Here, we read two simple dual inlet isodat files that are provided as examples in the module. isoread takes all the information directly from the binary, which makes it easy to record each step of what is happening with the data.

Installation (not run)

install.packages('devtools', depen=T) 
library(devtools)
install_github('sebkopf/isotopia')
install_github('sebkopf/isoread')

Dual inlet example 1

We start by loading the example dual inlet file (type = "DI") stored in the isoread package using the isoread command.

library(isoread)
path <- system.file(package="isoread", "extdata", "dual_inlet_example.did")
file <- isoread(path, type = "DI")

## Reading file /Library/Frameworks/R.framework/Versions/3.2/Resources/library/isoread/extdata/dual_inlet_example.did

The file variable now contains an isoread object with all the information that was extracted from the binary file and we can take a look at the data it holds.

Raw data

The raw voltages provide information on the signal stability between the sample and standard for all recorded masses. Here, we are using the k-table or kable command from the knitr package for lightly formatted table output. Instead, we can also just retrieve the raw mass data as a data frame using the get_mass_data() method, which, if needed, can be easily exported to a csv file (described in more details later).

library(knitr)
kable(file$get_mass_data())

analysis	cycle	mass28	mass29	mass32	mass33	mass34	mass38	mass40	mass44
Standard	1	2314.045	5754.992	427.1106	42.80679	593.5613	106.9198	4462.168	2578.955
Standard	2	2314.073	5752.840	427.1716	42.77963	593.6251	107.0572	4461.578	2618.840
Standard	3	2308.652	5740.336	426.2080	42.69747	592.3305	106.7632	4451.030	2631.241
Standard	4	2306.104	5735.285	425.7591	42.65157	591.6958	106.5660	4446.119	2639.536
Standard	5	2302.021	5724.794	425.0106	42.56889	590.5780	106.4758	4438.080	2640.291
Standard	6	2308.069	5739.984	426.1472	42.70022	592.1224	106.7954	4449.582	2651.911
Standard	7	2308.090	5739.708	426.1624	42.69850	592.1496	106.8122	4449.758	2655.171
Standard	8	2308.144	5739.896	426.1803	42.70228	592.2626	106.8325	4449.918	2658.405
Standard	9	2305.838	5734.350	425.7644	42.66567	591.6759	106.8660	4445.576	2658.389
Standard	10	2306.315	5735.724	425.8567	42.66567	591.7188	106.7118	4446.588	2660.560
Standard	11	2307.218	5737.932	426.0261	42.68440	592.0723	106.8456	4448.227	2662.468
Standard	12	2308.210	5740.555	426.2206	42.69283	592.3284	106.8522	4450.332	2664.312
Standard	13	2303.953	5729.707	425.4309	42.63369	591.1562	106.6712	4441.975	2661.175
Standard	14	2305.753	5734.431	425.7635	42.65260	591.6582	106.5983	4445.466	2662.850
Standard	15	2306.300	5735.799	425.8665	42.67357	591.8391	106.8433	4446.617	2664.359
Sample	1	2301.973	5724.794	424.8054	42.56047	590.4190	106.4125	4439.297	2526.243
Sample	2	2298.603	5716.512	424.2802	42.50254	589.6891	106.2093	4431.861	2591.896
Sample	3	2294.369	5703.757	423.5372	42.43292	588.5650	106.1346	4423.353	2613.448
Sample	4	2292.602	5701.618	423.2413	42.39906	588.2251	106.1388	4420.078	2625.208
Sample	5	2289.086	5692.840	422.6165	42.33993	587.2422	105.9075	4413.272	2629.914
Sample	6	2288.389	5691.215	422.4965	42.33408	587.1575	106.0384	4411.821	2633.810
Sample	7	2292.898	5702.283	423.3390	42.41419	588.3569	106.2021	4420.228	2642.814
Sample	8	2295.388	5708.688	423.8095	42.45699	588.9352	106.3133	4425.160	2648.109
Sample	9	2292.384	5701.034	423.2620	42.40164	588.1781	106.1250	4419.340	2647.268
Sample	10	2292.080	5700.124	423.2144	42.43034	588.1980	106.1328	4418.956	2649.154
Sample	11	2291.922	5700.017	423.1893	42.39218	588.0809	106.2410	4418.806	2649.913
Sample	12	2290.592	5696.548	422.9509	42.37912	587.7399	106.0916	4416.191	2649.625
Sample	13	2292.622	5701.611	423.3327	42.39855	588.3370	106.2643	4420.198	2653.452
Sample	14	2292.715	5701.894	423.3452	42.41316	588.3831	106.1967	4420.379	2653.427
Sample	15	2287.184	5688.116	422.3200	42.28922	586.8710	105.8699	4409.457	2647.124
Standard	0	2319.591	5768.939	427.8949	42.86850	594.7283	106.1920	4474.801	2419.137

