Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> devel diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 9b720e04..69792ba5 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,11 +17,7 @@ @@ -766,11 +762,7 @@License
-<<<<<<< HEAD
-
diff --git a/docs/articles/abfit-baseline-opts.html b/docs/articles/abfit-baseline-opts.html
index 224cba62..e75bd1cd 100644
--- a/docs/articles/abfit-baseline-opts.html
+++ b/docs/articles/abfit-baseline-opts.html
@@ -38,11 +38,7 @@
@@ -237,11 +233,7 @@ Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> develCustom analyses
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png
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diff --git a/docs/articles/index.html b/docs/articles/index.html
index 2b1f1a37..aad69369 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,11 +17,7 @@
@@ -99,11 +95,7 @@ All vignettes
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/articles/spant-basis-simulation.html b/docs/articles/spant-basis-simulation.html
index 9fc1bdd8..5c4ee20c 100644
--- a/docs/articles/spant-basis-simulation.html
+++ b/docs/articles/spant-basis-simulation.html
@@ -38,11 +38,7 @@
@@ -189,11 +185,7 @@ Basis simulation
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/articles/spant-intro.html b/docs/articles/spant-intro.html
index 938c488e..0ab4d399 100644
--- a/docs/articles/spant-intro.html
+++ b/docs/articles/spant-intro.html
@@ -38,11 +38,7 @@
@@ -180,57 +176,22 @@ Basis simulation#> GSH,Glu,GPC,Ins,Lac,Lip09,
#> Lip13a,Lip13b,Lip20,MM09,MM12,
#> MM14,MM17,MM20,NAA,NAAG,PCh,
-#> PCr,sIns,Tau
-
+#> PCr,sIns,Tau
+stackplot(basis, xlim = c(4, 0.5), labels = basis$names, y_offset = 5)
Perform ABfit analysis of the processed data
(mrs_proc):
-
+
fit_res <- fit_mrs(mrs_proc, basis)
Plot the fit result:
-
+
plot(fit_res)
Unscaled amplitudes, CRLB error estimates and other useful fitting
diagnostics, such as SNR, are given in the fit_res results
table:
-
+
fit_res$res_tab
-<<<<<<< HEAD
-#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr GABA
-#> 1 1 1 1 1 1 0 8.133932e-06 3.547065e-05 4.02672e-05 1.697281e-05
-#> Glc Gln GSH Glu GPC Ins
-#> 1 2.446596e-06 3.036132e-06 2.228048e-05 6.503217e-05 1.606706e-05 5.906155e-05
-#> Lac Lip09 Lip13a Lip13b Lip20 MM09 MM12
-#> 1 5.802284e-06 2.387704e-05 2.670653e-06 0 0 9.630788e-06 6.511381e-06
-#> MM14 MM17 MM20 NAA NAAG PCh
-#> 1 2.603855e-05 2.238405e-05 9.203743e-05 6.011109e-05 1.536531e-05 0
-#> PCr sIns Tau tNAA tCr tCho
-#> 1 2.101921e-05 6.504098e-06 0 7.54764e-05 6.12864e-05 1.606706e-05
-#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd
-#> 1 6.80683e-05 3.350783e-05 3.522059e-05 9.203743e-05 2.386861e-06 4.343919e-06
-#> Asp.sd Cr.sd GABA.sd Glc.sd Gln.sd GSH.sd
-#> 1 9.235326e-06 3.689004e-06 4.574407e-06 4.421681e-06 5.083001e-06 2.020426e-06
-#> Glu.sd GPC.sd Ins.sd Lac.sd Lip09.sd Lip13a.sd
-#> 1 5.082976e-06 2.602651e-06 2.093225e-06 5.301703e-06 4.119256e-06 1.328305e-05
-#> Lip13b.sd Lip20.sd MM09.sd MM12.sd MM14.sd MM17.sd
-#> 1 6.474481e-06 7.510908e-06 3.827554e-06 4.594019e-06 7.223367e-06 3.811301e-06
-#> MM20.sd NAA.sd NAAG.sd PCh.sd PCr.sd sIns.sd
-#> 1 8.595853e-06 1.017712e-06 1.208985e-06 2.236873e-06 3.084598e-06 7.240068e-07
-#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd
-#> 1 3.759956e-06 7.031383e-07 5.890481e-07 2.110662e-07 3.16966e-06 1.006794e-06
-#> tLM13.sd tLM20.sd phase lw shift asym
-#> 1 1.573147e-06 3.016809e-06 11.10963 5.023681 -0.00376505 0.1771067
-#> res.deviance res.niter res.info
-#> 1 7.307669e-05 28 2
-#> res.message bl_ed_pppm
-#> 1 Relative error between `par' and the solution is at most `ptol'. 2.364083
-#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN
-#> 1 FALSE 7.754368e-05 497 3.8 62.71687 51.3328 1.492722
-#> tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
-#> 1 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159
-=======
#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr
#> 1 1 1 1 1 1 0 8.133802e-06 3.547064e-05 4.026719e-05
#> GABA Glc Gln GSH Glu GPC
@@ -263,32 +224,19 @@ Basis simulation#> 1 FALSE 7.75437e-05 7.307671e-05 497 3.8 62.71686 51.33279
#> FQN tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
#> 1 1.492722 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159
->>>>>>> devel
#> auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844
#> 1 -8.977355 -9.000064 -9.013367 -9.02055
#> auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384
#> 1 -9.024177 -9.023462 -9.009854 -8.958654
#> auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743
-<<<<<<< HEAD
-#> 1 -8.844271 -8.690744 -8.562631 -8.485471
-#> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
-#> 1 -8.447136 -8.430174 -8.423053 -8.420086
-=======
#> 1 -8.844271 -8.690744 -8.56263 -8.485471
#> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
#> 1 -8.447135 -8.430173 -8.423052 -8.420085
->>>>>>> devel
#> auto_bl_crit_0.532 auto_bl_crit_0.529
#> 1 -8.418839 -8.418312
Note that signal names appended with “.sd” are the CRLB estimates for
the uncertainty (standard deviation) in the metabolite quantity
estimate. e.g. to calculate the percentage s.d. for tNAA:
-<<<<<<< HEAD
-
-fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
-#> [1] 0.9316001
-Spectral SNR:
-=======
fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
#> [1] 0.9316002
@@ -297,12 +245,7 @@ Basis simulationfit_res$res_tab$SNR
#> [1] 62.71686
Linewidth of the tNAA resonance in PPM:
->>>>>>> devel
-fit_res$res_tab$SNR
-#> [1] 62.71687
-Linewidth of the tNAA resonance in PPM:
-
fit_res$res_tab$tNAA_lw
#> [1] 0.04562445
@@ -313,53 +256,18 @@ Ratios to total-creatine
-
+
fit_res_tcr_sc <- scale_amp_ratio(fit_res, "tCr")
amps <- fit_amps(fit_res_tcr_sc)
print(t(amps))
#> [,1]
#> X.CrCH2 0.00000000
-<<<<<<< HEAD
-#> Ala 0.13272001
-#> Asp 0.57876874
-#> Cr 0.65703313
-#> GABA 0.27694252
-#> Glc 0.03992071
-#> Gln 0.04954005
-#> GSH 0.36354683
-#> Glu 1.06111906
-#> GPC 0.26216356
-#> Ins 0.96369746
-#> Lac 0.09467490
-#> Lip09 0.38959768
-#> Lip13a 0.04357660
-#> Lip13b 0.00000000
-#> Lip20 0.00000000
-#> MM09 0.15714395
-#> MM12 0.10624512
-#> MM14 0.42486672
-#> MM17 0.36523688
-#> MM20 1.50175937
-#> NAA 0.98082268
-#> NAAG 0.25071313
-#> PCh 0.00000000
-#> PCr 0.34296687
-#> sIns 0.10612627
-#> Tau 0.00000000
-#> tNAA 1.23153582
-#> tCr 1.00000000
-#> tCho 0.26216356
-#> Glx 1.11065912
-#> tLM09 0.54674163
-#> tLM13 0.57468844
-#> tLM20 1.50175937
-=======
#> Ala 0.13271789
#> Asp 0.57876852
#> Cr 0.65703306
#> GABA 0.27694176
#> Glc 0.03992062
-#> Gln 0.04953983
+#> Gln 0.04953982
#> GSH 0.36354693
#> Glu 1.06111932
#> GPC 0.26216353
@@ -387,7 +295,6 @@ Ratios to total-creatine#> tLM09 0.54674149
#> tLM13 0.57468661
#> tLM20 1.50175914
->>>>>>> devel
Water reference scaling, AKA “absolute-quantification”
@@ -395,14 +302,14 @@ Water reference sca
A more sophisticated approach to scaling metabolite values involves
the use of a separate water-reference acquisition - which can be
imported in the standard way:
-
+
fname_wref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant")
mrs_data_wref <- read_mrs(fname_wref)
The following code assumes the voxel contains 100% white matter
tissue and scales the metabolite values into molal (mM) units (mol / kg
tissue water) based on the method described by Gasparovic et al MRM 2006
55(6):1219-26:
-
+
p_vols <- c(WM = 100, GM = 0, CSF = 0)
TE = 0.03
TR = 2
@@ -414,14 +321,10 @@ Water reference sca
LCModel manual and references therein (section 10.2). This approach may
be preferred when comparing results to those obtained LCModel or
TARQUIN.
