Using jlmerclusterperm requires a prior installation of the Julia programming language, which can be downloaded from either the official website or using the command line utility juliaup. Julia version >=1.8 is required and 1.9 or higher is preferred for the substantial speed improvements.
+
Before using functions from jlmerclusterperm, an initial setup is required via calling jlmerclusterperm_setup(). The very first call on a system will install necessary dependencies (this only happens once and takes around 10-15 minutes).
+
Subsequent calls to jlmerclusterperm_setup() incur a small overhead of around 30 seconds, plus slight delays for first-time function calls. You pay up front for start-up and warm-up costs and get blazingly-fast functions from the package.
+
# Both lines must be run at the start of each new session
+library(jlmerclusterperm)
The paper Maris & Oostenveld (2007) which originally proposed the cluster-based permutation analysis.
+
The JuliaConnectoR package for powering the R interface to Julia.
+
The Julia packages GLM.jl and MixedModels.jl for fast implementations of (mixed effects) regression models.
+
Existing implementations of CPA in R (permuco, permutes, etc.) whose designs inspired the CPA interface in jlmerclusterperm.
+
+
+
+
Citations
+
If you use jlmerclusterperm for cluster-based permutation test with mixed-effects models in your research, please cite one (or more) of the following as you see fit.
Maris, E., & Oostenveld, R. (2007). Nonparametric statistical testing of EEG- and MEG-data. Journal of Neuroscience Methods, 164, 177–190. doi: 10.1016/j.jneumeth.2007.03.024.
+
+
To cite the Julia programming language:
+
+
Bezanson, J., Edelman, A., Karpinski, S., & Shah, V. B. (2017). Julia: A Fresh Approach to Numerical Computing. SIAM Review, 59(1), 65–98. doi: 10.1137/141000671.
+
+
To cite the GLM.jl and MixedModels.jl Julia libraries, consult their Zenodo pages:
diff --git a/docs/reference/figures/README-/CPA-io-dark.svg b/docs/reference/figures/README-/CPA-io-dark.svg
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+────────────────────────────────────────────────────────────────────────────────✔Detectingempiricalclustersandcalculatingcluster-massstatistics.[20ms]Progress:100%|████████████████████████████████████|Time:0:00:00(4.97ms/it)✔Samplingcluster-massstatisticsfromabootstrappednulldistribution.[912m✔Calculatingtheprobabilityoftheobservedcluster-massstatistics.[12ms]$null_cluster_dists──Nullcluster-massdistribution(t>2.5)────────────<null_cluster_dists>──Diet2(n=100)Mean(SD):-0.039(1.89)Coverageintervals:95%[-2.862,0.000]Diet3(n=100)Mean(SD):-0.129(2.02)Coverageintervals:95%[0.000,0.000]Diet4(n=100)Mean(SD):0.296(3.21)Coverageintervals:95%[0.000,5.797]$empirical_clusters──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121(p=0.0495)Diet3[3,12]:35.769(p=0.0099)Diet4[2,8]:32.442(p=0.0099)
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+──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121(p=0.0495)Diet3[3,12]:35.769(p=0.0099)Diet4[2,8]:32.442(p=0.0099)────────────────────────────────────────────────────────────────────────────────
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+──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121(p=0.0495)Diet3[3,12]:35.769(p=0.0099)Diet4[2,8]:32.442(p=0.0099)────────────────────────────────────────────────────────────────────────────────
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+
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diff --git a/docs/reference/figures/README-/empirical_clusters-dark.svg b/docs/reference/figures/README-/empirical_clusters-dark.svg
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+──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121Diet3[3,12]:35.769Diet4[2,8]:32.442────────────────────────────────────────────────────────────────────────────────
