer: Jonathan McPherson <jonathan@rstudio.com>
Diff between rsconnect versions 0.8.16 dated 2019-12-13 and 0.8.17 dated 2021-04-09
DESCRIPTION | 12 - MD5 | 113 ++++++------- NAMESPACE | 2 NEWS.md | 28 +++ R/accounts.R | 15 + R/applications.R | 103 +++++++++++- R/auth.R | 6 R/bundle.R | 333 ++++++++++++++++++++++++++++++---------- R/config.R | 27 ++- R/dependencies.R | 51 ++++-- R/deployApp.R | 18 +- R/deployDoc.R | 2 R/deployTFModel.R | 4 R/deployments.R | 28 ++- R/http-libcurl.R | 8 R/imports.R | 2 R/lint-utils.R | 4 R/lucid.R | 2 R/onLoad.R | 5 R/packages.R | 2 R/rpubs.R | 7 R/usage.R | 4 README.md | 10 - inst/resources/environment.py | 245 +++++++++++++++++++++++------ man/accountUsage.Rd | 10 - man/accounts.Rd | 6 man/addAuthorizedUser.Rd | 12 + man/applications.Rd | 9 - man/configureApp.Rd | 13 + man/connectApiUser.Rd | 9 - man/connectUser.Rd | 7 man/deployAPI.Rd | 9 - man/deployApp.Rd | 39 +++- man/deployDoc.Rd | 9 - man/deploySite.Rd | 25 ++- man/deployTFModel.Rd | 13 - man/deployments.Rd | 12 + man/forgetDeployment.Rd | 10 - man/generateAppName.Rd | 3 man/removeAuthorizedUser.Rd | 9 - man/rpubsUpload.Rd | 3 man/rsconnectPackages.Rd | 4 man/servers.Rd | 4 man/setAccountInfo.Rd | 6 man/setProperty.Rd | 10 - man/showInvited.Rd | 3 man/showLogs.Rd | 10 - man/showMetrics.Rd | 18 +- man/showUsage.Rd | 13 + man/showUsers.Rd | 3 man/syncAppMetadata.Rd |only man/unsetProperty.Rd | 9 - man/writeManifest.Rd | 14 + tests/testthat.R | 9 + tests/testthat/test-bundle.R | 42 +++++ tests/testthat/test-cert.R | 3 tests/testthat/test-connect.R | 2 tests/testthat/test-detection.R | 112 +++++++++++++ 58 files changed, 1137 insertions(+), 354 deletions(-)
Title: Exploration and Graphics for RivEr Trends
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS). The modeling
method is introduced and discussed in Hirsch et al. (2010) <doi:10.1111/j.1752-1688.2010.00482.x>,
and expanded in Hirsch and De Cicco (2015) <doi:10.3133/tm4A10>.
Author: Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>),
Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
Tim Cohn [ctb],
David Watkins [ctb],
Lindsay Carr [ctb],
Jennifer Murphy [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRET versions 3.0.2 dated 2019-02-08 and 3.0.5 dated 2021-04-09