-
+
fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref)
fit_res_molar$res_tab$tNAA
-<<<<<<< HEAD
-#> [1] 6.826336
-=======
#> [1] 6.826335
->>>>>>> devel
Note, while “absolute” units are attractive, a large number of
assumptions about metabolite and water relaxation rates are necessary to
arrive at these mM estimates. If you’re not confident at being able to
@@ -447,11 +350,7 @@
Water reference sca
diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png
index a8160510..3640c474 100644
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diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html
index 0b599b16..83e21ed5 100644
--- a/docs/articles/spant-metabolite-simulation.html
+++ b/docs/articles/spant-metabolite-simulation.html
@@ -38,11 +38,7 @@
@@ -281,9 +277,8 @@ Custom molecules#> L/G lineshape : 0
#>
#> nucleus chem_shift
-#> 1 1H 2.5
-
+#> 1 1H 2.5
+custom_mol |> sim_mol() |> lb(2) |> zf() |> plot(xlim = c(4.4, 0.5))
Once your happy the new molecule is correct, please consider
contributing it to the package if you think others would benefit.
@@ -305,11 +300,7 @@ Custom molecules
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html
index 2a477a86..733deb7e 100644
--- a/docs/articles/spant-preprocessing.html
+++ b/docs/articles/spant-preprocessing.html
@@ -38,11 +38,7 @@
@@ -179,11 +175,7 @@ Reading raw data and plotting
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/authors.html b/docs/authors.html
index a7fe7801..ee2d0e06 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,11 +17,7 @@
@@ -144,11 +140,7 @@ Citation
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/index.html b/docs/index.html
index 1cf2cb48..2632666f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -40,11 +40,7 @@
@@ -269,11 +265,7 @@ Developers
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/news/index.html b/docs/news/index.html
index 63380a9d..cf75257c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,11 +17,7 @@
@@ -77,17 +73,18 @@ Changelog
-<<<<<<< HEAD
-spant 2.22.0
-=======
-spant 2.23.0
+spant 2.24.0
+- Added argument to adjust the legend font size in ortho3 function.
+- Improved metabolite simulation performance thanks to the expm package recently adding support for complex matrices.
+
+
+spant 2.23.02024-08-27
- abfit options for lipid and MM maximum broadening and maximum frequency shift now default to be the same as the metabolite values unless explicitly changed.
- Added function to calculate the correlation matrix from a basis_set.
- Fix for RDA files where a comma is sometimes used as a decimal point.
spant 2.22.02024-07-11
->>>>>>> devel
- Added find_bids_mrs and mrs_data2bids helper functions.
- Improved handling of CMRR semi-LASER SVS water reference scans.
- Added functions for GLS coil combination.
@@ -604,11 +601,7 @@ spant 0.1.02
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 9f9c389c..384168c9 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,9 +1,5 @@
pandoc: 3.1.11
-<<<<<<< HEAD
-pkgdown: 2.0.9
-=======
pkgdown: 2.1.0
->>>>>>> devel
pkgdown_sha: ~
articles:
abfit-baseline-opts: abfit-baseline-opts.html
@@ -11,11 +7,7 @@ articles:
spant-intro: spant-intro.html
spant-metabolite-simulation: spant-metabolite-simulation.html
spant-preprocessing: spant-preprocessing.html
-<<<<<<< HEAD
-last_built: 2024-07-11T11:18Z
-=======
-last_built: 2024-08-27T13:06Z
->>>>>>> devel
+last_built: 2024-11-14T15:10Z
urls:
reference: https://martin3141.github.io/spant/reference
article: https://martin3141.github.io/spant/articles
diff --git a/docs/reference/Arg.mrs_data.html b/docs/reference/Arg.mrs_data.html
index 21cf298b..ec4791a6 100644
--- a/docs/reference/Arg.mrs_data.html
+++ b/docs/reference/Arg.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html
index c5ff53bb..a004e2df 100644
--- a/docs/reference/Conj.mrs_data.html
+++ b/docs/reference/Conj.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html
index efda9d95..e1b0443d 100644
--- a/docs/reference/Im.mrs_data.html
+++ b/docs/reference/Im.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html
index d24f6216..8860e06e 100644
--- a/docs/reference/Imzap.html
+++ b/docs/reference/Imzap.html
@@ -18,11 +18,7 @@
@@ -113,11 +109,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Mod.mrs_data.html b/docs/reference/Mod.mrs_data.html
index 10f3097a..f304f7a0 100644
--- a/docs/reference/Mod.mrs_data.html
+++ b/docs/reference/Mod.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html
index 8b9e62a0..df7091fb 100644
--- a/docs/reference/Ncoils.html
+++ b/docs/reference/Ncoils.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html
index 5cbcc56c..745b3df3 100644
--- a/docs/reference/Ndyns.html
+++ b/docs/reference/Ndyns.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html
index e6a89329..4a5cad73 100644
--- a/docs/reference/Npts.html
+++ b/docs/reference/Npts.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html
index 51bdc1c0..8fe4d378 100644
--- a/docs/reference/Nspec.html
+++ b/docs/reference/Nspec.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html
index 2493e772..a1614c98 100644
--- a/docs/reference/Ntrans.html
+++ b/docs/reference/Ntrans.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Nx.html b/docs/reference/Nx.html
index 4c619b3e..f46b2d22 100644
--- a/docs/reference/Nx.html
+++ b/docs/reference/Nx.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Ny.html b/docs/reference/Ny.html
index dd95a54b..8921fcbc 100644
--- a/docs/reference/Ny.html
+++ b/docs/reference/Ny.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html
index 6b13ee79..014d2535 100644
--- a/docs/reference/Nz.html
+++ b/docs/reference/Nz.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html
index 792e2b27..2c23aa81 100644
--- a/docs/reference/Re.mrs_data.html
+++ b/docs/reference/Re.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html
index 91e4014c..bd06536b 100644
--- a/docs/reference/abfit_opts.html
+++ b/docs/reference/abfit_opts.html
@@ -17,11 +17,7 @@
@@ -96,6 +92,7 @@ Return a list of options for an ABfit analysis.
bl_ed_pppm = 2,
auto_bl_flex = TRUE,
bl_comps_pppm = 15,
+ adaptive_bl_comps_pppm = FALSE,
export_sp_fit = FALSE,
max_asym = 0.25,
max_basis_shift = 0.0078,
@@ -126,16 +123,14 @@ Return a list of options for an ABfit analysis.
freq_reg = NULL,
freq_reg_naa = NULL,
lb_reg = NULL,
+ asym_reg = NULL,
output_all_paras = FALSE,
output_all_paras_raw = FALSE,
input_paras_raw = NULL,
optim_lw_only = FALSE,
optim_lw_only_limit = 20,
lb_init = 0.001,
-<<<<<<< HEAD
-=======
lb_init_approx_fit = FALSE,
->>>>>>> devel
zf_offset = NULL
)
@@ -203,6 +198,12 @@ Arguments
spline basis density (signals per ppm).
adaptive_bl_comps_pppm
+adjust the spline basis density in the detailed
+fit phase, based on the required level of smoothness, to reduce computation
+time.
export_sp_fit
add the fitted spline functions to the fit result.
Arguments
individual line broadening parameter.
asym_reg
+lineshape asymmetry parameter.
output_all_paras
include more fitting parameters in the fit table,
e.g. individual shift and damping factors for each basis set element.
Arguments
zero-fill. Default is NULL and will automatically set this to 50 points when
the FID distortion flag is set for the mrs_data.
-
-zf_offset
-offset in number of data points from the end of the FID to
-zero-fill. Default is NULL and will automatically set this to 50 points when
-the FID distortion flag is set for the mrs_data.
Value
@@ -411,11 +410,7 @@ Examples
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html
index 04268252..909deac5 100644
--- a/docs/reference/abfit_opts_v1_9_0.html
+++ b/docs/reference/abfit_opts_v1_9_0.html
@@ -18,11 +18,7 @@
@@ -112,11 +108,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/acquire.html b/docs/reference/acquire.html
index 05f23aaf..740c60f3 100644
--- a/docs/reference/acquire.html
+++ b/docs/reference/acquire.html
@@ -17,11 +17,7 @@
@@ -126,11 +122,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html
index 9ba363ba..306c6967 100644
--- a/docs/reference/add_noise.html
+++ b/docs/reference/add_noise.html
@@ -17,11 +17,7 @@
@@ -120,11 +116,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/add_noise_spec_snr.html b/docs/reference/add_noise_spec_snr.html
index 4785a76b..9f33f39b 100644
--- a/docs/reference/add_noise_spec_snr.html
+++ b/docs/reference/add_noise_spec_snr.html
@@ -17,11 +17,7 @@
@@ -109,11 +105,7 @@ Arguments
point.
-<<<<<<< HEAD
-ref_data
-=======
ref_data
->>>>>>> devel
measure the signal from the first scan in this reference data
and apply the same target noise level to mrs_data.
Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/align.html b/docs/reference/align.html
index a2a458ae..afae69c0 100644
--- a/docs/reference/align.html
+++ b/docs/reference/align.html
@@ -17,11 +17,7 @@
@@ -150,11 +146,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html
index 8144cf92..ee6d8a45 100644
--- a/docs/reference/apodise_xy.html
+++ b/docs/reference/apodise_xy.html
@@ -17,11 +17,7 @@
@@ -93,11 +89,7 @@ Arguments
MRSI data.
func
-=======
func
->>>>>>> devel
must be "hamming", "hanning" or "gaussian".
Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html
index 58f87125..0c5c39b0 100644
--- a/docs/reference/append_basis.html
+++ b/docs/reference/append_basis.html
@@ -17,11 +17,7 @@
@@ -114,11 +110,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/append_coils.html b/docs/reference/append_coils.html
index 6316e4ec..627192cf 100644
--- a/docs/reference/append_coils.html
+++ b/docs/reference/append_coils.html
@@ -18,11 +18,7 @@
@@ -112,11 +108,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/append_dyns.html b/docs/reference/append_dyns.html
index 9012cac6..b26793f7 100644
--- a/docs/reference/append_dyns.html
+++ b/docs/reference/append_dyns.html
@@ -18,11 +18,7 @@
@@ -112,11 +108,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/append_regs.html b/docs/reference/append_regs.html
index 148ffbbc..74188cae 100644
--- a/docs/reference/append_regs.html
+++ b/docs/reference/append_regs.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/apply_axes.html b/docs/reference/apply_axes.html
index 8f1baf51..a5f7ff98 100644
--- a/docs/reference/apply_axes.html
+++ b/docs/reference/apply_axes.html
@@ -17,11 +17,7 @@
@@ -134,11 +130,7 @@ Examples
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/apply_mrs.html b/docs/reference/apply_mrs.html
index f34191b5..5b220cb1 100644
--- a/docs/reference/apply_mrs.html
+++ b/docs/reference/apply_mrs.html
@@ -17,11 +17,7 @@
@@ -122,11 +118,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/apply_pulse.html b/docs/reference/apply_pulse.html
index 5277105c..2e6b988b 100644
--- a/docs/reference/apply_pulse.html
+++ b/docs/reference/apply_pulse.html
@@ -17,11 +17,7 @@
@@ -130,11 +126,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/array2mrs_data.html b/docs/reference/array2mrs_data.html
index 2e7ca3d6..72f05f62 100644
--- a/docs/reference/array2mrs_data.html
+++ b/docs/reference/array2mrs_data.html
@@ -18,11 +18,7 @@
@@ -103,19 +99,11 @@ Arguments
7d data array.
mrs_data
-example data to copy acquisition parameters from.
fs
-=======
mrs_data
example data to copy acquisition parameters from.
fs
->>>>>>> devel
sampling frequency in Hz.
Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/auto_phase.html b/docs/reference/auto_phase.html
index c1c1c981..e433d7eb 100644
--- a/docs/reference/auto_phase.html
+++ b/docs/reference/auto_phase.html
@@ -19,11 +19,7 @@
@@ -126,11 +122,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/back_extrap_ar.html b/docs/reference/back_extrap_ar.html
index 790e3383..c8415c2d 100644
--- a/docs/reference/back_extrap_ar.html
+++ b/docs/reference/back_extrap_ar.html
@@ -17,11 +17,7 @@
@@ -140,11 +136,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/basis2dyn_mrs_data.html b/docs/reference/basis2dyn_mrs_data.html
index 80b8fcfa..253f70c0 100644
--- a/docs/reference/basis2dyn_mrs_data.html
+++ b/docs/reference/basis2dyn_mrs_data.html
@@ -17,11 +17,7 @@
@@ -119,11 +115,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/basis2mrs_data.html b/docs/reference/basis2mrs_data.html
index fe710559..74a2966b 100644
--- a/docs/reference/basis2mrs_data.html
+++ b/docs/reference/basis2mrs_data.html
@@ -18,11 +18,7 @@
@@ -137,11 +133,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bbase.html b/docs/reference/bbase.html
index fb69df5f..fd5fdb57 100644
--- a/docs/reference/bbase.html
+++ b/docs/reference/bbase.html
@@ -18,11 +18,7 @@
@@ -120,11 +116,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_als.html b/docs/reference/bc_als.html
index 09652dc8..7fd5a49f 100644
--- a/docs/reference/bc_als.html
+++ b/docs/reference/bc_als.html
@@ -18,11 +18,7 @@
@@ -125,11 +121,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_constant.html b/docs/reference/bc_constant.html
index 6e27f5ed..e1c1193a 100644
--- a/docs/reference/bc_constant.html
+++ b/docs/reference/bc_constant.html
@@ -17,11 +17,7 @@
@@ -115,11 +111,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_gauss.html b/docs/reference/bc_gauss.html
index d5b57ebe..07d41694 100644
--- a/docs/reference/bc_gauss.html
+++ b/docs/reference/bc_gauss.html
@@ -17,11 +17,7 @@
@@ -114,11 +110,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_poly.html b/docs/reference/bc_poly.html
index 488abbd4..976204be 100644
--- a/docs/reference/bc_poly.html
+++ b/docs/reference/bc_poly.html
@@ -17,11 +17,7 @@
@@ -114,11 +110,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_spline.html b/docs/reference/bc_spline.html
index b44a93a9..364d0b1c 100644
--- a/docs/reference/bc_spline.html
+++ b/docs/reference/bc_spline.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/beta2lw.html b/docs/reference/beta2lw.html
index 2df9a7d7..6acdfc8c 100644
--- a/docs/reference/beta2lw.html
+++ b/docs/reference/beta2lw.html
@@ -18,11 +18,7 @@
@@ -112,11 +108,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bin_spec.html b/docs/reference/bin_spec.html
index 19601cba..5ee3bab5 100644
--- a/docs/reference/bin_spec.html
+++ b/docs/reference/bin_spec.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_basis_corr_mat.html b/docs/reference/calc_basis_corr_mat.html
index 25eed3ef..b9b7cc8c 100644
--- a/docs/reference/calc_basis_corr_mat.html
+++ b/docs/reference/calc_basis_corr_mat.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/calc_basis_crlbs.html b/docs/reference/calc_basis_crlbs.html
index 9b8b0c37..7cfd8c87 100644
--- a/docs/reference/calc_basis_crlbs.html
+++ b/docs/reference/calc_basis_crlbs.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/calc_coil_noise_cor.html b/docs/reference/calc_coil_noise_cor.html
index e4e58d8a..57d385a0 100644
--- a/docs/reference/calc_coil_noise_cor.html
+++ b/docs/reference/calc_coil_noise_cor.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_coil_noise_sd.html b/docs/reference/calc_coil_noise_sd.html
index 4c4a4218..772e9162 100644
--- a/docs/reference/calc_coil_noise_sd.html
+++ b/docs/reference/calc_coil_noise_sd.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_design_efficiency.html b/docs/reference/calc_design_efficiency.html
index eb470b7a..15560eb8 100644
--- a/docs/reference/calc_design_efficiency.html
+++ b/docs/reference/calc_design_efficiency.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_ed_from_lambda.html b/docs/reference/calc_ed_from_lambda.html
index 99ea03e7..534844d4 100644
--- a/docs/reference/calc_ed_from_lambda.html
+++ b/docs/reference/calc_ed_from_lambda.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_peak_info_vec.html b/docs/reference/calc_peak_info_vec.html
index 16a4310b..06cbf41b 100644
--- a/docs/reference/calc_peak_info_vec.html
+++ b/docs/reference/calc_peak_info_vec.html
@@ -17,11 +17,7 @@
@@ -115,11 +111,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_sd_poly.html b/docs/reference/calc_sd_poly.html
index 55b500d2..672e25c3 100644
--- a/docs/reference/calc_sd_poly.html
+++ b/docs/reference/calc_sd_poly.html
@@ -18,11 +18,7 @@
@@ -116,11 +112,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_spec_diff.html b/docs/reference/calc_spec_diff.html
index e258f6bb..a67f441b 100644
--- a/docs/reference/calc_spec_diff.html
+++ b/docs/reference/calc_spec_diff.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_spec_snr.html b/docs/reference/calc_spec_snr.html
index 34e74a11..00913709 100644
--- a/docs/reference/calc_spec_snr.html
+++ b/docs/reference/calc_spec_snr.html
@@ -18,11 +18,7 @@
@@ -149,11 +145,7 @@ Details
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/check_lcm.html b/docs/reference/check_lcm.html
index 99fb5614..ed92f5f5 100644
--- a/docs/reference/check_lcm.html
+++ b/docs/reference/check_lcm.html
@@ -17,11 +17,7 @@
@@ -98,11 +94,7 @@ Check LCModel can be run
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/check_tqn.html b/docs/reference/check_tqn.html
index aef1d677..df05510f 100644
--- a/docs/reference/check_tqn.html
+++ b/docs/reference/check_tqn.html
@@ -17,11 +17,7 @@
@@ -98,11 +94,7 @@ Check the TARQUIN binary can be run
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/circ_mask.html b/docs/reference/circ_mask.html
index dad70c51..a1405f51 100644
--- a/docs/reference/circ_mask.html
+++ b/docs/reference/circ_mask.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/coherence_filter.html b/docs/reference/coherence_filter.html
index 8d49462c..467a56af 100644
--- a/docs/reference/coherence_filter.html
+++ b/docs/reference/coherence_filter.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/collapse_to_dyns.html b/docs/reference/collapse_to_dyns.html
index 83bf2ca6..7bfbacb9 100644
--- a/docs/reference/collapse_to_dyns.html
+++ b/docs/reference/collapse_to_dyns.html
@@ -17,11 +17,7 @@
@@ -121,11 +117,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/comb_coils.html b/docs/reference/comb_coils.html
index 98cd6580..f52f39ad 100644
--- a/docs/reference/comb_coils.html
+++ b/docs/reference/comb_coils.html
@@ -19,11 +19,7 @@
@@ -165,11 +161,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/comb_coils_mrsi_gls.html b/docs/reference/comb_coils_mrsi_gls.html
index 57bc19d2..88872ccb 100644
--- a/docs/reference/comb_coils_mrsi_gls.html
+++ b/docs/reference/comb_coils_mrsi_gls.html
@@ -4,11 +4,7 @@
-<<<<<<< HEAD
-
-=======
->>>>>>> devel
@@ -37,11 +29,7 @@
Tutorials
-<<<<<<< HEAD
-
-=======
->>>>>>> devel
-<<<<<<< HEAD
-
-=======
->>>>>>> devel
@@ -105,13 +85,6 @@ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:14
Arguments
-<<<<<<< HEAD
- - metab
-MRSI data containing metabolite data.