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+──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121Diet3[3,12]:35.769Diet4[2,8]:32.442────────────────────────────────────────────────────────────────────────────────
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+
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+
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+──Nullcluster-massdistribution(t>2.5)────────────<null_cluster_dists>──Diet2(n=100)Mean(SD):-0.039(1.89)Coverageintervals:95%[-2.862,0.000]Diet3(n=100)Mean(SD):-0.129(2.02)Coverageintervals:95%[0.000,0.000]Diet4(n=100)Mean(SD):0.296(3.21)Coverageintervals:95%[0.000,5.797]────────────────────────────────────────────────────────────────────────────────
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+──Nullcluster-massdistribution(t>2.5)────────────<null_cluster_dists>──Diet2(n=100)Mean(SD):-0.039(1.89)Coverageintervals:95%[-2.862,0.000]Diet3(n=100)Mean(SD):-0.129(2.02)Coverageintervals:95%[0.000,0.000]Diet4(n=100)Mean(SD):0.296(3.21)Coverageintervals:95%[0.000,5.797]────────────────────────────────────────────────────────────────────────────────
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diff --git a/docs/reference/figures/README-/reCPA-io-dark.svg b/docs/reference/figures/README-/reCPA-io-dark.svg
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+✔Detectingempiricalclustersandcalculatingcluster-massstatistics.[5.2s]Progress:100%|████████████████████████████████████|Time:0:00:00(6.23ms/it)✔Samplingcluster-massstatisticsfromabootstrappednulldistribution.[821m✔Calculatingtheprobabilityoftheobservedcluster-massstatistics.[12ms]──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.387(p=0.0594)Diet3[2,12]:39.919(p=0.0099)Diet4[2,8]:33.853(p=0.0099)────────────────────────────────────────────────────────────────────────────────
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diff --git a/docs/reference/figures/README-/reCPA-io.svg b/docs/reference/figures/README-/reCPA-io.svg
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+✔Detectingempiricalclustersandcalculatingcluster-massstatistics.[5.2s]Progress:100%|████████████████████████████████████|Time:0:00:00(6.23ms/it)✔Samplingcluster-massstatisticsfromabootstrappednulldistribution.[821m✔Calculatingtheprobabilityoftheobservedcluster-massstatistics.[12ms]──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.387(p=0.0594)Diet3[2,12]:39.919(p=0.0099)Diet4[2,8]:33.853(p=0.0099)────────────────────────────────────────────────────────────────────────────────
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+✔StartingJuliawith7threads[2.9s]✔Activatingpackageenvironment[8.3s]✔Runningpackagesetupscripts(11/11)[7.1s]
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@@ -0,0 +1 @@
+✔StartingJuliawith7threads[2.9s]✔Activatingpackageenvironment[8.3s]✔Runningpackagesetupscripts(11/11)[7.1s]
\ No newline at end of file
diff --git a/docs/reference/figures/README-/spec-io-dark.svg b/docs/reference/figures/README-/spec-io-dark.svg
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+++ b/docs/reference/figures/README-/spec-io-dark.svg
@@ -0,0 +1 @@
+──jlmerspecification─────────────────────────────────────────<jlmer_spec>──Formula:weight~1+Diet2+Diet3+Diet4Predictors:Diet:Diet2,Diet3,Diet4Groupings:Subject:ChickTrial:Time:TimeData:weightDiet2Diet3Diet4ChickTime142000112510001235900013[reached'max'/getOption("max.print")--omitted575rows]────────────────────────────────────────────────────────────────────────────────
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@@ -0,0 +1 @@
