fps: Full pattern summation

Description Usage Arguments Details Value References Examples

View source: R/fps.R

Description

fps returns estimates of phase concentrations using full pattern summation of X-ray powder diffraction data. For more details see ?fps.powdRlib.

Usage

1
fps(lib, ...)

Arguments

lib

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

...

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

Details

Applies full pattern summation (Chipera & Bish, 2002, 2013; Eberl, 2003) 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.

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

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

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#Load the minerals library
data(minerals)

# Load the soils data
data(soils)

#Since the reference library is relatively small,
#the whole library can be used at once to get an
#estimate of the phases within each sample.
## Not run: 
fps_sand <-  fps(lib = minerals,
                 smpl = soils$sandstone,
                 refs = minerals$phases$phase_id,
                 std = "QUA.1",
                 align = 0.2)

fps_lime <- fps(lib = minerals,
                smpl = soils$limestone,
                refs = minerals$phases$phase_id,
                std = "QUA.1",
                align = 0.2)

fps_granite <- fps(lib = minerals,
                   smpl = soils$granite,
                   refs = minerals$phases$phase_id,
                   std = "QUA.1",
                   align = 0.2)

#Alternatively run all 3 at once using lapply

fps_soils <- lapply(soils, fps,
                    lib = minerals,
                    std = "QUA.2",
                    refs = minerals$phases$phase_id,
                    align = 0.2)

#Using the rockjock library:

data(rockjock)
data(rockjock_mixtures)

rockjock_1 <- fps(lib = rockjock,
                  smpl = rockjock_mixtures$Mix1,
                  refs = c("ORDERED_MICROCLINE",
                           "LABRADORITE",
                           "KAOLINITE_DRY_BRANCH",
                           "MONTMORILLONITE_WYO",
                           "ILLITE_1M_RM30",
                           "CORUNDUM"),
                  std = "CORUNDUM",
                  align = 0.3)

#Alternatively you can specify the internal standard
#concentration if known:
rockjock_1s <- fps(lib = rockjock,
                 smpl = rockjock_mixtures$Mix1,
                 refs = c("ORDERED_MICROCLINE",
                          "LABRADORITE",
                          "KAOLINITE_DRY_BRANCH",
                          "MONTMORILLONITE_WYO",
                          "ILLITE_1M_RM30",
                          "CORUNDUM"),
                 std = "CORUNDUM",
                 std_conc = 20,
                 align = 0.3)


## End(Not run)

benmbutler/powdR documentation built on Sept. 16, 2020, 5:03 a.m.