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Updating print function and messaging style (#122)
* Changed class name and generic name * Rename summarise_austraits to summarise_database * Updated format for print message for v<5 * Updated start up message
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,49 +1,89 @@ | ||
| #' @title Generic for outputting a nice summary for austraits objects | ||
| #' | ||
| #' @name print.austraits | ||
| #' @param database traits.build database | ||
| #' @name print.traits.build | ||
| #' @param x traits.build database | ||
| #' @param \dots passed to print | ||
| #' | ||
| #' @return nicely printed table | ||
| #' @export | ||
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| print.austraits <- function(database, ...){ | ||
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| print.traits.build <- function(x, ...){ | ||
| # browser() | ||
| # Setting up | ||
| version <- database$build_info$version %>% as.character() | ||
| nrecords <- nrow(database$traits) | ||
| nspecies <- unique(database$traits$taxon_name) %>% length() | ||
| ntraits <- unique(database$traits$trait_name) %>% length() | ||
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| cat("This is version", | ||
| version, | ||
| "of austraits!\n", | ||
| "\nThis object contains a total of", | ||
| nrecords, "records", | ||
| "for", nspecies, "taxa and", | ||
| ntraits, "traits.\n") | ||
| version <- x$build_info$version %>% as.character() | ||
| nrecords <- nrow(x$traits) | ||
| nspecies <- unique(x$traits$taxon_name) %>% length() | ||
| ntraits <- unique(x$traits$trait_name) %>% length() | ||
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| if(package_version(version) <= '3.0.2'){ | ||
| if(package_version(version) < '5.0.0'){ | ||
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| # Setting up | ||
| database_name <- x$definitions$austraits$description | ||
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| cat("\nThis object is a 'list' with the following components:\n\n", | ||
| database$definitions$austraits$elements %>% | ||
| purrr::map(~.x[["description"]]) %>% | ||
| as.vector() %>% | ||
| sprintf("- `%s`: %s", names(.), .) %>% | ||
| paste(collapse="\n") | ||
| ) | ||
| fun <- function() { | ||
| cli::cli_h1("This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits.") | ||
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| cli::cli_h2("This object is a 'list' with the following components:") | ||
| cli::cli_div(theme = list(span.emph = list(color = "forestgreen"))) | ||
| cli::cli_ul() | ||
| cli::cli_li("{.emph traits}: A table containing measurements of traits.") | ||
| cli::cli_li("{.emph locations}: A table containing observations of location/site characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `location_name`.") | ||
| cli::cli_li("{.emph contexts}: A table containing observations of contextual characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `link_id`, and `link_vals`.") | ||
| cli::cli_li("{.emph methods}: A table containing details on methods with which data were collected, including time frame and source. Cross referencing with the `traits` table is possible using combinations of the variables `dataset_id`, `trait_name`.") | ||
| cli::cli_li("{.emph excluded_data}: A table of data that did not pass quality test and so were excluded from the master dataset.") | ||
| cli::cli_li("{.emph taxonomic_updates}: A table of all taxonomic changes implemented in the construction of AusTraits. Changes are determined by comapring against the APC (Australian Plant Census) and APNI (Australian Plant Names Index).") | ||
| cli::cli_li("{.emph taxa}: A table containing details on taxa associated with information in `traits`. This information has been sourced from the APC (Australian Plant Census) and APNI (Australian Plant Names Index) and is released under a CC-BY3 license.") | ||
| cli::cli_li("{.emph definitions}: A copy of the definitions for all tables and terms. Information included here was used to process data and generate any documentation for the study.") | ||
| cli::cli_li("{.emph contributors}: A table of people contributing to each study.") | ||
| cli::cli_li("{.emph sources}: Bibtex entries for all primary and secondary sources in the compilation.") | ||
| cli::cli_li("{.emph build_info}: A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.") | ||
| cli::cli_end() | ||
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| cli::cli_alert_info("To access a component, try using the $ e.g. austraits$traits") | ||
| } | ||
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| fun() | ||
| } else{ | ||
| cat("\nThis object is a 'list' with the following components:\n\n", | ||
| database$schema$austraits$elements %>% | ||
| purrr::map(~.x[["description"]]) %>% | ||
| as.vector() %>% | ||
| sprintf("- `%s`: %s", names(.), .) %>% | ||
| paste(collapse="\n") | ||
| ) | ||
| database_name <- x$metadata$title | ||
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| traits.build_version <- x$metadata$related_identifiers |> | ||
| convert_list_to_df2() |> | ||
| dplyr::filter(resource_type == "software") |> | ||
| dplyr::pull(version) | ||
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| fun <- function() { | ||
| cli::cli_h1("This is {version} of {database_name}!") | ||
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| cli::cli_bullets(c( | ||
| "i" = "This database is built using traits.build version {traits.build_version}", | ||
| "i" = "This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits." | ||
| ) | ||
| ) | ||
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| cli::cli_h2("This object is a 'list' with the following components:") | ||
| cli::cli_div(theme = list(span.emph = list(color = "forestgreen"))) | ||
| cli::cli_ul() | ||
| cli::cli_li("{.emph traits}: A table containing measurements of traits.") | ||
| cli::cli_li("{.emph locations}: A table containing observations of location/site characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `location_name`.") | ||
| cli::cli_li("{.emph contexts}: A table containing observations of contextual characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `link_id`, and `link_vals`.") | ||
| cli::cli_li("{.emph methods}: A table containing details on methods with which data were collected, including time frame and source. Cross referencing with the `traits` table is possible using combinations of the variables `dataset_id`, `trait_name`.") | ||
| cli::cli_li("{.emph excluded_data}: A table of data that did not pass quality test and so were excluded from the master dataset.") | ||
| cli::cli_li("{.emph taxonomic_updates}: A table of all taxonomic changes implemented in the construction of AusTraits. Changes are determined by comapring against the APC (Australian Plant Census) and APNI (Australian Plant Names Index).") | ||
| cli::cli_li("{.emph taxa}: A table containing details on taxa associated with information in `traits`. This information has been sourced from the APC (Australian Plant Census) and APNI (Australian Plant Names Index) and is released under a CC-BY3 license.") | ||
| cli::cli_li("{.emph contributors}: A table of people contributing to each study.") | ||
| cli::cli_li("{.emph sources}: Bibtex entries for all primary and secondary sources in the compilation.") | ||
| cli::cli_li("{.emph definitions}: A copy of the definitions for all tables and terms. Information included here was used to process data and generate any documentation for the study.") | ||
| cli::cli_li("{.emph schema}: A copy of the schema for all tables and terms. Information included here was used to process data and generate any documentation for the study.") | ||
| cli::cli_li("{.emph metadata}: Metadata associated with the dataset, including title, creators, license, subject, funding sources.") | ||
| cli::cli_li("{.emph build_info}: A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.") | ||
| cli::cli_end() | ||
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| cli::cli_alert_info("To access a component, try using the $ e.g. austraits$traits") | ||
| } | ||
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| fun() | ||
| } | ||
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| cat("\n\nTo access a component, try using the $ e.g. austraits$traits") | ||
| } | ||
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