NEWS
germinationmetrics 0.1.9
NEW FUNCTIONS:
geom_line2 - A modification of ggplot2::geom_line to plot both lines and points together.
UPDATED FUNCTIONS:
FourPHFfit - Added better error handling. Now gracefully fails by returning empty output due to convergence errors or when fitting is not possible.FourPHFfit.bulk - Added better convergence error handling. Added grid search for finding starting values.plot.FourPHFfit.bulk - Now uses geom_errorbar for showing uniformity. Added better plotting without overlap using geom_line2.t50 - Fixes bug causing incorrect results when multiple values of Ni and Nj are present (Thanks to Aude Maugarny @amaugarn).
germinationmetrics 0.1.8 (2023-08-18)
UPDATED FUNCTIONS:
FirstGermTime, LastGermTime, TimeSpreadGerm - Fixed issue with incorrect display of results in case of intervals which are not in days (Thanks to D. Vijay Dunna.Vijay[at]icar.gov.in).FourPHFfit, plot.FourPHFfit FourPHFfit.bulk and plot.FourPHFfit.bulk - Replaced fitting using minpack.lm::nlsLM with gslnls::gsl_nls.FourPHFfit.bulk and plot.FourPHFfit.bulk - Fixed issue with plotting of cumulative data with show.points = TRUE (Thanks to D. Vijay for Dunna.Vijay[at]icar.gov.in).FourPHFfit.bulk - Added fit quality evaluation in output.VarGermTime, SEGermTime, SEGermRate, CUGerm - Fixed calculation bug with cumulative data.
OTHER NOTES:
- Added unit tests with
testthat.
- Fixed
inst/CITATION.
germinationmetrics 0.1.7 (2022-08-28)
UPDATED FUNCTIONS:
FourPHFfit.bulk - Fixed false "total number of seeds tested is less than the total number of germinated seeds" warning when germination count data is cumulative (Thanks to D. Vijay for Dunna.Vijay[at]icar.gov.in).FourPHFfit - Updated computation of starting values.
VIGNETTE:
- Resolved duplicate chunk labels.
OTHER NOTES:
- Updated documentation for
WeightGermPercent and germination.indices to fix HTML validation problems.
germinationmetrics 0.1.6 (2022-06-15)
NEW FUNCTIONS:
PeakGermPercent - Compute peak germination percentage.
UPDATED FUNCTIONS:
FirstGermTime, LastGermTime and PeakGermTime - Updated documentation with formula.EmergenceRateIndex - Depreciate erroneous method argument options of melville and melvillesantanaranal and replace them with shmueligoldberg and sgsantanaranal respectively.
GermSpeedCorrected - Use germination percentage instead of counts.EmergenceRateIndex, GermIndex, GermSpeedCorrected, GermValue, GermRateRecip and TimsonsIndex - Minor documentation update.
VIGNETTE:
- Fixed fetching CRAN page for version history to fail gracefully when access is down.
- Updated units in Table 3.
germinationmetrics 0.1.5 (2021-02-17)
NEW FUNCTIONS:
plot.FourPHFfit.bulk - Wrapper function around FourPHFfit for multiple samples.
UPDATED FUNCTIONS:
FourPHFfit - Added warning for low germination percentages. Modified to return NA output for zero total germination inputs with non-converging fits so as not to break FourPHFfit.bulk.
VIGNETTE:
- Removed cairo dependency.
germinationmetrics 0.1.4 (2020-06-16)
NEW FUNCTIONS:
FourPHFfit.bulk - Wrapper function around FourPHFfit for multiple samples.GermIndex - Compute germination index according to Melville et al., (1980).EmergenceRateIndex - Compute emergence rate index according to Shmueli and
Goldberg (1971), Bilbro and Wanjura (1982), and Fakorede and Ayoola (1980).
UPDATED FUNCTIONS:
FourPHFfit - Added more checks for the input arguments umax, umin, xp, tries and tmax.MeanGermPercent, MeanGermNumber, GermSynchrony, GermUncertainty, TimsonsIndex, GermRateGeorge, GermSpeed, GermSpeedAccumulated, FirstGermTime, GermValue, PeakValue, WeightGermPercent, t50, MeanGermRate, MeanGermTime, germination.indices, FourPHFfit and FourPHFfit.bulk - Fixed the check for uniformity of intervals to handle non-integer values correctly. Closes issue #3.(Thanks to Jonas Ohlsson [@jonasoh])TimsonsIndex and GermRateGeorge- Fixed to handle interval data other than days.
VIGNETTE:
- Fixed details of Median germination time in Table 3.
- Fixed typo in formula for CUG in Table 3.
- Added reference for Coefficient of variation of the germination time in Table 3.
- Reverted to using system certificates instead of RCurl ones for fetching and displaying version history as suggested by Prof. Brian Ripley ([email protected]).
OTHER NOTES:
- Error in case of non-uniform intervals converted to warning.
- Fixed documentation errors in
FourPHFfit and CVGermTime.
- Updated documentation for
GermSpeed, GermSpeedAccumulated, CUGerm MeanGermRate, SEGermRate, CVG, MeanGermTime, VarGermTime, SEGermTime, GermUncertainty, GermSynchrony, MeanGermPercent, MeanGermNumber, WeightGermPercent, TimsonsIndex, GermRateGeorge and GermSynchrony.
- Converted all equations in Rd files to
MathJaxusing mathjaxr
- Added long running examples to
\donttest in germination.indices, plot.FourPHFfit, gcdata and FourPHFfit.bulk.
germinationmetrics 0.1.3 (2019-01-19)
NEW FUNCTIONS:
WeightGermPercent - Compute the Weighted germination percentage.germination.indices - wrapper function to compute germination indices in batch.
UPDATED FUNCTIONS:
CVGermTime - Fixed error in function name (CVSEGermTime).TimsonsIndex - Fixed error in method name (khanungar).GermSpeed and GermSpeedAccumulated - Updated with option to use percentage germination in addition to germination counts.GermSpeedCorrected - Updated with option to use GermSpeedAccumulated in addition to GermSpeed.GermValue - Updated with option to consider time from start of test in addition to time from onset of germination.
VIGNETTE:
- Fixed LATEX xcolor options clash issue in vignette.
OTHER NOTES:
- Updated documentation -
GermValue, MeanGermTime and TimsonsIndex.
germinationmetrics 0.1.2 (2018-10-31)
OTHER NOTES:
- Removed non-ASCII symbols in
inst/REFERENCES.bib being used by Rdpack macro to enforce UTF-8 encoding.
- Added inline citations in documentation with Rdpack
\insertCite{}{} and replaced all \insertRef{}{} with \insertAllCited{}.
- Fixed https link issue in vignette.
- Added mirror set command in vignette.
- Added
XML, RCurl and httr to suggests.
germinationmetrics 0.1.1 (2018-07-26)
NEW FUNCTIONS:
plot.FourPHFfit - plot method for FourPHFfit.
UPDATED FUNCTIONS:
FourPHFfit - Fixed code to accommodate changes in the new release of broom package.FourPHFfit - Separated plot method to new function plot.FourPHFfit.
VIGNETTE:
- Fixed LATEX xcolor options clash issue in vignette.
- Fixed issue with missing pandoc in case of r-release-osx-x86_64.
OTHER NOTES:
- Fixed citation information.
- Added zenodo and rdocumentation badges.
- Added CRAN installation instructions in Readme.
- Added logo.
germinationmetrics 0.1.0 (2018-04-17)
germinationmetrics 0.0.0.9000