Package: drcSeedGerm 1.1.1

drcSeedGerm: Utilities for Data Analyses in Seed Germination/Emergence Assays

Utility functions to be used to analyse datasets obtained from seed germination/emergence assays. Fits several types of seed germination/emergence models, including those reported in Onofri et al. (2018) "Hydrothermal-time-to-event models for seed germination", European Journal of Agronomy, 101, 129-139 <doi:10.1016/j.eja.2018.08.011>. Contains several datasets for practicing.

Authors:Andrea Onofri <[email protected]>

drcSeedGerm_1.1.1.tar.gz
drcSeedGerm_1.1.1.zip(r-4.7)drcSeedGerm_1.1.1.zip(r-4.6)drcSeedGerm_1.1.1.zip(r-4.5)
drcSeedGerm_1.1.1.tgz(r-4.6-any)drcSeedGerm_1.1.1.tgz(r-4.5-any)
drcSeedGerm_1.1.1.tar.gz(r-4.7-any)drcSeedGerm_1.1.1.tar.gz(r-4.6-any)
drcSeedGerm_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
drcSeedGerm/json (API)
NEWS

# Install 'drcSeedGerm' in R:
install.packages('drcSeedGerm', repos = c('https://onofriandreapg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/onofriandreapg/drcseedgerm/issues

Datasets:
  • alfalfaSG - Field-book for a germination assay with alfalfa
  • barley - A series of germination assays with barley
  • excalibur - Relationship between germination rate and water potential in oilseed rape
  • festuca - Relationship between germination rate and water potential in Festuca arundinacea L.
  • hordeum - Germination of Hordeum spontaneum at different temperatures and water potentials
  • phalaris - A series of germination assays with Phalaris minor
  • rape - Germination data from an assay of rapeseed at decreasing water potential levels
  • rape2G - Germination data from an assay of rapeseed at decreasing water potential levels

On CRAN:

Conda:

nonlinear-regressionseed-germination-assaystime-to-event

4.02 score 5 stars 42 scripts 166 downloads 84 exports 81 dependencies

Last updated from:d68b6e2e8b. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK186
source / vignettesOK190
linux-release-x86_64OK172
macos-release-arm64OK160
macos-oldrel-arm64OK115
windows-develOK136
windows-releaseOK123
windows-oldrelOK126
wasm-releaseOK127

Exports:GRPsi.LinGRPsi.PolGRPsi.Pol2GRPsiLinGRPsiLin.funGRPsiPolGRPsiPol.funGRPsiPol2GRPsiPol2.funGRT.BSGRT.BS.funGRT.BSbGRT.BSb.funGRT.ExGRT.Ex.funGRT.ExbGRT.Exb.funGRT.GHGRT.GH.funGRT.GH2GRT.GH2.funGRT.MGRT.M.funGRT.MbGRT.Mb.funGRT.RFGRT.RF.funGRT.RFbGRT.RFb.funGRT.YLGRT.YL.funGRTPsi.BSGRTPsi.BS.funGRTPsi.MGRTPsi.M.funHaloTLHaloTL.funHaloTLLHaloTLL.funHaloTnormHaloTnorm.funHTE1HTE1.funHTE2HTE2.funHTE3HTE3.funHTexHTex.funHTGHTG.funHTLHTL.funHTLLHTLL.funHTnormHTnorm.funHTTEMHTTEM.funHTTLL.BSHTTLL.BS.funHTTLL.MHTTLL.M.funHTTnorm.BSHTTnorm.BS.funHTTnorm.MHTTnorm.M.funHTW1HTW1.funHTW2HTW2.funjackGroupSEmakeDrmmakeDrm2PmaxPsi1PmaxPsi1.funPmaxT1PmaxT1.funTTEMTTEM.funTTERFTTERF.funTTERFcTTERFc.fun

Dependencies:abindbackportsbootbroomcarcarDataclicodetoolscolorspacecowplotcpp11DerivdoBydplyrdrcdrctefarverforecastFormulafracdiffgenericsggplot2gluegtablegtoolsisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmclustmgcvmicrobenchmarkminqamodelrmultcompmvtnormnlmenloptrnnetnor1mixnumDerivpbkrtestpillarpkgconfigplotrixplyrpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangS7sandwichscalesSparseMstringistringrsurvivalTH.datatibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzoo

