Reading isotope files | ir_find_isofiles() * | ir_read_isofiles() * | bonus combine collections with c() | bonus ir_save_isofiles() / ir_load_isofiles() | Aggregating data | ir_aggregate_isofiles() * | bonus intensity units | bonus ir_get_aggregator() | bonus ir_register_aggregator() | bonus ir_get_problems() / ir_show_problems() | Accessing the data | ir_get_data() | shortcuts ir_get_metadata() / ir_get_traces() / ... | bonus ir_get_vendor_data_table() | ir_filter_metadata() / ir_mutate_metadata() / ir_join_metadata() | bonus ir_filter_for_continuous_flow() / ir_filter_for_dual_inlet() / ir_filter_for_scans() | bonus ir_save_aggregated_data() / ir_load_aggregated_data() | Calculating ratios | ir_calculate_ratios() | bonus base mass, additive offsets, and normalization | Visualizing data | ir_plot_continuous_flow() | bonus ir_generate_traces_tibble() / ir_generate_cycles_tibble() / ir_generate_scans_tibble() | ir_plot_dual_inlet() | ir_plot_scans() | Exporting data | ir_export_to_excel() | Package options | bonus ir_options() / ir_get_option()
Package: isoreader2 0.6.1
Sebastian Kopf
isoreader2: Read Stable Isotope Data Files
Interface to the raw data and metadata stored in the file formats commonly encountered in scientific disciplines that make use of stable isotopes. Supports Isodat (.dxf, .cf, .did, .caf, .scn), IonOS (.iarc), LyticOS (.larc), Callisto (.bch), and Qtegra (.imexp) file formats. Provides a consistent data structure together with tools to aggregate, convert signal units, filter, and visualize the extracted data. The approach is described in Kopf et al. (2021) <doi:10.21105/joss.02878>.
Authors:
isoreader2_0.6.1.tar.gz
isoreader2_0.6.1.tar.gz(r-4.7-any)isoreader2_0.6.1.tar.gz(r-4.6-any)
isoreader2_0.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
isoreader2/json (API)
| # Install 'isoreader2' in R: |
| install.packages('isoreader2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/isoverse/isoreader2/issues
Pkgdown/docs site:https://isoreader2.isoverse.org
Last updated from:aa7fb1a05c. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 186 | ||
| source / vignettes | OK | 237 | ||
| linux-release-x86_64 | OK | 187 | ||
| wasm-release | OK | 130 |
Exports:autoir_add_to_aggregatorir_aggregate_isofilesir_calculate_ratiosir_check_isoextractir_check_isosolfsir_convert_intensityir_copy_examplesir_default_themeir_examples_folderir_export_to_excelir_extract_isofilesir_filter_for_continuous_flowir_filter_for_dual_inletir_filter_for_scansir_filter_metadatair_find_continuous_flowir_find_dual_inletir_find_isofilesir_find_scansir_generate_cycles_tibbleir_generate_scans_tibbleir_generate_traces_tibbleir_get_aggregatorir_get_cyclesir_get_datair_get_isoextract_versionir_get_metadatair_get_optionir_get_optionsir_get_problemsir_get_resistorsir_get_scansir_get_supported_file_typesir_get_tracesir_get_vendor_data_tableir_join_metadatair_load_aggregated_datair_load_isofilesir_mutate_metadatair_optionsir_plot_continuous_flowir_plot_dual_inletir_plot_scansir_read_isofilesir_register_aggregatorir_save_aggregated_datair_save_isofilesir_show_problemsir_start_aggregator
Dependencies:bitbit64clicliprcpp11crayondplyrevaluatefansifarvergenericsggplot2gluegtablehighrhmsisobandknitrlabelinglifecyclemagrittrpillarpkgconfigprettyunitsprocessxprogresspspurrrR6RColorBrewerRcppRcppSimdJsonreadrrlangS7scalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| isoreader2: Read Stable Isotope Data Files | isoreader2-package isoreader2 |
| Automatic / default behavior | auto |
| Combine aggregated isofile data | c.ir_aggregated_data |
| Combine isofiles | c.ir_isofiles |
| Aggregate data from isofiles | ir_aggregate_isofiles |
| Calculate isotope ratios | ir_calculate_ratios |
| Check for the isoextract executables | ir_check_isoextract ir_check_isosolfs |
| Convert intensity between units | ir_convert_intensity |
| Default isoreader2 plotting theme | ir_default_theme |
| Bundled example files | ir_copy_examples ir_examples_folder |
| Export data to Excel | ir_export_to_excel |
| run the isoextract executable on a vector of file paths this is usually not called directly | ir_extract_isofiles ir_get_isoextract_version |
| Filter isofiles by measurement type | ir_filter_for ir_filter_for_continuous_flow ir_filter_for_dual_inlet ir_filter_for_scans |
| Find isodat files | ir_find_continuous_flow ir_find_dual_inlet ir_find_isofiles ir_find_scans |
| Generate the tibble used by the plotting functions | ir_generate_cycles_tibble ir_generate_scans_tibble ir_generate_tibble ir_generate_traces_tibble |
| Get data frame from aggregated data | ir_get_cycles ir_get_data ir_get_metadata ir_get_resistors ir_get_scans ir_get_traces ir_get_vendor_data_table |
| Retrieve parsing problems | ir_get_problems ir_show_problems |
| Get supported file types | ir_get_supported_file_types |
| Save and load isofiles | ir_isofiles_storage ir_load_isofiles ir_save_isofiles |
| Filter, mutate, or join the metadata of isofiles | ir_filter_metadata ir_join_metadata ir_metadata ir_mutate_metadata |
| Package options | get_pkg_options ir_get_option ir_get_options ir_options |
| Plot continuous flow data | ir_plot_continuous_flow |
| Plot dual inlet cycle data | ir_plot_dual_inlet |
| Plot scan data | ir_plot_scans |
| Read isotope data files | ir_read_isofiles |
| Dynamic data aggregator | ir_add_to_aggregator ir_get_aggregator ir_register_aggregator ir_start_aggregator |
| Save and load aggregated isofile data | ir_load_aggregated_data ir_save_aggregated_data ir_storage |