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EGRET-3.0.5/EGRET/NEWS | 7 EGRET-3.0.5/EGRET/R/EGRET.R | 44 - EGRET-3.0.5/EGRET/R/boxConcMonth.R | 4 EGRET-3.0.5/EGRET/R/boxConcThree.R | 3 EGRET-3.0.5/EGRET/R/boxQTwice.R | 6 EGRET-3.0.5/EGRET/R/calculateMonthlyResults.R | 29 EGRET-3.0.5/EGRET/R/cumQdate.R |only EGRET-3.0.5/EGRET/R/egret_objects.R | 14 EGRET-3.0.5/EGRET/R/errorStats.R |only EGRET-3.0.5/EGRET/R/estCrossVal.R | 4 EGRET-3.0.5/EGRET/R/estDailyFromSurfacesJ.R | 13 EGRET-3.0.5/EGRET/R/estSurfaces.R | 2 EGRET-3.0.5/EGRET/R/flexFN.R | 4 EGRET-3.0.5/EGRET/R/flowDuration.R | 14 EGRET-3.0.5/EGRET/R/fluxBiasEight.R | 10 EGRET-3.0.5/EGRET/R/fluxBiasStat.R | 4 EGRET-3.0.5/EGRET/R/generalAxis.R | 2 EGRET-3.0.5/EGRET/R/kalman_functions.R |only EGRET-3.0.5/EGRET/R/makeAnnualSeries.R | 7 EGRET-3.0.5/EGRET/R/makeRandomResiduals.R | 4 EGRET-3.0.5/EGRET/R/mergeReport.r | 8 EGRET-3.0.5/EGRET/R/modelEstimation.R | 47 - EGRET-3.0.5/EGRET/R/plot15.R | 18 EGRET-3.0.5/EGRET/R/plot1of15.R | 11 EGRET-3.0.5/EGRET/R/plotConcHist.R | 165 ++-- EGRET-3.0.5/EGRET/R/plotConcPred.R | 8 EGRET-3.0.5/EGRET/R/plotConcQ.R | 19 EGRET-3.0.5/EGRET/R/plotConcQSmooth.R | 28 EGRET-3.0.5/EGRET/R/plotConcTime.R | 22 EGRET-3.0.5/EGRET/R/plotConcTimeDaily.R | 7 EGRET-3.0.5/EGRET/R/plotConcTimeSmooth.R | 24 EGRET-3.0.5/EGRET/R/plotContours.R | 41 EGRET-3.0.5/EGRET/R/plotDiffContours.R | 38 EGRET-3.0.5/EGRET/R/plotFlowSingle.R | 18 EGRET-3.0.5/EGRET/R/plotFluxHist.R | 125 ++- EGRET-3.0.5/EGRET/R/plotFluxPred.R | 2 EGRET-3.0.5/EGRET/R/plotFluxQ.R | 2 EGRET-3.0.5/EGRET/R/plotFluxTimeDaily.R | 56 - 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Title: Thermodynamic Calculations and Diagrams for Geochemistry
Description: An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
balanced reactions to form species from user-selected basis species and for
calculating the standard molal properties of species and reactions, including
the standard Gibbs energy and equilibrium constant. Calculations of the
non-equilibrium chemical affinity and equilibrium chemical activity of species
can be portrayed on diagrams as a function of temperature, pressure, or
activity of basis species; in two dimensions, this gives a maximum affinity or
predominance diagram. The diagrams have formatted chemical formulas and axis
labels, and water stability limits can be added to Eh-pH, oxygen fugacity-
temperature, and other diagrams with a redox variable. The package has been
developed to handle common calculations in aqueous geochemistry, such as
solubility due to complexation of metal ions, mineral buffers of redox or pH,
and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ
also has unique capabilities for comparing the compositional and thermodynamic
properties of different proteins.