- noise_pts
-=======
Value
-<<<<<<< HEAD
-
-
-coil combined MRSI data.
-=======
coil combined MRSI data.
->>>>>>> devel
@@ -155,26 +117,15 @@ Value
-<<<<<<< HEAD
-
-
-
-
-=======
->>>>>>> devel
Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> develSite built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> devel diff --git a/docs/articles/spant-intro.html b/docs/articles/spant-intro.html index 938c488e..0ab4d399 100644 --- a/docs/articles/spant-intro.html +++ b/docs/articles/spant-intro.html @@ -38,11 +38,7 @@ @@ -180,57 +176,22 @@Basis simulation#> GSH,Glu,GPC,Ins,Lac,Lip09,
#> Lip13a,Lip13b,Lip20,MM09,MM12,
#> MM14,MM17,MM20,NAA,NAAG,PCh,
-#> PCr,sIns,Tau
-
+#> PCr,sIns,Tau
+stackplot(basis, xlim = c(4, 0.5), labels = basis$names, y_offset = 5)
Perform ABfit analysis of the processed data
(mrs_proc):
-
+
fit_res <- fit_mrs(mrs_proc, basis)
Plot the fit result:
-
+
plot(fit_res)
Unscaled amplitudes, CRLB error estimates and other useful fitting
diagnostics, such as SNR, are given in the fit_res results
table:
-
+
fit_res$res_tab
-<<<<<<< HEAD
-#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr GABA
-#> 1 1 1 1 1 1 0 8.133932e-06 3.547065e-05 4.02672e-05 1.697281e-05
-#> Glc Gln GSH Glu GPC Ins
-#> 1 2.446596e-06 3.036132e-06 2.228048e-05 6.503217e-05 1.606706e-05 5.906155e-05
-#> Lac Lip09 Lip13a Lip13b Lip20 MM09 MM12
-#> 1 5.802284e-06 2.387704e-05 2.670653e-06 0 0 9.630788e-06 6.511381e-06
-#> MM14 MM17 MM20 NAA NAAG PCh
-#> 1 2.603855e-05 2.238405e-05 9.203743e-05 6.011109e-05 1.536531e-05 0
-#> PCr sIns Tau tNAA tCr tCho
-#> 1 2.101921e-05 6.504098e-06 0 7.54764e-05 6.12864e-05 1.606706e-05
-#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd
-#> 1 6.80683e-05 3.350783e-05 3.522059e-05 9.203743e-05 2.386861e-06 4.343919e-06
-#> Asp.sd Cr.sd GABA.sd Glc.sd Gln.sd GSH.sd
-#> 1 9.235326e-06 3.689004e-06 4.574407e-06 4.421681e-06 5.083001e-06 2.020426e-06
-#> Glu.sd GPC.sd Ins.sd Lac.sd Lip09.sd Lip13a.sd
-#> 1 5.082976e-06 2.602651e-06 2.093225e-06 5.301703e-06 4.119256e-06 1.328305e-05
-#> Lip13b.sd Lip20.sd MM09.sd MM12.sd MM14.sd MM17.sd
-#> 1 6.474481e-06 7.510908e-06 3.827554e-06 4.594019e-06 7.223367e-06 3.811301e-06
-#> MM20.sd NAA.sd NAAG.sd PCh.sd PCr.sd sIns.sd
-#> 1 8.595853e-06 1.017712e-06 1.208985e-06 2.236873e-06 3.084598e-06 7.240068e-07
-#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd
-#> 1 3.759956e-06 7.031383e-07 5.890481e-07 2.110662e-07 3.16966e-06 1.006794e-06
-#> tLM13.sd tLM20.sd phase lw shift asym
-#> 1 1.573147e-06 3.016809e-06 11.10963 5.023681 -0.00376505 0.1771067
-#> res.deviance res.niter res.info
-#> 1 7.307669e-05 28 2
-#> res.message bl_ed_pppm
-#> 1 Relative error between `par' and the solution is at most `ptol'. 2.364083
-#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN
-#> 1 FALSE 7.754368e-05 497 3.8 62.71687 51.3328 1.492722
-#> tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
-#> 1 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159
-=======
#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr
#> 1 1 1 1 1 1 0 8.133802e-06 3.547064e-05 4.026719e-05
#> GABA Glc Gln GSH Glu GPC
@@ -263,32 +224,19 @@ Basis simulation#> 1 FALSE 7.75437e-05 7.307671e-05 497 3.8 62.71686 51.33279
#> FQN tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
#> 1 1.492722 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159
->>>>>>> devel
#> auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844
#> 1 -8.977355 -9.000064 -9.013367 -9.02055
#> auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384
#> 1 -9.024177 -9.023462 -9.009854 -8.958654
#> auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743
-<<<<<<< HEAD
-#> 1 -8.844271 -8.690744 -8.562631 -8.485471
-#> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
-#> 1 -8.447136 -8.430174 -8.423053 -8.420086
-=======
#> 1 -8.844271 -8.690744 -8.56263 -8.485471
#> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
#> 1 -8.447135 -8.430173 -8.423052 -8.420085
->>>>>>> devel
#> auto_bl_crit_0.532 auto_bl_crit_0.529
#> 1 -8.418839 -8.418312
Note that signal names appended with “.sd” are the CRLB estimates for
the uncertainty (standard deviation) in the metabolite quantity
estimate. e.g. to calculate the percentage s.d. for tNAA:
-<<<<<<< HEAD
-
-fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
-#> [1] 0.9316001
-Spectral SNR:
-=======
fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
#> [1] 0.9316002
@@ -297,12 +245,7 @@ Basis simulationfit_res$res_tab$SNR
#> [1] 62.71686
Linewidth of the tNAA resonance in PPM:
->>>>>>> devel
-fit_res$res_tab$SNR
-#> [1] 62.71687
-Linewidth of the tNAA resonance in PPM:
-
fit_res$res_tab$tNAA_lw
#> [1] 0.04562445
@@ -313,53 +256,18 @@ Ratios to total-creatine
-
+
fit_res_tcr_sc <- scale_amp_ratio(fit_res, "tCr")
amps <- fit_amps(fit_res_tcr_sc)
print(t(amps))
#> [,1]
#> X.CrCH2 0.00000000
-<<<<<<< HEAD
-#> Ala 0.13272001
-#> Asp 0.57876874
-#> Cr 0.65703313
-#> GABA 0.27694252
-#> Glc 0.03992071
-#> Gln 0.04954005
-#> GSH 0.36354683
-#> Glu 1.06111906
-#> GPC 0.26216356
-#> Ins 0.96369746
-#> Lac 0.09467490
-#> Lip09 0.38959768
-#> Lip13a 0.04357660
-#> Lip13b 0.00000000
-#> Lip20 0.00000000
-#> MM09 0.15714395
-#> MM12 0.10624512
-#> MM14 0.42486672
-#> MM17 0.36523688
-#> MM20 1.50175937
-#> NAA 0.98082268
-#> NAAG 0.25071313
-#> PCh 0.00000000
-#> PCr 0.34296687
-#> sIns 0.10612627
-#> Tau 0.00000000
-#> tNAA 1.23153582
-#> tCr 1.00000000
-#> tCho 0.26216356
-#> Glx 1.11065912
-#> tLM09 0.54674163
-#> tLM13 0.57468844
-#> tLM20 1.50175937
-=======
#> Ala 0.13271789
#> Asp 0.57876852
#> Cr 0.65703306
#> GABA 0.27694176
#> Glc 0.03992062
-#> Gln 0.04953983
+#> Gln 0.04953982
#> GSH 0.36354693
#> Glu 1.06111932
#> GPC 0.26216353
@@ -387,7 +295,6 @@ Ratios to total-creatine#> tLM09 0.54674149
#> tLM13 0.57468661
#> tLM20 1.50175914
->>>>>>> devel
Water reference scaling, AKA “absolute-quantification”
@@ -395,14 +302,14 @@ Water reference sca
A more sophisticated approach to scaling metabolite values involves
the use of a separate water-reference acquisition - which can be
imported in the standard way:
-
+
fname_wref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant")
mrs_data_wref <- read_mrs(fname_wref)
The following code assumes the voxel contains 100% white matter
tissue and scales the metabolite values into molal (mM) units (mol / kg
tissue water) based on the method described by Gasparovic et al MRM 2006
55(6):1219-26:
-
+
p_vols <- c(WM = 100, GM = 0, CSF = 0)
TE = 0.03
TR = 2
@@ -414,14 +321,10 @@ Water reference sca
LCModel manual and references therein (section 10.2). This approach may
be preferred when comparing results to those obtained LCModel or
TARQUIN.
