NEWS

avidaR 1.2.1 (2024-06-21)

Bug fixes

New features

Added function convert_org_into_seq to convert a digital organism file into a genome instruction sequence.
Added function get_doi_from_experiment_id to get the DOI of the scientific publication that documents the experiment carried out.
Added function get_experiment_id_from_organism_id to get the experiment identifier from which a digital organism is derived.
Added function get_docker_image_from_experiment_id to get the docker image built to run the experiment, which guarantees reproducibility.

Improvements

Updated colors for better comprehension on figures generated by plot_transcriptome() function.
The plot_transcriptome function can now plot multiple transcriptomes in a single function call.
The instruction_set function has been extended to use the "head", "head-sex", and "transsmt" instruction sets.

Bug fixes

Fixed issues to comply with the CRAN policy: 'Packages which use Internet resources should fail gracefully with an informative message if the resource is not available or has changed (and not give a check warning nor error)'.
Fixed issue 'Use of .data in tidyselect expressions was deprecated' on convert_seq_into_org() function.

Improvements

More friendly error messages for helping in solving issues caused by service availability, not valid user requests, unauthorized access, and others.

New features

Added timeout parameter in method set_access_options() to limit the amount of time waiting data from the service.

Bug fixes

Removed top-level code which creates triplestore object and set default access options. Read more about how to properly connect to 'avidaDB'.

Improvements

If seed_id is not specified, a randomly-chosen seed_id value is used to speed up the execution of the following functions:
- get_genome_id_from_logic_operation
- get_genome_id_from_phenotype_id
- get_transcriptome_id_from_logic_operation
- get_transcriptome_id_from_phenotype_id
- get_transcriptome_id_from_logic_operation
- get_transcriptome_id_from_phenotype_id
The function get_mutant_at_pos has been expanded:
- The function parameter genome_id has been added, and the previous parameters (inst_replaced , inst_replaced_by, and pos) can be now omitted by the user.
- If genome_id is not specified, a randomly chosen genome_id (between those provided by the function get_genome_id_of_wild_type_organisms) will be used.
- If inst_replaced and/or inst_replaced_by is/are not specified, all mutations at the specified position on the genome are shown.
- If the parameter pos is not specified, all mutations at all positions on the genome are shown (depending on the values of inst_replaced and inst_replaced_by).

New features

Added function get_db_summary that will provide a summary of the database.
Added get_genome_id_of_wild_type_organisms to identify the genomes of the organisms that were used as wild-type organisms.

Bug fixes

Removed a line from the clause WHERE that was slowing down the execution of the function get_transcriptome_id_from_phenotype_id.
The use of exponential notation was prevented because it provided empty results when requesting data by identifiers like genome_10000000.