Visualization

For convenience, isoread also implements several plotting functions so we can quickly visualize the raw data. The make_ggplot() method generates a ggplot2 plot object which can be printed (or saved as a PDF) as is, or modified using all functionality provided by the ggplot2 - here for example, with the addition of a figure caption.

file$make_ggplot() + labs(title = "Raw mass voltages plot")

ggsave("my_file.pdf", width = 10, height = 7)

Or only a few masses

The make_ggplot() method can take additional parameters to plot only specific masses of interest.

file$make_ggplot(masses = c("mass32", "mass34"))

Processed data

Whole table

In theory, the data reduction could be performed ab initio from the raw voltage counts, but in practice it is often easier to start with the precomputed processed data from Isodat and pipe those information to the standard data processing procedure that comes traditionally after this step. That’s why isoread attempts to read the whole data table from the binary file as well, although this is the step that often requires some fine tuning to make sure the processor really captures all relevant data columns in the right format (see clumped CO2 isodat file example below).

kable(file$get_data_table())

cycle	d 32O2/28N2	d 32O2/29N2	d 40Ar/28N2	d 32O2/40Ar	d 44CO2/28N2	d 44CO2/40Ar
1	0.0980921	0.1421863	-0.1250340	0.2230465	17.361331	17.481194
2	-0.0190026	-0.1986415	-0.0477705	0.0287593	4.011599	4.059004
3	-0.0368937	0.0652816	-0.0425848	0.0056908	2.953237	2.995911
4	-0.0340016	-0.1304614	-0.0021110	-0.0318906	2.556024	2.558140
5	-0.0078191	-0.0158211	0.0104945	-0.0183139	2.728998	2.718456
6	-0.0168540	-0.0604423	0.0228565	-0.0397103	2.601003	2.578072
7	-0.0301186	-0.0634252	-0.0394053	0.0092870	2.551532	2.591048
8	-0.0272254	-0.1218628	-0.0311020	0.0038767	2.260614	2.291790
9	-0.0310329	-0.0727141	-0.0551547	0.0241232	2.158959	2.214241
10	-0.0274719	-0.0092828	-0.0317104	0.0042385	2.202047	2.233831
11	-0.0259919	-0.0447872	0.0042289	-0.0302208	2.090056	2.085817
12	-0.0254705	-0.0056133	-0.0173751	-0.0080958	2.268057	2.285474
13	-0.0182514	-0.0099826	-0.0010664	-0.0171851	2.360382	2.361445
14	-0.0252622	-0.0271131	0.0135928	-0.0388544	2.051568	2.037947
15	-0.0372995	-0.0128886	-0.0581892	0.0208909	1.999905	2.058216

Summary

Or to summarize the information quickly, use the parameter summarize = TRUE.

kable(file$get_data_table(summarize = TRUE))