-
+
fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref)
fit_res_molar$res_tab$tNAA
-<<<<<<< HEAD
-#> [1] 6.826336
-=======
#> [1] 6.826335
->>>>>>> devel
Note, while “absolute” units are attractive, a large number of
assumptions about metabolite and water relaxation rates are necessary to
arrive at these mM estimates. If you’re not confident at being able to
@@ -447,11 +350,7 @@
Water reference sca
diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png
index a8160510..3640c474 100644
Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png differ
diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html
index 0b599b16..83e21ed5 100644
--- a/docs/articles/spant-metabolite-simulation.html
+++ b/docs/articles/spant-metabolite-simulation.html
@@ -38,11 +38,7 @@
@@ -281,9 +277,8 @@ Custom molecules#> L/G lineshape : 0
#>
#> nucleus chem_shift
-#> 1 1H 2.5
-
+#> 1 1H 2.5
+custom_mol |> sim_mol() |> lb(2) |> zf() |> plot(xlim = c(4.4, 0.5))
Once your happy the new molecule is correct, please consider
contributing it to the package if you think others would benefit.
@@ -305,11 +300,7 @@ Custom molecules
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html
index 2a477a86..733deb7e 100644
--- a/docs/articles/spant-preprocessing.html
+++ b/docs/articles/spant-preprocessing.html
@@ -38,11 +38,7 @@
@@ -179,11 +175,7 @@ Reading raw data and plotting
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/authors.html b/docs/authors.html
index a7fe7801..ee2d0e06 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,11 +17,7 @@
@@ -144,11 +140,7 @@ Citation
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/index.html b/docs/index.html
index 1cf2cb48..2632666f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -40,11 +40,7 @@
@@ -269,11 +265,7 @@ Developers
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/news/index.html b/docs/news/index.html
index 63380a9d..cf75257c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,11 +17,7 @@
@@ -77,17 +73,18 @@ Changelog
-<<<<<<< HEAD
-spant 2.22.0
-=======
-spant 2.23.0
+spant 2.24.0
+- Added argument to adjust the legend font size in ortho3 function.
+- Improved metabolite simulation performance thanks to the expm package recently adding support for complex matrices.
+
+
+spant 2.23.02024-08-27
- abfit options for lipid and MM maximum broadening and maximum frequency shift now default to be the same as the metabolite values unless explicitly changed.
- Added function to calculate the correlation matrix from a basis_set.
- Fix for RDA files where a comma is sometimes used as a decimal point.
spant 2.22.02024-07-11
->>>>>>> devel
- Added find_bids_mrs and mrs_data2bids helper functions.
- Improved handling of CMRR semi-LASER SVS water reference scans.
- Added functions for GLS coil combination.
@@ -604,11 +601,7 @@ spant 0.1.02
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 9f9c389c..384168c9 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,9 +1,5 @@
pandoc: 3.1.11
-<<<<<<< HEAD
-pkgdown: 2.0.9
-=======
pkgdown: 2.1.0
->>>>>>> devel
pkgdown_sha: ~
articles:
abfit-baseline-opts: abfit-baseline-opts.html
@@ -11,11 +7,7 @@ articles:
spant-intro: spant-intro.html
spant-metabolite-simulation: spant-metabolite-simulation.html
spant-preprocessing: spant-preprocessing.html
-<<<<<<< HEAD
-last_built: 2024-07-11T11:18Z
-=======
-last_built: 2024-08-27T13:06Z
->>>>>>> devel
+last_built: 2024-11-14T15:10Z
urls:
reference: https://martin3141.github.io/spant/reference
article: https://martin3141.github.io/spant/articles
diff --git a/docs/reference/Arg.mrs_data.html b/docs/reference/Arg.mrs_data.html
index 21cf298b..ec4791a6 100644
--- a/docs/reference/Arg.mrs_data.html
+++ b/docs/reference/Arg.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html
index c5ff53bb..a004e2df 100644
--- a/docs/reference/Conj.mrs_data.html
+++ b/docs/reference/Conj.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html
index efda9d95..e1b0443d 100644
--- a/docs/reference/Im.mrs_data.html
+++ b/docs/reference/Im.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html
index d24f6216..8860e06e 100644
--- a/docs/reference/Imzap.html
+++ b/docs/reference/Imzap.html
@@ -18,11 +18,7 @@
@@ -113,11 +109,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Mod.mrs_data.html b/docs/reference/Mod.mrs_data.html
index 10f3097a..f304f7a0 100644
--- a/docs/reference/Mod.mrs_data.html
+++ b/docs/reference/Mod.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html
index 8b9e62a0..df7091fb 100644
--- a/docs/reference/Ncoils.html
+++ b/docs/reference/Ncoils.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html
index 5cbcc56c..745b3df3 100644
--- a/docs/reference/Ndyns.html
+++ b/docs/reference/Ndyns.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html
index e6a89329..4a5cad73 100644
--- a/docs/reference/Npts.html
+++ b/docs/reference/Npts.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html
index 51bdc1c0..8fe4d378 100644
--- a/docs/reference/Nspec.html
+++ b/docs/reference/Nspec.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html
index 2493e772..a1614c98 100644
--- a/docs/reference/Ntrans.html
+++ b/docs/reference/Ntrans.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Nx.html b/docs/reference/Nx.html
index 4c619b3e..f46b2d22 100644
--- a/docs/reference/Nx.html
+++ b/docs/reference/Nx.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Ny.html b/docs/reference/Ny.html
index dd95a54b..8921fcbc 100644
--- a/docs/reference/Ny.html
+++ b/docs/reference/Ny.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html
index 6b13ee79..014d2535 100644
--- a/docs/reference/Nz.html
+++ b/docs/reference/Nz.html
@@ -17,11 +17,7 @@
@@ -106,11 +102,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html
index 792e2b27..2c23aa81 100644
--- a/docs/reference/Re.mrs_data.html
+++ b/docs/reference/Re.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html
index 91e4014c..bd06536b 100644
--- a/docs/reference/abfit_opts.html
+++ b/docs/reference/abfit_opts.html
@@ -17,11 +17,7 @@
@@ -96,6 +92,7 @@ Return a list of options for an ABfit analysis.
bl_ed_pppm = 2,
auto_bl_flex = TRUE,
bl_comps_pppm = 15,
+ adaptive_bl_comps_pppm = FALSE,
export_sp_fit = FALSE,
max_asym = 0.25,
max_basis_shift = 0.0078,
@@ -126,16 +123,14 @@ Return a list of options for an ABfit analysis.
freq_reg = NULL,
freq_reg_naa = NULL,
lb_reg = NULL,
+ asym_reg = NULL,
output_all_paras = FALSE,
output_all_paras_raw = FALSE,
input_paras_raw = NULL,
optim_lw_only = FALSE,
optim_lw_only_limit = 20,
lb_init = 0.001,
-<<<<<<< HEAD
-=======
lb_init_approx_fit = FALSE,
->>>>>>> devel
zf_offset = NULL
)
@@ -203,6 +198,12 @@ Arguments
spline basis density (signals per ppm).
adaptive_bl_comps_pppm
+adjust the spline basis density in the detailed
+fit phase, based on the required level of smoothness, to reduce computation
+time.
export_sp_fit
add the fitted spline functions to the fit result.
Arguments
individual line broadening parameter.
asym_reg
+lineshape asymmetry parameter.
output_all_paras
include more fitting parameters in the fit table,
e.g. individual shift and damping factors for each basis set element.
Arguments
zero-fill. Default is NULL and will automatically set this to 50 points when
the FID distortion flag is set for the mrs_data.
-
-zf_offset
-offset in number of data points from the end of the FID to
-zero-fill. Default is NULL and will automatically set this to 50 points when
-the FID distortion flag is set for the mrs_data.
Value
@@ -411,11 +410,7 @@ Examples
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html
index 04268252..909deac5 100644
--- a/docs/reference/abfit_opts_v1_9_0.html
+++ b/docs/reference/abfit_opts_v1_9_0.html
@@ -18,11 +18,7 @@
@@ -112,11 +108,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/acquire.html b/docs/reference/acquire.html
index 05f23aaf..740c60f3 100644
--- a/docs/reference/acquire.html
+++ b/docs/reference/acquire.html
@@ -17,11 +17,7 @@
@@ -126,11 +122,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html
index 9ba363ba..306c6967 100644
--- a/docs/reference/add_noise.html
+++ b/docs/reference/add_noise.html
@@ -17,11 +17,7 @@
@@ -120,11 +116,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/add_noise_spec_snr.html b/docs/reference/add_noise_spec_snr.html
index 4785a76b..9f33f39b 100644
--- a/docs/reference/add_noise_spec_snr.html
+++ b/docs/reference/add_noise_spec_snr.html
@@ -17,11 +17,7 @@
@@ -109,11 +105,7 @@ Arguments
point.