+──jlmerspecification─────────────────────────────────────────<jlmer_spec>──Formula:weight~1+Diet2+Diet3+Diet4Predictors:Diet:Diet2,Diet3,Diet4Groupings:Subject:ChickTrial:Time:TimeData:weightDiet2Diet3Diet4ChickTime142000112510001235900013[reached'max'/getOption("max.print")--omitted575rows]────────────────────────────────────────────────────────────────────────────────
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+thresholdpredictoridstartendlengthsum_statisticpvalue12.0Diet213538.4963760.0792079222.0Diet312121138.2160350.0099009932.0Diet412121141.6514680.0099009942.5Diet213426.1211410.0495049552.5Diet313121035.7689570.0099009962.5Diet4128732.4423520.00990099313.0Diet3135312.7192310.00990099213.0Diet32912414.0376220.00990099413.0Diet4127629.6594020.00990099
\ No newline at end of file
diff --git a/docs/reference/figures/README-/walk_threshold_steps.svg b/docs/reference/figures/README-/walk_threshold_steps.svg
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+thresholdpredictoridstartendlengthsum_statisticpvalue12.0Diet213538.4963760.0792079222.0Diet312121138.2160350.0099009932.0Diet412121141.6514680.0099009942.5Diet213426.1211410.0495049552.5Diet313121035.7689570.0099009962.5Diet4128732.4423520.00990099313.0Diet3135312.7192310.00990099213.0Diet32912414.0376220.00990099413.0Diet4127629.6594020.00990099
\ No newline at end of file
diff --git a/man/figures/README-/CPA-io-dark.svg b/man/figures/README-/CPA-io-dark.svg
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+────────────────────────────────────────────────────────────────────────────────✔Detectingempiricalclustersandcalculatingcluster-massstatistics.[20ms]Progress:100%|████████████████████████████████████|Time:0:00:00(4.97ms/it)✔Samplingcluster-massstatisticsfromabootstrappednulldistribution.[912m✔Calculatingtheprobabilityoftheobservedcluster-massstatistics.[12ms]$null_cluster_dists──Nullcluster-massdistribution(t>2.5)────────────<null_cluster_dists>──Diet2(n=100)Mean(SD):-0.039(1.89)Coverageintervals:95%[-2.862,0.000]Diet3(n=100)Mean(SD):-0.129(2.02)Coverageintervals:95%[0.000,0.000]Diet4(n=100)Mean(SD):0.296(3.21)Coverageintervals:95%[0.000,5.797]$empirical_clusters──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121(p=0.0495)Diet3[3,12]:35.769(p=0.0099)Diet4[2,8]:32.442(p=0.0099)
\ No newline at end of file
diff --git a/man/figures/README-/CPA-io.svg b/man/figures/README-/CPA-io.svg
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+++ b/man/figures/README-/CPA-io.svg
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+────────────────────────────────────────────────────────────────────────────────✔Detectingempiricalclustersandcalculatingcluster-massstatistics.[20ms]Progress:100%|████████████████████████████████████|Time:0:00:00(4.97ms/it)✔Samplingcluster-massstatisticsfromabootstrappednulldistribution.[912m✔Calculatingtheprobabilityoftheobservedcluster-massstatistics.[12ms]$null_cluster_dists──Nullcluster-massdistribution(t>2.5)────────────<null_cluster_dists>──Diet2(n=100)Mean(SD):-0.039(1.89)Coverageintervals:95%[-2.862,0.000]Diet3(n=100)Mean(SD):-0.129(2.02)Coverageintervals:95%[0.000,0.000]Diet4(n=100)Mean(SD):0.296(3.21)Coverageintervals:95%[0.000,5.797]$empirical_clusters──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121(p=0.0495)Diet3[3,12]:35.769(p=0.0099)Diet4[2,8]:32.442(p=0.0099)
\ No newline at end of file
diff --git a/man/figures/README-/calculate_clusters_pvalues-dark.svg b/man/figures/README-/calculate_clusters_pvalues-dark.svg
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index 0000000..a18265e
--- /dev/null
+++ b/man/figures/README-/calculate_clusters_pvalues-dark.svg
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+──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121(p=0.0495)Diet3[3,12]:35.769(p=0.0099)Diet4[2,8]:32.442(p=0.0099)────────────────────────────────────────────────────────────────────────────────
