Isoreader supports several continuous flow IRMS data formats. This vignette shows some of the functionality for continuous flow files. For additional information on operations more generally (caching, combining read files, data export, etc.), please consult the operations vignette. For details on downstream data processing and visualization, see the isoprocessor package.
Reading continuous flow files is as simple as passing one or multiple file or folder paths to the
iso_read_continuous_flow() function. If folders are provided, any files that have a recognized continuous flow file extensions within those folders will be processed (e.g. all
.iarc). Here we read several files that are bundled with the package as examples (and whose paths can be retrieved using the
iso_get_reader_example() function). Note that some of the files (.cf, .dxf) are individual analysis files whereas others (.iarc) are collections of several files.
# read a few of the continuous flow examples iso_files <- iso_read_continuous_flow( iso_get_reader_example("continuous_flow_example.cf"), iso_get_reader_example("continuous_flow_example.iarc"), iso_get_reader_example("continuous_flow_example.dxf"), iso_get_reader_example("linearity_example.dxf") ) #> Info: preparing to read 4 data files (all will be cached)... #> Info: reading file 'continuous_flow_example.cf' with '.cf' reader #> Info: reading file 'continuous_flow_example.iarc' with '.iarc' reader #> unpacking isoprime archieve file... #> found 1 processing list(s) in .iarc: 'ProcessingList_1' #> found 2 method(s) in .iarc: 'Method_320', 'Method_77' #> found 4 sample(s) in .iarc #> searching processing list 'ProcessingList_1' for gas configurati... #> found configurations for 'CO', 'SO2', 'CO2', 'H2', 'N2' #> processing sample '6632_WSL-2 wood' (IRMS data '133.hdf5', '135.... #> processing sample '6605_USGS41' (IRMS data '40.hdf5', '43.hdf5') #> processing sample '6617_IAEA600' (IRMS data '80.hdf5', '82.hdf5') #> processing sample '6630_GlutamicAcid04' (IRMS data '124.hdf5', '... #> Info: reading file 'continuous_flow_example.dxf' with '.dxf' reader #> Info: reading file 'linearity_example.dxf' with '.dxf' reader #> Info: finished reading 4 files in 8.81 secs
iso_files variable now contains a set of isoreader objects, one for each file. Take a look at what information was retrieved from the files using the
In case there was any trouble with reading any of the files, the following functions provide an overview summary as well as details of all errors and warnings, respectively. The examples here contain no errors but if you run into any unexpected file read problems, please file a bug report in the isoreader issue tracker.
Detailed file information can be aggregated for all isofiles using the
iso_get_file_info() function which supports the full select syntax of the dplyr package to specify which columns are of interest (by default, all file information is retrieved). Additionally, file information from different file formats can be renamed to the same column name for easy of downstream processing. The following provides a few examples for how this can be used (the names of the interesting info columns may vary between different file formats):
# select file information iso_files %>% iso_get_file_info( select = c( # rename sample id columns from the different file types to a new ID column ID = `Identifier 1`, ID = `Name`, # select columns without renaming Analysis, `Peak Center`, `H3 Factor`, # select the time stamp and rename it to `Date & Time` `Date & Time` = file_datetime ) ) %>% rmarkdown::paged_table() #> Info: aggregating file info from 7 data file(s), selecting info columns 'c(ID = `Identifier 1`, ID = Name, Analysis, `Peak Center`, `H3 Factor`, #> `Date & Time` = file_datetime)'
Rather than retrieving specific file info columns using the above example of
iso_get_file_info(select = ...), these information can also be modified across an entire collection of isofiles using the
iso_rename_file_info() functions. For example, the above example could be similarly achieved with the following use of
# select + rename specific file info columns iso_files2 <- iso_files %>% iso_select_file_info( ID = `Identifier 1`, ID = `Name`, Analysis, `Peak Center`, `H3 Factor`, `Date & Time` = file_datetime ) #> Info: keeping 7 file info column(s) wherever they exist across 7 isofile(s): #> - 'Analysis' in 3 files #> - 'file_datetime' (renamed to 'Date & Time') in 7 files #> - 'file_id' in 7 files #> - 'H3 Factor' in 3 files #> - 'Identifier 1' (renamed to 'ID') in 3 files #> - 'Name' (renamed to 'ID') in 4 files #> - 'Peak Center' in 3 files # fetch all file info iso_files2 %>% iso_get_file_info() %>% rmarkdown::paged_table() #> Info: aggregating file info from 7 data file(s)
Any collection of isofiles can also be filtered based on the available file information using the function
iso_filter_files. This function can operate on any column available in the file information and supports full dplyr syntax.
