NEWS.md

In HOPE-UIB-BIO/R-Ratepol-package: R-Ratepol: Estimating Rate of Change in Temporal Sequences

RRatepol 1.2.3

• fix an issue with subsetting the uncertainty matrix to correctly align with the rest of the data (thanks to Giacomo Galli for reporting the bug)
• replace all not a basic ASCII character in documentation

RRatepol 1.2.2

• add more information about additional resources and workshops
• use {neotoma2} from CRAN
• fix an issue with a case, where the age difference between samples is zero. The zeros are replaced by arbitrary 0.1.

RRatepol 1.2.1

Uncertainty sampling

• fix an issue with an error message for a large number of iterations in sampling age-sequence

RRatepol 1.2.0

Name uniformity

• In order to make all (exported) functions easier to use (use verbs, snake_style,...), rename all functions and their argument. For back-compatibility, the original functions and arguments are kept but flagged as deprecated. More details here.
• main exported function name change:
• rename fc_estimate_RoC() to estimate_roc() (#23)
• rename fc_plot_RoC_sequence() to plot_roc() (#24)
• rename fc_detect_peak_points() to detect_peak_points() (#25)
• rename all internal functions (#26)
• Update README (#27)

RRatepol 1.1.0

neotoma -> neotoma2

• update the vignette to use neotoma2 package (neotoma was deprecated)

utility functions Internal checks

• change util_* functions to use RUtilpol package

Function references

• remove several functions references by flagging them as internal

Bug fixes

• correctly not transform to proportions when selected by a user.

Other

• within select() replace .data$foo with "foo" (suggested in tidyselect)
• replace 1:length(... with seq_along

RRatepol 1.0.0

General

• package has been re-factored (most internal processes have been updated)
• several arguments of functions have been changed and marked with lifecycle
• add several more checks while data sourcing

Dissimilarity calculation

• use vegan package to calculate all dissimilarities except of standardised euclidean.

parallel computation

• use the pbapply package
• data for iteration is prepared separately
• added progress bar

example data

• names for example columns as been adjusted to avoid using .

RRatepol 0.6.1

Dissimilarity calculation

• use vegan package to calculate Gower and Bray-Curtis (new) dissimilarity

Univariate RoC estimation

• fix issues when using only single-taxon dataset

Code cosmetics changes

• TRUE/FALSE written as full
• all arguments are written for each function
• spelling fixes

RRatepol 0.6.0

Overhaul change of the estimation of RoC

• RoC score is now returned in units selected by user (time_standardisation)
• Method of sample selection from bin is now optional (bin_selection)
• RoC is estimated only for subsequent bins (only_subsequent == TRUE)
• Bins are now created form the beginning of the core (instead of 0)

Console outputs

• General overhaul of console outputs presented to user while running RRatepol
• more information and warning messages are presented with each run

doParallel

have been curated by you during the last years packages doSNOW and snow are replaced by doParallel

• progress bar for randomisation is currently not present

Other

• Added various checks for correct argument selection
• all hyphens are replaced with dashes (–) in the whole package
• examples are wrapped into dontrun

RRatepol 0.5.6

README

• Figures are now saved in the new folder (man folder) with the new names.
• cosmetics changes in the code (spaces, new lines, etc)

Vignette

• stop using pre-saved data
• decrease the i_multiplier to 0.5 to speed up the vignette building
• change the treads arguments in fc_estimate_RoC to FALSE so the vignette can be build in machines without multiple cores.
• rename r chunks to remove empty spaces in names

Other

• remove RRatepol namespace inside package for internal functions
• fix couple of typos in function descriptions
• add cran-comments

RRatepol 0.5.5

• sample.id or sample_id can be used in as the sample identification
• RRatepol::fc_plot_RoC_sequence: fix typo in argument age_threshold
• citation(package = "RRatepol") now show correct citation
• update the Figure in README file

HOPE-UIB-BIO/R-Ratepol-package documentation built on March 6, 2024, 7:10 a.m.