Author: Jeffrey Dick [aut, cre] (<https://orcid.org/0000-0002-0687-5890>)
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.4.0 dated 2020-11-11 and 1.4.1 dated 2021-04-09
CHNOSZ-1.4.0/CHNOSZ/demo/berman.R |only CHNOSZ-1.4.0/CHNOSZ/inst/ONEWS |only CHNOSZ-1.4.1/CHNOSZ/DESCRIPTION | 10 CHNOSZ-1.4.1/CHNOSZ/MD5 | 206 - CHNOSZ-1.4.1/CHNOSZ/R/add.OBIGT.R | 16 CHNOSZ-1.4.1/CHNOSZ/R/diagram.R | 132 - CHNOSZ-1.4.1/CHNOSZ/R/examples.R | 4 CHNOSZ-1.4.1/CHNOSZ/R/info.R | 24 CHNOSZ-1.4.1/CHNOSZ/R/ionize.aa.R | 7 CHNOSZ-1.4.1/CHNOSZ/R/mosaic.R | 39 CHNOSZ-1.4.1/CHNOSZ/R/solubility.R | 145 - CHNOSZ-1.4.1/CHNOSZ/R/species.R | 5 CHNOSZ-1.4.1/CHNOSZ/R/subcrt.R | 12 CHNOSZ-1.4.1/CHNOSZ/R/thermo.R | 23 CHNOSZ-1.4.1/CHNOSZ/R/util.affinity.R | 2 CHNOSZ-1.4.1/CHNOSZ/R/util.data.R | 6 CHNOSZ-1.4.1/CHNOSZ/R/util.fasta.R | 4 CHNOSZ-1.4.1/CHNOSZ/R/util.units.R | 2 CHNOSZ-1.4.1/CHNOSZ/build/partial.rdb |only CHNOSZ-1.4.1/CHNOSZ/build/vignette.rds |binary CHNOSZ-1.4.1/CHNOSZ/demo/00Index | 4 CHNOSZ-1.4.1/CHNOSZ/demo/AkDi.R | 4 CHNOSZ-1.4.1/CHNOSZ/demo/E_coli.R |only CHNOSZ-1.4.1/CHNOSZ/demo/Pourbaix.R |only CHNOSZ-1.4.1/CHNOSZ/demo/affinity.R | 36 CHNOSZ-1.4.1/CHNOSZ/demo/contour.R | 29 CHNOSZ-1.4.1/CHNOSZ/demo/gold.R | 94 CHNOSZ-1.4.1/CHNOSZ/demo/mosaic.R | 73 CHNOSZ-1.4.1/CHNOSZ/demo/potassium.R |only CHNOSZ-1.4.1/CHNOSZ/demo/solubility.R | 44 CHNOSZ-1.4.1/CHNOSZ/demo/sphalerite.R | 31 CHNOSZ-1.4.1/CHNOSZ/demo/zinc.R | 44 CHNOSZ-1.4.1/CHNOSZ/inst/CHECKLIST | 3 CHNOSZ-1.4.1/CHNOSZ/inst/NEWS.Rd | 2095 ---------------- CHNOSZ-1.4.1/CHNOSZ/inst/ONEWS.Rd |only CHNOSZ-1.4.1/CHNOSZ/inst/OONEWS |only CHNOSZ-1.4.1/CHNOSZ/inst/TODO | 17 CHNOSZ-1.4.1/CHNOSZ/inst/doc/OBIGT.Rmd | 2 CHNOSZ-1.4.1/CHNOSZ/inst/doc/OBIGT.bib | 69 CHNOSZ-1.4.1/CHNOSZ/inst/doc/OBIGT.html | 56 CHNOSZ-1.4.1/CHNOSZ/inst/doc/anintro.R | 12 CHNOSZ-1.4.1/CHNOSZ/inst/doc/anintro.Rmd | 43 CHNOSZ-1.4.1/CHNOSZ/inst/doc/anintro.html | 242 - CHNOSZ-1.4.1/CHNOSZ/inst/doc/eos-regress.Rmd | 2 CHNOSZ-1.4.1/CHNOSZ/inst/doc/eos-regress.html | 14 CHNOSZ-1.4.1/CHNOSZ/inst/doc/equilibrium.Rmd | 14 CHNOSZ-1.4.1/CHNOSZ/inst/doc/equilibrium.html | 8 CHNOSZ-1.4.1/CHNOSZ/inst/doc/multi-metal.R | 873 +++++- CHNOSZ-1.4.1/CHNOSZ/inst/doc/multi-metal.Rmd | 503 +++ CHNOSZ-1.4.1/CHNOSZ/inst/doc/multi-metal.html | 1263 +++++---- CHNOSZ-1.4.1/CHNOSZ/inst/extdata/OBIGT/AkDi.csv | 48 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv | 70 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv | 2 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/OBIGT/SUPCRT92.csv | 1 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv | 28 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv | 4 