-<<<<<<< HEAD
-ref_data
-=======
ref_data
->>>>>>> devel
measure the signal from the first scan in this reference data
and apply the same target noise level to mrs_data.
Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/align.html b/docs/reference/align.html
index a2a458ae..afae69c0 100644
--- a/docs/reference/align.html
+++ b/docs/reference/align.html
@@ -17,11 +17,7 @@
@@ -150,11 +146,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html
index 8144cf92..ee6d8a45 100644
--- a/docs/reference/apodise_xy.html
+++ b/docs/reference/apodise_xy.html
@@ -17,11 +17,7 @@
@@ -93,11 +89,7 @@ Arguments
MRSI data.
func
-=======
func
->>>>>>> devel
must be "hamming", "hanning" or "gaussian".
Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html
index 58f87125..0c5c39b0 100644
--- a/docs/reference/append_basis.html
+++ b/docs/reference/append_basis.html
@@ -17,11 +17,7 @@
@@ -114,11 +110,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/append_coils.html b/docs/reference/append_coils.html
index 6316e4ec..627192cf 100644
--- a/docs/reference/append_coils.html
+++ b/docs/reference/append_coils.html
@@ -18,11 +18,7 @@
@@ -112,11 +108,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/append_dyns.html b/docs/reference/append_dyns.html
index 9012cac6..b26793f7 100644
--- a/docs/reference/append_dyns.html
+++ b/docs/reference/append_dyns.html
@@ -18,11 +18,7 @@
@@ -112,11 +108,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/append_regs.html b/docs/reference/append_regs.html
index 148ffbbc..74188cae 100644
--- a/docs/reference/append_regs.html
+++ b/docs/reference/append_regs.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/apply_axes.html b/docs/reference/apply_axes.html
index 8f1baf51..a5f7ff98 100644
--- a/docs/reference/apply_axes.html
+++ b/docs/reference/apply_axes.html
@@ -17,11 +17,7 @@
@@ -134,11 +130,7 @@ Examples
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/apply_mrs.html b/docs/reference/apply_mrs.html
index f34191b5..5b220cb1 100644
--- a/docs/reference/apply_mrs.html
+++ b/docs/reference/apply_mrs.html
@@ -17,11 +17,7 @@
@@ -122,11 +118,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/apply_pulse.html b/docs/reference/apply_pulse.html
index 5277105c..2e6b988b 100644
--- a/docs/reference/apply_pulse.html
+++ b/docs/reference/apply_pulse.html
@@ -17,11 +17,7 @@
@@ -130,11 +126,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/array2mrs_data.html b/docs/reference/array2mrs_data.html
index 2e7ca3d6..72f05f62 100644
--- a/docs/reference/array2mrs_data.html
+++ b/docs/reference/array2mrs_data.html
@@ -18,11 +18,7 @@
@@ -103,19 +99,11 @@ Arguments
7d data array.
mrs_data
-example data to copy acquisition parameters from.
fs
-=======
mrs_data
example data to copy acquisition parameters from.
fs
->>>>>>> devel
sampling frequency in Hz.
Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/auto_phase.html b/docs/reference/auto_phase.html
index c1c1c981..e433d7eb 100644
--- a/docs/reference/auto_phase.html
+++ b/docs/reference/auto_phase.html
@@ -19,11 +19,7 @@
@@ -126,11 +122,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/back_extrap_ar.html b/docs/reference/back_extrap_ar.html
index 790e3383..c8415c2d 100644
--- a/docs/reference/back_extrap_ar.html
+++ b/docs/reference/back_extrap_ar.html
@@ -17,11 +17,7 @@
@@ -140,11 +136,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/basis2dyn_mrs_data.html b/docs/reference/basis2dyn_mrs_data.html
index 80b8fcfa..253f70c0 100644
--- a/docs/reference/basis2dyn_mrs_data.html
+++ b/docs/reference/basis2dyn_mrs_data.html
@@ -17,11 +17,7 @@
@@ -119,11 +115,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/basis2mrs_data.html b/docs/reference/basis2mrs_data.html
index fe710559..74a2966b 100644
--- a/docs/reference/basis2mrs_data.html
+++ b/docs/reference/basis2mrs_data.html
@@ -18,11 +18,7 @@
@@ -137,11 +133,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bbase.html b/docs/reference/bbase.html
index fb69df5f..fd5fdb57 100644
--- a/docs/reference/bbase.html
+++ b/docs/reference/bbase.html
@@ -18,11 +18,7 @@
@@ -120,11 +116,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_als.html b/docs/reference/bc_als.html
index 09652dc8..7fd5a49f 100644
--- a/docs/reference/bc_als.html
+++ b/docs/reference/bc_als.html
@@ -18,11 +18,7 @@
@@ -125,11 +121,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_constant.html b/docs/reference/bc_constant.html
index 6e27f5ed..e1c1193a 100644
--- a/docs/reference/bc_constant.html
+++ b/docs/reference/bc_constant.html
@@ -17,11 +17,7 @@
@@ -115,11 +111,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_gauss.html b/docs/reference/bc_gauss.html
index d5b57ebe..07d41694 100644
--- a/docs/reference/bc_gauss.html
+++ b/docs/reference/bc_gauss.html
@@ -17,11 +17,7 @@
@@ -114,11 +110,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_poly.html b/docs/reference/bc_poly.html
index 488abbd4..976204be 100644
--- a/docs/reference/bc_poly.html
+++ b/docs/reference/bc_poly.html
@@ -17,11 +17,7 @@
@@ -114,11 +110,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bc_spline.html b/docs/reference/bc_spline.html
index b44a93a9..364d0b1c 100644
--- a/docs/reference/bc_spline.html
+++ b/docs/reference/bc_spline.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/beta2lw.html b/docs/reference/beta2lw.html
index 2df9a7d7..6acdfc8c 100644
--- a/docs/reference/beta2lw.html
+++ b/docs/reference/beta2lw.html
@@ -18,11 +18,7 @@
@@ -112,11 +108,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/bin_spec.html b/docs/reference/bin_spec.html
index 19601cba..5ee3bab5 100644
--- a/docs/reference/bin_spec.html
+++ b/docs/reference/bin_spec.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_basis_corr_mat.html b/docs/reference/calc_basis_corr_mat.html
index 25eed3ef..b9b7cc8c 100644
--- a/docs/reference/calc_basis_corr_mat.html
+++ b/docs/reference/calc_basis_corr_mat.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/calc_basis_crlbs.html b/docs/reference/calc_basis_crlbs.html
index 9b8b0c37..7cfd8c87 100644
--- a/docs/reference/calc_basis_crlbs.html
+++ b/docs/reference/calc_basis_crlbs.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/calc_coil_noise_cor.html b/docs/reference/calc_coil_noise_cor.html
index e4e58d8a..57d385a0 100644
--- a/docs/reference/calc_coil_noise_cor.html
+++ b/docs/reference/calc_coil_noise_cor.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_coil_noise_sd.html b/docs/reference/calc_coil_noise_sd.html
index 4c4a4218..772e9162 100644
--- a/docs/reference/calc_coil_noise_sd.html
+++ b/docs/reference/calc_coil_noise_sd.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_design_efficiency.html b/docs/reference/calc_design_efficiency.html
index eb470b7a..15560eb8 100644
--- a/docs/reference/calc_design_efficiency.html
+++ b/docs/reference/calc_design_efficiency.html
@@ -17,11 +17,7 @@
@@ -110,11 +106,7 @@ Arguments
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_ed_from_lambda.html b/docs/reference/calc_ed_from_lambda.html
index 99ea03e7..534844d4 100644
--- a/docs/reference/calc_ed_from_lambda.html
+++ b/docs/reference/calc_ed_from_lambda.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_peak_info_vec.html b/docs/reference/calc_peak_info_vec.html
index 16a4310b..06cbf41b 100644
--- a/docs/reference/calc_peak_info_vec.html
+++ b/docs/reference/calc_peak_info_vec.html
@@ -17,11 +17,7 @@
@@ -115,11 +111,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_sd_poly.html b/docs/reference/calc_sd_poly.html
index 55b500d2..672e25c3 100644
--- a/docs/reference/calc_sd_poly.html
+++ b/docs/reference/calc_sd_poly.html
@@ -18,11 +18,7 @@
@@ -116,11 +112,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_spec_diff.html b/docs/reference/calc_spec_diff.html
index e258f6bb..a67f441b 100644
--- a/docs/reference/calc_spec_diff.html
+++ b/docs/reference/calc_spec_diff.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/calc_spec_snr.html b/docs/reference/calc_spec_snr.html
index 34e74a11..00913709 100644
--- a/docs/reference/calc_spec_snr.html
+++ b/docs/reference/calc_spec_snr.html
@@ -18,11 +18,7 @@
@@ -149,11 +145,7 @@ Details
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/check_lcm.html b/docs/reference/check_lcm.html
index 99fb5614..ed92f5f5 100644
--- a/docs/reference/check_lcm.html
+++ b/docs/reference/check_lcm.html
@@ -17,11 +17,7 @@
@@ -98,11 +94,7 @@ Check LCModel can be run
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/check_tqn.html b/docs/reference/check_tqn.html
index aef1d677..df05510f 100644
--- a/docs/reference/check_tqn.html
+++ b/docs/reference/check_tqn.html
@@ -17,11 +17,7 @@
@@ -98,11 +94,7 @@ Check the TARQUIN binary can be run
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/circ_mask.html b/docs/reference/circ_mask.html
index dad70c51..a1405f51 100644
--- a/docs/reference/circ_mask.html
+++ b/docs/reference/circ_mask.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/coherence_filter.html b/docs/reference/coherence_filter.html
index 8d49462c..467a56af 100644
--- a/docs/reference/coherence_filter.html
+++ b/docs/reference/coherence_filter.html
@@ -17,11 +17,7 @@
@@ -118,11 +114,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/collapse_to_dyns.html b/docs/reference/collapse_to_dyns.html
index 83bf2ca6..7bfbacb9 100644
--- a/docs/reference/collapse_to_dyns.html
+++ b/docs/reference/collapse_to_dyns.html
@@ -17,11 +17,7 @@
@@ -121,11 +117,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/comb_coils.html b/docs/reference/comb_coils.html
index 98cd6580..f52f39ad 100644
--- a/docs/reference/comb_coils.html
+++ b/docs/reference/comb_coils.html
@@ -19,11 +19,7 @@
@@ -165,11 +161,7 @@ Value
-<<<<<<< HEAD
- Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
diff --git a/docs/reference/comb_coils_mrsi_gls.html b/docs/reference/comb_coils_mrsi_gls.html
index 57bc19d2..88872ccb 100644
--- a/docs/reference/comb_coils_mrsi_gls.html
+++ b/docs/reference/comb_coils_mrsi_gls.html
@@ -4,11 +4,7 @@
-<<<<<<< HEAD
-
-=======
->>>>>>> devel
@@ -37,11 +29,7 @@
Tutorials
-<<<<<<< HEAD
-
-=======
->>>>>>> devel
-<<<<<<< HEAD
-
-=======
->>>>>>> devel
@@ -105,13 +85,6 @@ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:14
Arguments
-<<<<<<< HEAD
- - metab
-MRSI data containing metabolite data.
