Changelog • RRatepol

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