Variable	Mean	Std. Devi.	Std. Error.
d 32O2/28N2	-0.0176402	0.0329837	0.0085163
d 32O2/29N2	-0.0377045	0.0805434	0.0207962
d 40Ar/28N2	-0.0266887	0.0379295	0.0097934
d 32O2/40Ar	0.0090428	0.0633772	0.0163639
d 44CO2/28N2	3.4770208	3.8734844	1.0001294
d 44CO2/40Ar	3.5033723	3.8997987	1.0069237

Or to display only a few of these

kable(file$get_data_table(select = c("d 32O2/28N2", "d 44CO2/40Ar"), sum = T))

Variable	Mean	Std. Devi.	Std. Error.
d 32O2/28N2	-0.0176402	0.0329837	0.0085163
d 44CO2/40Ar	3.5033723	3.8997987	1.0069237

File information

Since isoread has access to the original raw binary data file, it can extract other parameters stored with the data. These are the ones currently retrieved for dual inlet files:

kable(file$get_info())

Property	Value
File location	/Library/Frameworks/R.framework/Versions/3.2/Resources/library/isoread/extdata/dual_inlet_example.did
Date	2016-05-30 21:16:05
Info_Peak	Peak Center found at [58910]
Info_Background	Background: 1.75 mV,4.88 mV,2.34 mV,-2.04 mV,2.61 mV,22.83 mV,2.93 mV,242.96 mV (Bender-Lab-User)
Row	1
Peak Center	1
Background	1
Pressadjust	0
Identifier 1	Stability
Identifier 2	ON
Analysis	1481
Comment	Test System
Preparation
Method	dual inlet Paul.met

Data export

Lastly, isoread provides a convenience method (export_data()) to export all of these data to comma-separated-value (csv) files.

file$export_data(file = "my_file_raw.csv", type = "raw")

## Creating raw export for dual_inlet_example.did ...

## raw data exported to my_file_raw.csv

file$export_data(file = "my_file_table.csv", type = "table")

## Creating table export for dual_inlet_example.did ...

## table data exported to my_file_table.csv

file$export_data(file = "my_file_summary.csv", type = "summary")

## Creating summary export for dual_inlet_example.did ...

## summary data exported to my_file_summary.csv

file$export_data(file = "my_file_info.csv", type = "info")

## Creating info export for dual_inlet_example.did ...

## info data exported to my_file_info.csv

Extensions

For reading entire folders of isodat files, you can use the isoread_folder function which returns a vector of all contained isodat files as isoread objects. This whole group of files can be e.g. exported at once using the export_data function. For additional information on functionality provided by the isoread package, please pull up the package help via help(package="isoread").

For all bug reports and feature requests, please use the Issue Tracker on the project’s GitHub page.

Example 2: Clumped carbonate isotope data

The second example is a slightly more specialized dual inlet analysis for clumped CO2 measurements. Here, the specialized implementation of the “CO2_CLUMPED” data type ensures direct acess to all the relevant data summary values in addition to the raw voltage readings of the dual inlet data.

library(isoread)
file <- isoread(system.file("extdata", "dual_inlet_clumped_carbonate.did", package="isoread"), type = "CO2_CLUMPED")

## Reading file /Library/Frameworks/R.framework/Versions/3.2/Resources/library/isoread/extdata/dual_inlet_clumped_carbonate.did

Raw data

library(knitr)
kable(file$get_mass_data())