- noise_pts
-=======
Value
-<<<<<<< HEAD
-
-
-coil combined MRSI data.
-=======
coil combined MRSI data.
->>>>>>> devel
@@ -155,26 +117,15 @@ Value
-<<<<<<< HEAD
-
-
-
-
-=======
->>>>>>> devel
mrs_proc):+fit_res <- fit_mrs(mrs_proc, basis)Plot the fit result:
-@@ -313,53 +256,18 @@+plot(fit_res)
Unscaled amplitudes, CRLB error estimates and other useful fitting diagnostics, such as SNR, are given in the
-fit_resresults table:+fit_res$res_tab -<<<<<<< HEAD -#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr GABA -#> 1 1 1 1 1 1 0 8.133932e-06 3.547065e-05 4.02672e-05 1.697281e-05 -#> Glc Gln GSH Glu GPC Ins -#> 1 2.446596e-06 3.036132e-06 2.228048e-05 6.503217e-05 1.606706e-05 5.906155e-05 -#> Lac Lip09 Lip13a Lip13b Lip20 MM09 MM12 -#> 1 5.802284e-06 2.387704e-05 2.670653e-06 0 0 9.630788e-06 6.511381e-06 -#> MM14 MM17 MM20 NAA NAAG PCh -#> 1 2.603855e-05 2.238405e-05 9.203743e-05 6.011109e-05 1.536531e-05 0 -#> PCr sIns Tau tNAA tCr tCho -#> 1 2.101921e-05 6.504098e-06 0 7.54764e-05 6.12864e-05 1.606706e-05 -#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd -#> 1 6.80683e-05 3.350783e-05 3.522059e-05 9.203743e-05 2.386861e-06 4.343919e-06 -#> Asp.sd Cr.sd GABA.sd Glc.sd Gln.sd GSH.sd -#> 1 9.235326e-06 3.689004e-06 4.574407e-06 4.421681e-06 5.083001e-06 2.020426e-06 -#> Glu.sd GPC.sd Ins.sd Lac.sd Lip09.sd Lip13a.sd -#> 1 5.082976e-06 2.602651e-06 2.093225e-06 5.301703e-06 4.119256e-06 1.328305e-05 -#> Lip13b.sd Lip20.sd MM09.sd MM12.sd MM14.sd MM17.sd -#> 1 6.474481e-06 7.510908e-06 3.827554e-06 4.594019e-06 7.223367e-06 3.811301e-06 -#> MM20.sd NAA.sd NAAG.sd PCh.sd PCr.sd sIns.sd -#> 1 8.595853e-06 1.017712e-06 1.208985e-06 2.236873e-06 3.084598e-06 7.240068e-07 -#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd -#> 1 3.759956e-06 7.031383e-07 5.890481e-07 2.110662e-07 3.16966e-06 1.006794e-06 -#> tLM13.sd tLM20.sd phase lw shift asym -#> 1 1.573147e-06 3.016809e-06 11.10963 5.023681 -0.00376505 0.1771067 -#> res.deviance res.niter res.info -#> 1 7.307669e-05 28 2 -#> res.message bl_ed_pppm -#> 1 Relative error between `par' and the solution is at most `ptol'. 2.364083 -#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN -#> 1 FALSE 7.754368e-05 497 3.8 62.71687 51.3328 1.492722 -#> tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901 -#> 1 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159 -======= #> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr #> 1 1 1 1 1 1 0 8.133802e-06 3.547064e-05 4.026719e-05 #> GABA Glc Gln GSH Glu GPC @@ -263,32 +224,19 @@Basis simulation#> 1 FALSE 7.75437e-05 7.307671e-05 497 3.8 62.71686 51.33279 #> FQN tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901 #> 1 1.492722 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159 ->>>>>>> devel #> auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844 #> 1 -8.977355 -9.000064 -9.013367 -9.02055 #> auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384 #> 1 -9.024177 -9.023462 -9.009854 -8.958654 #> auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743 -<<<<<<< HEAD -#> 1 -8.844271 -8.690744 -8.562631 -8.485471 -#> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54 -#> 1 -8.447136 -8.430174 -8.423053 -8.420086 -======= #> 1 -8.844271 -8.690744 -8.56263 -8.485471 #> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54 #> 1 -8.447135 -8.430173 -8.423052 -8.420085 ->>>>>>> devel #> auto_bl_crit_0.532 auto_bl_crit_0.529 #> 1 -8.418839 -8.418312
Note that signal names appended with “.sd” are the CRLB estimates for the uncertainty (standard deviation) in the metabolite quantity estimate. e.g. to calculate the percentage s.d. for tNAA:
-<<<<<<< HEAD ---fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100 -#> [1] 0.9316001Spectral SNR:
-=======@@ -297,12 +245,7 @@fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100 #> [1] 0.9316002Basis simulationfit_res$res_tab$SNR #> [1] 62.71686
Linewidth of the tNAA resonance in PPM:
->>>>>>> devel--fit_res$res_tab$SNR -#> [1] 62.71687Linewidth of the tNAA resonance in PPM:
-fit_res$res_tab$tNAA_lw #> [1] 0.04562445Ratios to total-creatine -
->>>>>>> devel+-======= #> Ala 0.13271789 #> Asp 0.57876852 #> Cr 0.65703306 #> GABA 0.27694176 #> Glc 0.03992062 -#> Gln 0.04953983 +#> Gln 0.04953982 #> GSH 0.36354693 #> Glu 1.06111932 #> GPC 0.26216353 @@ -387,7 +295,6 @@fit_res_tcr_sc <- scale_amp_ratio(fit_res, "tCr") amps <- fit_amps(fit_res_tcr_sc) print(t(amps)) #> [,1] #> X.CrCH2 0.00000000 -<<<<<<< HEAD -#> Ala 0.13272001 -#> Asp 0.57876874 -#> Cr 0.65703313 -#> GABA 0.27694252 -#> Glc 0.03992071 -#> Gln 0.04954005 -#> GSH 0.36354683 -#> Glu 1.06111906 -#> GPC 0.26216356 -#> Ins 0.96369746 -#> Lac 0.09467490 -#> Lip09 0.38959768 -#> Lip13a 0.04357660 -#> Lip13b 0.00000000 -#> Lip20 0.00000000 -#> MM09 0.15714395 -#> MM12 0.10624512 -#> MM14 0.42486672 -#> MM17 0.36523688 -#> MM20 1.50175937 -#> NAA 0.98082268 -#> NAAG 0.25071313 -#> PCh 0.00000000 -#> PCr 0.34296687 -#> sIns 0.10612627 -#> Tau 0.00000000 -#> tNAA 1.23153582 -#> tCr 1.00000000 -#> tCho 0.26216356 -#> Glx 1.11065912 -#> tLM09 0.54674163 -#> tLM13 0.57468844 -#> tLM20 1.50175937Ratios to total-creatine#> tLM09 0.54674149 #> tLM13 0.57468661 #> tLM20 1.50175914
Water reference scaling, AKA “absolute-quantification”
@@ -395,14 +302,14 @@ Water reference sca
A more sophisticated approach to scaling metabolite values involves the use of a separate water-reference acquisition - which can be imported in the standard way:
-+fname_wref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant") mrs_data_wref <- read_mrs(fname_wref)The following code assumes the voxel contains 100% white matter tissue and scales the metabolite values into molal (mM) units (mol / kg tissue water) based on the method described by Gasparovic et al MRM 2006 55(6):1219-26:
-- +#> 1 1H 2.5 +custom_mol |> sim_mol() |> lb(2) |> zf() |> plot(xlim = c(4.4, 0.5))+@@ -281,9 +277,8 @@p_vols <- c(WM = 100, GM = 0, CSF = 0) TE = 0.03 TR = 2 @@ -414,14 +321,10 @@Water reference sca LCModel manual and references therein (section 10.2). This approach may be preferred when comparing results to those obtained LCModel or TARQUIN. -
->>>>>>> devel+-======= #> [1] 6.826335fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref) fit_res_molar$res_tab$tNAA -<<<<<<< HEAD -#> [1] 6.826336Note, while “absolute” units are attractive, a large number of assumptions about metabolite and water relaxation rates are necessary to arrive at these mM estimates. If you’re not confident at being able to @@ -447,11 +350,7 @@
Water reference sca diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png index a8160510..3640c474 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html index 0b599b16..83e21ed5 100644 --- a/docs/articles/spant-metabolite-simulation.html +++ b/docs/articles/spant-metabolite-simulation.html @@ -38,11 +38,7 @@
Custom molecules#> L/G lineshape : 0 #> #> nucleus chem_shift -#> 1 1H 2.5
Once your happy the new molecule is correct, please consider contributing it to the package if you think others would benefit.