Readme and manuals

Help Manual

Help pageTopics
Field-book for a germination assay with alfalfaalfalfaSG
A series of germination assays with barleybarley
Relationship between germination rate and water potential in oilseed rape (var. Excalibur)excalibur
Relationship between germination rate and water potential in Festuca arundinacea L.festuca
Hydro-time models based on the germination rateGRPsi.Lin GRPsi.Pol GRPsi.Pol2 GRPsiLin GRPsiLin.fun GRPsiPol GRPsiPol.fun GRPsiPol2 GRPsiPol2.fun
Thermal-time models based on the germination rateGRT.BS GRT.BS.fun GRT.BSb GRT.BSb.fun GRT.Ex GRT.Ex.fun GRT.Exb GRT.Exb.fun GRT.GH GRT.GH.fun GRT.GH2 GRT.GH2.fun GRT.M GRT.M.fun GRT.Mb GRT.Mb.fun GRT.RF GRT.RF.fun GRT.RFb GRT.RFb.fun GRT.YL GRT.YL.fun
Hydro-Thermal-time models based on the germination rateGRTPsi.BS GRTPsi.BS.fun GRTPsi.M GRTPsi.M.fun
Halotime model with logistic distribution of base salt concentration (derived from Bakhshandeh et al., 2020)HaloTL HaloTL.fun
Halotime model with log-logistic distribution of base salt concentration (derived from Bakhshandeh et al., 2020)HaloTLL HaloTLL.fun
Halotime model with normal distribution of base salt concentration (derived from Bakhshandeh et al., 2020)HaloTnorm HaloTnorm.fun
Germination of Hordeum spontaneum at different temperatures and water potentialshordeum
Hydrotime model with log-logistic distribution of germination time (Onofri et al., 2018)HTE1 HTE1.fun
Hydrotime model with log-logistic distribution of germination time (Onofri et al., 2018)HTE2 HTE2.fun
Hydrotime model with log-logistic distribution of germination time (Onofri et al., 2018)HTE3 HTE3.fun
Hydrotime model with Type II Extreme Value distribution of base water potential (Mesgaran et al., 2013)HTex HTex.fun
Hydrotime model with Gumbel distribution of base water potential (Mesgaran et al., 2013)HTG HTG.fun
Hydrotime model with logistic distribution of base water potential (Mesgaran et al., 2013)HTL HTL.fun
Hydrotime model with log-logistic distribution of base water potential (Mesgaran et al., 2013)HTLL HTLL.fun
Hydrotime model with normal distribution of base water potential (Bradford, 2002)HTnorm HTnorm.fun
Hydro-thermal-time model with log-logistic distribution of germination time (Onofri et al., 2018)HTTEM HTTEM.fun
Hydro-thermal-time model with log-logistic distribution of base water potential (Mesgaran et al., 2017)HTTLL.BS HTTLL.BS.fun HTTLL.M HTTLL.M.fun
Hydro-thermal-time model with normal distribution of base water potential (Bradford, 2002)HTTnorm.BS HTTnorm.BS.fun HTTnorm.M HTTnorm.M.fun
Hydrotime model with Weibull Type I distribution of base water potential (Mesgaran et al., 2013)HTW1 HTW1.fun
Hydrotime model with Weibull Type II distribution of base water potential (Mesgaran et al., 2013)HTW2 HTW2.fun
Delete-a-Petri-dish jackknifejackGroupSE
Reshape a seed germination datasets for time-to-event analyses (deprecated)makeDrm
Reshape a seed germination datasets for time-to-event model fitting.makeDrm2
A series of germination assays with Phalaris minorphalaris
Effect of environmental water potential or temperature on the germination capability of a seed lotPmaxPsi1 PmaxPsi1.fun PmaxT1 PmaxT1.fun
Germination data from an assay of rapeseed at decreasing water potential levelsrape
Germination data from an assay of rapeseed at decreasing water potential levelsrape2G
Thermal-time models with log-logistic distribution of germination time (Onofri et al., 2018)TTEM TTEM.fun TTERF TTERF.fun TTERFc TTERFc.fun