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diff --git a/man/figures/README-/calculate_clusters_pvalues.svg b/man/figures/README-/calculate_clusters_pvalues.svg
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index 0000000..5d4516e
--- /dev/null
+++ b/man/figures/README-/calculate_clusters_pvalues.svg
@@ -0,0 +1 @@
+──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121(p=0.0495)Diet3[3,12]:35.769(p=0.0099)Diet4[2,8]:32.442(p=0.0099)────────────────────────────────────────────────────────────────────────────────
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diff --git a/man/figures/README-/empirical_clusters-dark.svg b/man/figures/README-/empirical_clusters-dark.svg
new file mode 100644
index 0000000..ad64e7d
--- /dev/null
+++ b/man/figures/README-/empirical_clusters-dark.svg
@@ -0,0 +1 @@
+──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121Diet3[3,12]:35.769Diet4[2,8]:32.442────────────────────────────────────────────────────────────────────────────────
\ No newline at end of file
diff --git a/man/figures/README-/empirical_clusters.svg b/man/figures/README-/empirical_clusters.svg
new file mode 100644
index 0000000..90b6352
--- /dev/null
+++ b/man/figures/README-/empirical_clusters.svg
@@ -0,0 +1 @@
+──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.121Diet3[3,12]:35.769Diet4[2,8]:32.442────────────────────────────────────────────────────────────────────────────────
\ No newline at end of file
diff --git a/man/figures/README-/null_statistics-dark.svg b/man/figures/README-/null_statistics-dark.svg
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--- /dev/null
+++ b/man/figures/README-/null_statistics-dark.svg
@@ -0,0 +1 @@
+──Nullcluster-massdistribution(t>2.5)────────────<null_cluster_dists>──Diet2(n=100)Mean(SD):-0.039(1.89)Coverageintervals:95%[-2.862,0.000]Diet3(n=100)Mean(SD):-0.129(2.02)Coverageintervals:95%[0.000,0.000]Diet4(n=100)Mean(SD):0.296(3.21)Coverageintervals:95%[0.000,5.797]────────────────────────────────────────────────────────────────────────────────
\ No newline at end of file
diff --git a/man/figures/README-/null_statistics.svg b/man/figures/README-/null_statistics.svg
new file mode 100644
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--- /dev/null
+++ b/man/figures/README-/null_statistics.svg
@@ -0,0 +1 @@
+──Nullcluster-massdistribution(t>2.5)────────────<null_cluster_dists>──Diet2(n=100)Mean(SD):-0.039(1.89)Coverageintervals:95%[-2.862,0.000]Diet3(n=100)Mean(SD):-0.129(2.02)Coverageintervals:95%[0.000,0.000]Diet4(n=100)Mean(SD):0.296(3.21)Coverageintervals:95%[0.000,5.797]────────────────────────────────────────────────────────────────────────────────
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diff --git a/man/figures/README-/reCPA-io-dark.svg b/man/figures/README-/reCPA-io-dark.svg
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--- /dev/null
+++ b/man/figures/README-/reCPA-io-dark.svg
@@ -0,0 +1 @@
+✔Detectingempiricalclustersandcalculatingcluster-massstatistics.[5.2s]Progress:100%|████████████████████████████████████|Time:0:00:00(6.23ms/it)✔Samplingcluster-massstatisticsfromabootstrappednulldistribution.[821m✔Calculatingtheprobabilityoftheobservedcluster-massstatistics.[12ms]──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.387(p=0.0594)Diet3[2,12]:39.919(p=0.0099)Diet4[2,8]:33.853(p=0.0099)────────────────────────────────────────────────────────────────────────────────
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diff --git a/man/figures/README-/reCPA-io.svg b/man/figures/README-/reCPA-io.svg
new file mode 100644
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--- /dev/null
+++ b/man/figures/README-/reCPA-io.svg
@@ -0,0 +1 @@