@@ -305,11 +300,7 @@Custom molecules
-<<<<<<< HEAD
-Site built with pkgdown 2.0.9.
-=======
Site built with pkgdown 2.1.0.
->>>>>>> devel
Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> devel diff --git a/docs/authors.html b/docs/authors.html index a7fe7801..ee2d0e06 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,11 +17,7 @@ @@ -144,11 +140,7 @@Citation
-<<<<<<< HEAD
-
diff --git a/docs/index.html b/docs/index.html
index 1cf2cb48..2632666f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -40,11 +40,7 @@
@@ -269,11 +265,7 @@ Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> develDevelopers
-<<<<<<< HEAD
-
diff --git a/docs/news/index.html b/docs/news/index.html
index 63380a9d..cf75257c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,11 +17,7 @@
@@ -77,17 +73,18 @@ Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> develChangelog
-<<<<<<< HEAD
-
+ spant 2.22.0
-======= -spant 2.23.0
+spant 2.24.0
+- Added argument to adjust the legend font size in ortho3 function. +
- Improved metabolite simulation performance thanks to the expm package recently adding support for complex matrices. +
+
spant 2.23.02024-08-27
- abfit options for lipid and MM maximum broadening and maximum frequency shift now default to be the same as the metabolite values unless explicitly changed.
- Added function to calculate the correlation matrix from a basis_set.
- Fix for RDA files where a comma is sometimes used as a decimal point.
spant 2.22.02024-07-11
->>>>>>> devel- Added find_bids_mrs and mrs_data2bids helper functions.
- Improved handling of CMRR semi-LASER SVS water reference scans.
- Added functions for GLS coil combination. @@ -604,11 +601,7 @@
spant 0.1.02
-<<<<<<< HEAD
-
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 9f9c389c..384168c9 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,9 +1,5 @@
pandoc: 3.1.11
-<<<<<<< HEAD
-pkgdown: 2.0.9
-=======
pkgdown: 2.1.0
->>>>>>> devel
pkgdown_sha: ~
articles:
abfit-baseline-opts: abfit-baseline-opts.html
@@ -11,11 +7,7 @@ articles:
spant-intro: spant-intro.html
spant-metabolite-simulation: spant-metabolite-simulation.html
spant-preprocessing: spant-preprocessing.html
-<<<<<<< HEAD
-last_built: 2024-07-11T11:18Z
-=======
-last_built: 2024-08-27T13:06Z
->>>>>>> devel
+last_built: 2024-11-14T15:10Z
urls:
reference: https://martin3141.github.io/spant/reference
article: https://martin3141.github.io/spant/articles
diff --git a/docs/reference/Arg.mrs_data.html b/docs/reference/Arg.mrs_data.html
index 21cf298b..ec4791a6 100644
--- a/docs/reference/Arg.mrs_data.html
+++ b/docs/reference/Arg.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> develValue
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diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html
index c5ff53bb..a004e2df 100644
--- a/docs/reference/Conj.mrs_data.html
+++ b/docs/reference/Conj.mrs_data.html
@@ -17,11 +17,7 @@
@@ -111,11 +107,7 @@ Site built with pkgdown 2.0.9.
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diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html
index efda9d95..e1b0443d 100644
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+++ b/docs/reference/Im.mrs_data.html
@@ -17,11 +17,7 @@
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diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html
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diff --git a/docs/reference/Mod.mrs_data.html b/docs/reference/Mod.mrs_data.html
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diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html
index 8b9e62a0..df7091fb 100644
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diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html
index 5cbcc56c..745b3df3 100644
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diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html
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diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html
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diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html
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diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html
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diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html
index 792e2b27..2c23aa81 100644
--- a/docs/reference/Re.mrs_data.html
+++ b/docs/reference/Re.mrs_data.html
@@ -17,11 +17,7 @@
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diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html
index 91e4014c..bd06536b 100644
--- a/docs/reference/abfit_opts.html
+++ b/docs/reference/abfit_opts.html
@@ -17,11 +17,7 @@
@@ -96,6 +92,7 @@ Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> develReturn a list of options for an ABfit analysis.
bl_ed_pppm = 2, auto_bl_flex = TRUE, bl_comps_pppm = 15, + adaptive_bl_comps_pppm = FALSE, export_sp_fit = FALSE, max_asym = 0.25, max_basis_shift = 0.0078, @@ -126,16 +123,14 @@Return a list of options for an ABfit analysis.
freq_reg = NULL, freq_reg_naa = NULL, lb_reg = NULL, + asym_reg = NULL, output_all_paras = FALSE, output_all_paras_raw = FALSE, input_paras_raw = NULL, optim_lw_only = FALSE, optim_lw_only_limit = 20, lb_init = 0.001, -<<<<<<< HEAD -======= lb_init_approx_fit = FALSE, ->>>>>>> devel zf_offset = NULL ) @@ -203,6 +198,12 @@Arguments
spline basis density (signals per ppm).
adjust the spline basis density in the detailed +fit phase, based on the required level of smoothness, to reduce computation +time.
add the fitted spline functions to the fit result.
Arguments
individual line broadening parameter.
lineshape asymmetry parameter.
include more fitting parameters in the fit table, e.g. individual shift and damping factors for each basis set element.
Arguments
zero-fill. Default is NULL and will automatically set this to 50 points when the FID distortion flag is set for the mrs_data. - -offset in number of data points from the end of the FID to -zero-fill. Default is NULL and will automatically set this to 50 points when -the FID distortion flag is set for the mrs_data.
Value
@@ -411,11 +410,7 @@Examples
-<<<<<<< HEAD
-
diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html
index 04268252..909deac5 100644
--- a/docs/reference/abfit_opts_v1_9_0.html
+++ b/docs/reference/abfit_opts_v1_9_0.html
@@ -18,11 +18,7 @@
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-=======Site built with pkgdown 2.1.0.
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diff --git a/docs/reference/acquire.html b/docs/reference/acquire.html
index 05f23aaf..740c60f3 100644
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@@ -17,11 +17,7 @@
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diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html
index 9ba363ba..306c6967 100644
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@@ -17,11 +17,7 @@
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diff --git a/docs/reference/add_noise_spec_snr.html b/docs/reference/add_noise_spec_snr.html
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@@ -17,11 +17,7 @@
@@ -109,11 +105,7 @@ Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> develArguments
point. -<<<<<<< HEAD -measure the signal from the first scan in this reference data and apply the same target noise level to mrs_data.
Value
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diff --git a/docs/reference/align.html b/docs/reference/align.html
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diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html
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@@ -17,11 +17,7 @@
@@ -93,11 +89,7 @@ Site built with pkgdown 2.0.9.
-=======Site built with pkgdown 2.1.0.
->>>>>>> develArguments
MRSI data.
must be "hamming", "hanning" or "gaussian".
Value
-<<<<<<< HEAD
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diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html
index 58f87125..0c5c39b0 100644
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diff --git a/docs/reference/append_coils.html b/docs/reference/append_coils.html
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diff --git a/docs/reference/append_dyns.html b/docs/reference/append_dyns.html
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diff --git a/docs/reference/append_regs.html b/docs/reference/append_regs.html
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diff --git a/docs/reference/apply_axes.html b/docs/reference/apply_axes.html
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diff --git a/docs/reference/apply_mrs.html b/docs/reference/apply_mrs.html
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diff --git a/docs/reference/apply_pulse.html b/docs/reference/apply_pulse.html
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diff --git a/docs/reference/array2mrs_data.html b/docs/reference/array2mrs_data.html
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7d data array.
example data to copy acquisition parameters from.
example data to copy acquisition parameters from.
sampling frequency in Hz.
Value
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diff --git a/docs/reference/auto_phase.html b/docs/reference/auto_phase.html
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Arguments
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-MRSI data containing metabolite data.
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Value
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-
-coil combined MRSI data.
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coil combined MRSI data.
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Arguments
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MRSI data containing metabolite data.
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-
-- noise_pts -=======
Value
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