Add SDM-PSI Estimator

docs/api.rst

@@ -39,8 +39,11 @@ For more information about the components of coordinate-based meta-analysis in N
    meta.ibma
    meta.cbma.ale
    meta.cbma.mkda
+   meta.cbma.sdm
+   meta.cbma.sdm_simulations
    meta.cbma.base
    meta.kernel
+   meta.utils
 
 .. _api_results_ref:
 

docs/conf.py

@@ -51,6 +51,7 @@
     "sphinx.ext.intersphinx",  # links code to other packages
     "sphinx.ext.linkcode",  # links to code from api
     "sphinx.ext.napoleon",  # alternative to numpydoc
+    "sphinx.ext.todo",  # todo directives, only for in-progress SDM implementation
     "sphinx_copybutton",  # for copying code snippets
     "sphinx_gallery.gen_gallery",  # example gallery
     "sphinxarg.ext",  # argparse
@@ -240,3 +241,7 @@ def generate_example_rst(app, what, name, obj, options, lines):
     if not os.path.exists(examples_path):
         # touch file
         open(examples_path, "w").close()
+
+
+todo_include_todos = True
+todo_emit_warnings = False

docs/references.bib

@@ -1,3 +1,39 @@
+@article{albajes2019meta,
+  title={Meta-analysis of voxel-based neuroimaging studies using seed-based d mapping with permutation of subject images (SDM-PSI)},
+  author={Albajes-Eizagirre, Anton and Solanes, Aleix and Fullana, Miquel Angel and Ioannidis, John PA and Fusar-Poli, Paolo and Torrent, Carla and Sol{\'e}, Brisa and Bonn{\'\i}n, Caterina Mar and Vieta, Eduard and Mataix-Cols, David and others},
+  journal={JoVE (Journal of Visualized Experiments)},
+  number={153},
+  pages={e59841},
+  year={2019},
+  url={https://doi.org/10.3791/59841},
+  doi={10.3791/59841}
+}
+
+@article{albajes2019meta2,
+  title={Meta-analysis of non-statistically significant unreported effects},
+  author={Albajes-Eizagirre, Anton and Solanes, Aleix and Radua, Joaquim},
+  journal={Statistical methods in medical research},
+  volume={28},
+  number={12},
+  pages={3741--3754},
+  year={2019},
+  publisher={SAGE Publications Sage UK: London, England},
+  url={https://doi.org/10.1177%2F0962280218811349},
+  doi={10.1177%2F0962280218811349}
+}
+
+@article{albajes2019voxel,
+  title={Voxel-based meta-analysis via permutation of subject images (PSI): theory and implementation for SDM},
+  author={Albajes-Eizagirre, Anton and Solanes, Aleix and Vieta, Eduard and Radua, Joaquim},
+  journal={Neuroimage},
+  volume={186},
+  pages={174--184},
+  year={2019},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2018.10.077},
+  doi={10.1016/j.neuroimage.2018.10.077}
+}
+
 @article{amft2015definition,
   title={Definition and characterization of an extended social-affective default network},
   author={Amft, Maren and Bzdok, Danilo and Laird, Angela R and Fox, Peter T and Schilbach, Leonhard and Eickhoff, Simon B},
@@ -83,6 +119,17 @@ @article{bullmore1999global
   doi={10.1109/42.750253}
 }
 
+@article{cochran1954combination,
+  title={The combination of estimates from different experiments},
+  author={Cochran, William G},
+  journal={Biometrics},
+  volume={10},
+  number={1},
+  pages={101--129},
+  year={1954},
+  publisher={JSTOR}
+}
+
 @article{dersimonian1986meta,
   title={Meta-analysis in clinical trials},
   author={DerSimonian, Rebecca and Laird, Nan},
@@ -172,6 +219,17 @@ @book{hedges2014statistical
   publisher={Academic press}
 }
 
+@article{higgins2002quantifying,
+  title={Quantifying heterogeneity in a meta-analysis},
+  author={Higgins, Julian PT and Thompson, Simon G},
+  journal={Statistics in medicine},
+  volume={21},
+  number={11},
+  pages={1539--1558},
+  year={2002},
+  publisher={Wiley Online Library}
+}
+
 @article{hughett2008accurate,
   title={Accurate computation of the F-to-z and t-to-z transforms for large arguments},
   author={Hughett, Paul},
@@ -221,6 +279,18 @@ @article{langner2014meta
   doi={10.1016/j.neuroimage.2014.06.007}
 }
 
+@article{marshall2009combining,
+  title={Combining estimates of interest in prognostic 498 modelling studies after multiple imputation: current practice and guidelines},
+  author={Marshall, A and Altman, DG and Holder, RL and Royston, P},
+  journal={BMC Med Res 499 Methodol},
+  volume={9},
+  number={57},
+  pages={500},
+  year={2009},
+  url={https://doi.org/10.1186/1471-2288-9-57},
+  doi={10.1186/1471-2288-9-57}
+}
+
 @article{newman2009distributed,
   title={Distributed algorithms for topic models.},
   author={Newman, David and Asuncion, Arthur and Smyth, Padhraic and Welling, Max},
@@ -266,6 +336,18 @@ @article{poldrack2012discovering
   doi={10.1371/journal.pcbi.1002707}
 }
 
+@article{radua2014anisotropic,
+  title={Anisotropic kernels for coordinate-based meta-analyses of neuroimaging studies},
+  author={Radua, Joaquim and Rubia, Katya and Canales, Erick Jorge and Pomarol-Clotet, Edith and Fusar-Poli, Paolo and Mataix-Cols, David},
+  journal={Frontiers in psychiatry},
+  volume={5},
+  pages={13},
+  year={2014},
+  publisher={Frontiers},
+  url={https://doi.org/10.3389/fpsyt.2014.00013},
+  doi={10.3389/fpsyt.2014.00013}
+}
+
 @article{rubin2017decoding,
   title={Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition},
   author={Rubin, Timothy N and Koyejo, Oluwasanmi and Gorgolewski, Krzysztof J and Jones, Michael N and Poldrack, Russell A and Yarkoni, Tal},

nimare/meta/__init__.py

@@ -1,7 +1,7 @@
 """Coordinate-, image-, and effect-size-based meta-analysis estimators."""
 
 from . import ibma, kernel
-from .cbma import ALE, KDA, SCALE, ALESubtraction, MKDAChi2, MKDADensity, ale, mkda
+from .cbma import ALE, KDA, SCALE, ALESubtraction, MKDAChi2, MKDADensity, ale, mkda, sdm
 from .ibma import (
     DerSimonianLaird,
     Fishers,
@@ -36,4 +36,5 @@
     "ibma",
     "ale",
     "mkda",
+    "sdm",
 ]

nimare/meta/cbma/__init__.py

@@ -1,5 +1,6 @@
 """Coordinate-based meta-analytic estimators."""
 from .ale import ALE, SCALE, ALESubtraction
 from .mkda import KDA, MKDAChi2, MKDADensity
+from .sdm import run_sdm
 
-__all__ = ["ALE", "ALESubtraction", "SCALE", "MKDADensity", "MKDAChi2", "KDA"]
+__all__ = ["ALE", "ALESubtraction", "SCALE", "MKDADensity", "MKDAChi2", "KDA", "run_sdm"]