+✔Detectingempiricalclustersandcalculatingcluster-massstatistics.[5.2s]Progress:100%|████████████████████████████████████|Time:0:00:00(6.23ms/it)✔Samplingcluster-massstatisticsfromabootstrappednulldistribution.[821m✔Calculatingtheprobabilityoftheobservedcluster-massstatistics.[12ms]──Empiricalclusters(t>2.5)────────────────────────<empirical_clusters>──Diet2[3,4]:6.387(p=0.0594)Diet3[2,12]:39.919(p=0.0099)Diet4[2,8]:33.853(p=0.0099)────────────────────────────────────────────────────────────────────────────────
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diff --git a/man/figures/README-/setup-io-dark.svg b/man/figures/README-/setup-io-dark.svg
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--- /dev/null
+++ b/man/figures/README-/setup-io-dark.svg
@@ -0,0 +1 @@
+✔StartingJuliawith7threads[2.9s]✔Activatingpackageenvironment[8.3s]✔Runningpackagesetupscripts(11/11)[7.1s]
\ No newline at end of file
diff --git a/man/figures/README-/setup-io.svg b/man/figures/README-/setup-io.svg
new file mode 100644
index 0000000..2b1bf31
--- /dev/null
+++ b/man/figures/README-/setup-io.svg
@@ -0,0 +1 @@
+✔StartingJuliawith7threads[2.9s]✔Activatingpackageenvironment[8.3s]✔Runningpackagesetupscripts(11/11)[7.1s]
\ No newline at end of file
diff --git a/man/figures/README-/spec-io-dark.svg b/man/figures/README-/spec-io-dark.svg
new file mode 100644
index 0000000..fcc9cfa
--- /dev/null
+++ b/man/figures/README-/spec-io-dark.svg
@@ -0,0 +1 @@
+──jlmerspecification─────────────────────────────────────────<jlmer_spec>──Formula:weight~1+Diet2+Diet3+Diet4Predictors:Diet:Diet2,Diet3,Diet4Groupings:Subject:ChickTrial:Time:TimeData:weightDiet2Diet3Diet4ChickTime142000112510001235900013[reached'max'/getOption("max.print")--omitted575rows]────────────────────────────────────────────────────────────────────────────────
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diff --git a/man/figures/README-/spec-io.svg b/man/figures/README-/spec-io.svg
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+++ b/man/figures/README-/spec-io.svg
@@ -0,0 +1 @@
+──jlmerspecification─────────────────────────────────────────<jlmer_spec>──Formula:weight~1+Diet2+Diet3+Diet4Predictors:Diet:Diet2,Diet3,Diet4Groupings:Subject:ChickTrial:Time:TimeData:weightDiet2Diet3Diet4ChickTime142000112510001235900013[reached'max'/getOption("max.print")--omitted575rows]────────────────────────────────────────────────────────────────────────────────
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diff --git a/man/figures/README-/walk_threshold_steps-dark.svg b/man/figures/README-/walk_threshold_steps-dark.svg
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@@ -0,0 +1 @@
+thresholdpredictoridstartendlengthsum_statisticpvalue12.0Diet213538.4963760.0792079222.0Diet312121138.2160350.0099009932.0Diet412121141.6514680.0099009942.5Diet213426.1211410.0495049552.5Diet313121035.7689570.0099009962.5Diet4128732.4423520.00990099313.0Diet3135312.7192310.00990099213.0Diet32912414.0376220.00990099413.0Diet4127629.6594020.00990099
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diff --git a/man/figures/README-/walk_threshold_steps.svg b/man/figures/README-/walk_threshold_steps.svg
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index 0000000..19869e5
--- /dev/null
+++ b/man/figures/README-/walk_threshold_steps.svg
@@ -0,0 +1 @@
+thresholdpredictoridstartendlengthsum_statisticpvalue12.0Diet213538.4963760.0792079222.0Diet312121138.2160350.0099009932.0Diet412121141.6514680.0099009942.5Diet213426.1211410.0495049552.5Diet313121035.7689570.0099009962.5Diet4128732.4423520.00990099313.0Diet3135312.7192310.00990099213.0Diet32912414.0376220.00990099413.0Diet4127629.6594020.00990099
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diff --git a/man/figures/README-plot-empirical_statistics-1.png b/man/figures/README-plot-empirical_statistics-1.png
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