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv | 21 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/OBIGT/refs.csv | 7 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/adds/OBIGT_check.csv | 470 +-- CHNOSZ-1.4.1/CHNOSZ/inst/extdata/thermo/opt.csv | 4 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/thermo/protein.csv | 2 CHNOSZ-1.4.1/CHNOSZ/inst/extdata/thermo/stoich.csv.xz |binary CHNOSZ-1.4.1/CHNOSZ/man/CHNOSZ-package.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/DEW.Rd | 4 CHNOSZ-1.4.1/CHNOSZ/man/EOSregress.Rd | 4 CHNOSZ-1.4.1/CHNOSZ/man/IAPWS95.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/add.OBIGT.Rd | 21 CHNOSZ-1.4.1/CHNOSZ/man/affinity.Rd | 4 CHNOSZ-1.4.1/CHNOSZ/man/basis.Rd | 4 CHNOSZ-1.4.1/CHNOSZ/man/berman.Rd | 8 CHNOSZ-1.4.1/CHNOSZ/man/buffer.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/diagram.Rd | 27 CHNOSZ-1.4.1/CHNOSZ/man/eos.Rd | 19 CHNOSZ-1.4.1/CHNOSZ/man/equilibrate.Rd | 7 CHNOSZ-1.4.1/CHNOSZ/man/examples.Rd | 122 CHNOSZ-1.4.1/CHNOSZ/man/extdata.Rd | 38 CHNOSZ-1.4.1/CHNOSZ/man/ionize.aa.Rd | 4 CHNOSZ-1.4.1/CHNOSZ/man/mosaic.Rd | 24 CHNOSZ-1.4.1/CHNOSZ/man/nonideal.Rd | 18 CHNOSZ-1.4.1/CHNOSZ/man/objective.Rd | 4 CHNOSZ-1.4.1/CHNOSZ/man/palply.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/protein.info.Rd | 4 CHNOSZ-1.4.1/CHNOSZ/man/solubility.Rd | 227 - CHNOSZ-1.4.1/CHNOSZ/man/species.Rd | 3 CHNOSZ-1.4.1/CHNOSZ/man/subcrt.Rd | 16 CHNOSZ-1.4.1/CHNOSZ/man/thermo.Rd | 28 CHNOSZ-1.4.1/CHNOSZ/man/util.blast.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/util.data.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/util.formula.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/util.protein.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/util.water.Rd | 2 CHNOSZ-1.4.1/CHNOSZ/man/water.Rd | 22 CHNOSZ-1.4.1/CHNOSZ/tests/testthat/test-eos.R | 4 CHNOSZ-1.4.1/CHNOSZ/tests/testthat/test-info.R | 8 CHNOSZ-1.4.1/CHNOSZ/tests/testthat/test-ionize.aa.R | 11 CHNOSZ-1.4.1/CHNOSZ/tests/testthat/test-mix.R | 3 CHNOSZ-1.4.1/CHNOSZ/tests/testthat/test-mod.OBIGT.R | 2 CHNOSZ-1.4.1/CHNOSZ/tests/testthat/test-mosaic.R | 12 CHNOSZ-1.4.1/CHNOSZ/tests/testthat/test-solubility.R | 40 CHNOSZ-1.4.1/CHNOSZ/vignettes/CHNOSZ.dia |binary CHNOSZ-1.4.1/CHNOSZ/vignettes/CHNOSZ.png |binary CHNOSZ-1.4.1/CHNOSZ/vignettes/OBIGT.Rmd | 2 CHNOSZ-1.4.1/CHNOSZ/vignettes/OBIGT.bib | 69 CHNOSZ-1.4.1/CHNOSZ/vignettes/anintro.Rmd | 43 CHNOSZ-1.4.1/CHNOSZ/vignettes/eos-regress.Rmd | 2 CHNOSZ-1.4.1/CHNOSZ/vignettes/equilibrium.Rmd | 14 CHNOSZ-1.4.1/CHNOSZ/vignettes/multi-metal.Rmd | 503 +++ CHNOSZ-1.4.1/CHNOSZ/vignettes/vig.bib | 116 108 files changed, 4095 insertions(+), 4229 deletions(-)