analysis	cycle	mass44	mass45	mass46	mass47	mass48	mass49
Standard	1	15941.14	18995.66	21954.19	2512.345	29.80048	-180.9752
Standard	2	15933.54	18986.64	21943.58	2511.280	29.81818	-180.7748
Standard	3	15916.58	18966.34	21919.97	2508.497	29.78074	-180.4583
Standard	4	15901.62	18948.60	21899.17	2506.104	29.76304	-180.2311
Standard	5	15896.00	18941.97	21891.49	2505.600	29.75818	-180.3095
Standard	6	15884.63	18928.51	21876.19	2503.555	29.72923	-180.2013
Standard	7	15875.89	18918.12	21863.96	2502.444	29.69513	-180.0340
Sample	1	15955.18	19122.71	22237.99	2559.245	31.09436	-181.2460
Sample	2	15945.64	19111.16	22224.65	2557.857	31.09153	-180.9976
Sample	3	15925.90	19087.57	22197.05	2554.388	31.06846	-180.7002
Sample	4	15911.10	19069.70	22176.18	2552.023	31.01948	-180.4653
Sample	5	15909.83	19068.24	22174.62	2551.665	31.02819	-180.2734
Sample	6	15912.56	19071.57	22178.48	2552.281	31.04205	-180.5112
Sample	7	15914.03	19073.47	22180.52	2552.800	31.05845	-180.3734
Standard	0	15946.42	19001.94	21960.62	2513.280	29.78742	-181.2712

file$make_ggplot()

Or only a few masses

file$make_ggplot(masses = c("mass44", "mass47"))

Processed data

Whole table

The entire table of processed data.

kable(file$get_data_table())

cycle	d 45CO2/44CO2	d 46CO2/44CO2	d13C	d18O	d17O	at% 13C	at% 18O
1	3.328777	37.33065	2.192992	37.36646	6.202321	1.108056	0.2075809
2	3.320955	37.31180	2.185295	37.34760	6.192886	1.108048	0.2075772
3	3.326338	37.31751	2.190857	37.35331	6.195743	1.108054	0.2075783
4	3.320030	37.31721	2.184106	37.35302	6.195597	1.108047	0.2075782
5	3.318741	37.32977	2.182264	37.36560	6.201893	1.108045	0.2075808
6	3.317755	37.32285	2.181460	37.35868	6.198427	1.108044	0.2075794
7	3.321752	37.31837	2.185909	37.35418	6.196176	1.108049	0.2075785

Summary

kable(file$get_data_table(summarize = TRUE))

Variable	Mean	Std. Devi.	Std. Error.
d 45CO2/44CO2	3.322050	0.0040499	0.0015307
d 46CO2/44CO2	37.321165	0.0069678	0.0026336
d13C	2.186126	0.0043016	0.0016259
d18O	37.356979	0.0069742	0.0026360
d17O	6.197578	0.0034906	0.0013193
at% 13C	1.108049	0.0000047	0.0000018
at% 18O	0.207579	0.0000014	0.0000005

Or only a few of these

kable(file$get_data_table(select = c("d13C", "d18O"), sum = T))

Variable	Mean	Std. Devi.	Std. Error.
d13C	2.186126	0.0043016	0.0016259
d18O	37.356979	0.0069742	0.0026360

Other info

And whatever other information was pulled out of the file.

kable(file$get_info())

Property	Value
File location	/Library/Frameworks/R.framework/Versions/3.2/Resources/library/isoread/extdata/dual_inlet_clumped_carbonate.did
Date	2016-05-30 21:16:05
Info_Peak	Peak Center found at [61032]
Info_Background	Background: 8.87 mV,11.31 mV,12.98 mV,6.40 mV,1.90 mV,5.88 mV (old253)
Info_PressAdjust	PressAdjust: L: 15972.5 R: 15971.6 ( Manual Adjustment )
Line	158
Peak Center	1
Pressadjust	1
Background	1
Identifier 1	CIT Carrara
Identifier 2	13
Analysis	49077
Comment
Preparation
Post Script
Method	CO2_multiply_16V.met

Dual Inlet Intro

Sebastian Kopf

2016-05-30

Installation (not run)

Dual inlet example 1

Raw data

Visualization

Or only a few masses

Processed data

Whole table

Summary

Or to display only a few of these

File information

Data export

Extensions

Example 2: Clumped carbonate isotope data

Raw data

Or only a few masses

Processed data

Whole table

Summary

Or only a few of these

Other info