The file information in any collection of isofiles can also be mutated using the function
iso_mutate_file_info. This function can introduce new columns and operate on any existing columns available in the file information (even if it does not exist in all files) and supports full dplyr syntax.
iso_files3 <- iso_files2 %>% iso_mutate_file_info( # update existing column ID = paste("ID:", ID), # introduce new column `Run since 2015?` = `Date & Time` > "2015-01-01" ) #> Info: mutating file info for 7 data file(s) iso_files3 %>% iso_get_file_info() %>% rmarkdown::paged_table() #> Info: aggregating file info from 7 data file(s)
Additionally, a wide range of new file information can be added in the form of a data frame with any number of columns (usually read from a comma-separated-value/csv file or an Excel/xlsx file) using the function
iso_add_file_info and specifying which existing file information should be used to merge in the new information. It is similar to dplyr’s left_join but with additional safety checks and the possibility to join the new information sequentially as illustrated below.
# this kind of information data frame is frequently read in from a csv or xlsx file new_info <- dplyr::bind_rows( # new information based on new vs. old samples dplyr::tribble( ~file_id, ~`Run since 2015?`, ~process, ~info, NA, TRUE, "yes", "new runs", NA, FALSE, "yes", "old runs" ), # new information for a single specific file dplyr::tribble( ~file_id, ~process, ~note, "6617_IAEA600", "no", "did not inject properly" ) ) new_info %>% rmarkdown::paged_table()
# adding it to the isofiles iso_files3 %>% iso_add_file_info(new_info, by1 = "Run since 2015?", by2 = "file_id") %>% iso_get_file_info(select = names(new_info)) %>% rmarkdown::paged_table() #> Info: adding new file information ('process', 'info', 'note') to 7 data file(s), joining by 'Run since 2015?' then 'file_id'... #> - 'Run since 2015?' join: 2/2 new info rows matched 7/7 data files - 1 of these was/were also matched by subsequent joins which took precedence #> - 'file_id' join: 1/1 new info rows matched 1/7 data files #> Info: aggregating file info from 7 data file(s), selecting info columns 'names(new_info)'
Most file information is initially read as text to avoid cumbersome specifications during the read process and compatibility issues between different IRMS file formats. However, many file info columns are not easily processed as text. The isoreader package therefore provides several parsing and data extraction functions to facilitate processing the text-based data (some via functionality implemented by the readr package). See code block below for examples. For a complete overview, see the
# use parsing and extraction in iso_mutate_file_info iso_files2 %>% iso_mutate_file_info( # change type of Peak Center to logical `Peak Center` = parse_logical(`Peak Center`), # retrieve first word of file_id file_id_1st = extract_word(file_id), # retrieve second word of ID column file_id_2nd = extract_word(file_id, 2), # retrieve file extension from the file_id using regular expression name = extract_substring(ID, "(\\w+)-?(.*)?", capture_bracket = 1) ) %>% iso_get_file_info(select = c(matches("file_id"), ID, name, `Peak Center`)) %>% rmarkdown::paged_table() #> Info: mutating file info for 7 data file(s) #> Info: aggregating file info from 7 data file(s), selecting info columns 'c(matches("file_id"), ID, name, `Peak Center`)'
# use iso_parse_file_info for simplified parsing of column data types iso_files2 %>% iso_parse_file_info( integer = Analysis, number = `H3 Factor`, logical = `Peak Center` ) %>% iso_get_file_info() %>% rmarkdown::paged_table() #> Info: parsing 3 file info columns for 7 data file(s): #> - to integer: 'Analysis' #> - to logical: 'Peak Center' #> - to number: 'H3 Factor' #> Warning: 1 parsing failure. #> row col expected actual #> 7 -- an integer MAT25391411 #> Info: aggregating file info from 7 data file(s)
Additionally, some IRMS data files contain resistor information that are useful for downstream calculations (see e.g. section on signal conversion later in this vignette):
As well as isotopic reference values for the different gases:
The raw data read from the IRMS files can be retrieved similarly using the
iso_get_raw_data() function. Most data aggregation functions also allow for inclusion of file information using the
include_file_info parameter, which functions identically to the
select parameter of the
iso_get_file_info function discussed earlier.
