germinationmetrics 0.1.9

NEW FUNCTIONS:

• geom_line2 - A modification of ggplot2::geom_line to plot both lines and points together as an internal function.

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).
• GermValue & GermSpeed - Updated calculations to ignroe NaN values.
• EmergenceRateIndex - Fix error due to missing total.seeds argument.

germinationmetrics 0.1.8

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

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

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

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

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 (ripley@stats.ox.ac.uk).

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

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

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

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

• First release

germinationmetrics 0.0.0.9000

• Pre-release