powdR (version 1.1.0)

afps: Automated full pattern summation

Description

afps returns estimates of phase concentrations using automated full pattern summation of X-ray powder diffraction data. It is designed for high-throughput cases involving mineral quantification from large reference libraries. For more details see ?afps.powdRlib.

Usage

afps(lib, ...)

Arguments

lib

A powdRlib object representing the reference library. Created using the powdRlib constructor function.

...

Other parameters passed to methods e.g. afps.powdRlib

Value

a list with components:

tth

a vector of the 2theta scale of the fitted data

fitted

a vector of the fitted XRPD pattern

measured

a vector of the original XRPD measurement (aligned)

residuals

a vector of the residuals (fitted vs measured)

phases

a dataframe of the phases used to produce the fitted pattern

phases_grouped

the phases dataframe grouped by phase_name and summed

rwp

the Rwp of the fitted vs measured pattern

weighted_pure_patterns

a dataframe of reference patterns used to produce the fitted pattern. All patterns have been weighted according to the coefficients used in the fit

coefficients

a named vector of coefficients used to produce the fitted pattern

inputs

a list of input arguments used in the function call

Details

Applies automated full pattern summation to an XRPD measurement to quantify phase concentrations. Requires a powdRlib library of reference patterns with reference intensity ratios in order to derive mineral concentrations.

References

Chipera, S.J., Bish, D.L., 2013. Fitting Full X-Ray Diffraction Patterns for Quantitative Analysis: A Method for Readily Quantifying Crystalline and Disordered Phases. Adv. Mater. Phys. Chem. 03, 47-53. doi:10.4236/ampc.2013.31A007

Chipera, S.J., Bish, D.L., 2002. FULLPAT: A full-pattern quantitative analysis program for X-ray powder diffraction using measured and calculated patterns. J. Appl. Crystallogr. 35, 744-749. doi:10.1107/S0021889802017405

Eberl, D.D., 2003. User's guide to RockJock - A program for determining quantitative mineralogy from powder X-ray diffraction data. Boulder, CA.

Examples

# NOT RUN {
#Load the minerals library
data(minerals)

# Load the soils data
data(soils)

# }
# NOT RUN {
afps_sand <-  afps(lib = minerals,
                 smpl = soils$sandstone,
                 std = "QUA.2",
                 align = 0.2,
                 lod = 0.2,
                 amorphous = "ORG",
                 amorphous_lod = 1)

afps_lime <- afps(lib = minerals,
                smpl = soils$limestone,
                std = "QUA.2",
                align = 0.2,
                lod = 0.2,
                amorphous = "ORG",
                amorphous_lod = 1)

afps_granite <- afps(lib = minerals,
                   smpl = soils$granite,
                   std = "QUA.2",
                   align = 0.2,
                   lod = 0.2,
                   amorphous = "ORG",
                   amorphous_lod = 1)

#Alternatively run all 3 at once using lapply

afps_soils <- lapply(soils, afps,
                     lib = minerals,
                     std = "QUA.2",
                     align = 0.2,
                     lod = 0.2,
                     amorphous = "ORG",
                     amorphous_lod = 1)

#Automated quantification using the rockjock library

data(rockjock)
data(rockjock_mixtures)

#This takes a few minutes to run
rockjock_a1 <- afps(lib = rockjock,
                    smpl = rockjock_mixtures$Mix1,
                    std = "CORUNDUM",
                    align = 0.3,
                    lod = 1)

#Quantifying the same sample but defining the internal standard
#concentration (also takes a few minutes to run):
rockjock_a1s <- afps(lib = rockjock,
                     smpl = rockjock_mixtures$Mix1,
                     std = "CORUNDUM",
                     std_conc = 20,
                     align = 0.3,
                     lod = 1)

# }