# get specific raw data and add some file information iso_files %>% iso_get_raw_data( # select just time and the m/z 2 and 3 ions select = c(time.s, v2.mV, v3.mV), # include the Analysis number fron the file info and rename it to 'run' include_file_info = c(run = Analysis) ) %>% # look at first few records only head(n=10) %>% rmarkdown::paged_table() #> Info: aggregating raw data from 7 data file(s), selecting data columns 'c(time.s, v2.mV, v3.mV)', including file info 'c(run = Analysis)'
The isoreader package is intended to make raw stable isotope data easily accessible. However, as with most analytical data, there is significant downstream processing required to turn these raw intensity chromatograms into peak-specific, properly referenced isotopic measurements. This and similar functionality as well as data visualization is part of the isoprocessor package which takes isotopic data through the various corrections in a transparent, efficient and reproducible manner.
That said, most vendor software also performs some of these calculations and it can be useful to be able to compare new data reduction procecures against those implemented in the vendor software. For this purpose, isoreader retrieves vendor computed data tables whenver possible, as illustrated below.
As with most data retrieval funtions, the
iso_get_vendor_data_table() function also allows specific column selection (by default, all columns are selected) and easy addition of file information via the
include_file_info parameter (by default, none is included).
# get specific parts and add some file information iso_files %>% iso_get_vendor_data_table( # select peak number, ret. time, overall intensity and all H delta columns select = c(Nr., Rt, area = `rIntensity All`, matches("^d \\d+H")), # include the Analysis number fron the file info and rename it to 'run' include_file_info = c(run = Analysis) ) %>% rmarkdown::paged_table() #> Info: aggregating vendor data table without units from 7 data file(s), including file info 'c(run = Analysis)'
# the data table also provides units if included in the original data file # caution however: it may require changes to the `select` parameter iso_files %>% iso_get_vendor_data_table( with_units = TRUE, # select peak number, ret. time, overall intensity and all H delta columns select = c(Nr., matches("^Rt"), matches("rIntensity All"), matches("^d \\d+H")), # include the Analysis number fron the file info and rename it to 'run' include_file_info = c(run = Analysis) ) %>% rmarkdown::paged_table() #> Info: aggregating vendor data table with units from 7 data file(s), including file info 'c(run = Analysis)'
For users familiar with the nested data frames from the tidyverse (particularly tidyr’s
unnest), there is an easy way to retrieve all data from the iso file objects in a single nested data frame. Use the
include_vendor_data_table parameters to specify which columns to include. By default, everything is included:
Saving entire collections of isofiles for retrieval at a later point is easily done using the
iso_save function which stores collections or individual isoreader file objects in the efficient R data storage format
.rds (if not specified, the extension
.cf.rds will be automatically appended). These saved collections can be convientiently read back using the same
iso_read_continuous_flow command used for raw data files.
# export to R data archive iso_files %>% iso_save("iso_files_export.cf.rds") #> Info: exporting data from 7 iso_files into R Data Storage 'iso_files_export.cf.rds' # read back the exported R data archive iso_files <- iso_read_continuous_flow("iso_files_export.cf.rds") #> Info: preparing to read 1 data files (all will be cached)... #> Info: reading file 'iso_files_export.cf.rds' with '.cf.rds' reader #> Info: loaded data for 7 data files from R Data Storage - checking load... #> Info: finished reading 1 files in 0.09 secs iso_files %>% iso_get_data_summary() %>% rmarkdown::paged_table() #> Info: aggregating data summary from 7 data file(s)
At the moment, isoreader supports export of all data to R Data archives, Excel, and the Feather file format (a Python/R cross-over format). Note that both export methods have similar syntax and append the appropriate file extension for each type of export file (
# export to excel iso_files %>% iso_export_to_excel("iso_files_export") #> Info: exporting data from 7 iso_files into Excel 'iso_files_export.cf.xlsx' #> Note: zip::zip() is deprecated, please use zip::zipr() instead # data sheets available in the exported data file: readxl::excel_sheets("iso_files_export.cf.xlsx") #>  "raw data" "file info" "method info" #>  "vendor data table" "problems"
# export to feather iso_files %>% iso_export_to_feather("iso_files_export") #> Info: exporting data from 7 iso_files into .cf.feather files at 'iso_files_export' # exported feather files list.files(pattern = ".cf.feather") #>  "iso_files_export_file_info.cf.feather" #>  "iso_files_export_method_info-resistors.cf.feather" #>  "iso_files_export_method_info-standards.cf.feather" #>  "iso_files_export_problems.cf.feather" #>  "iso_files_export_raw_data.cf.feather" #>  "iso_files_export_vendor_data_table.cf.feather"