Source code for mb.core.regression.lmer

from mb.core.regression.core import *

#####################################
#
# REGRESSION EXECUTABLE TYPES
#
#####################################


[docs]class RegressionExecutableLMER(RegressionExecutable):
    MANIP = 'regress-lmer'
    STATIC_PREREQ_TYPES = ['scripts/regress-lmer.sh', 'scripts/lmer-tools.R', 'scripts/regress-lmer.R']
    DESCR_SHORT = 'LMER regression executable'
    DESCR_LONG = "Exectuable for fitting a linear mixed-effects (LMER) regression model"

    def body(self):
        out = 'cp %s %s' % (
            self.static_prereqs()[0].path,
            self.path
        )

        return out





#####################################
#
# PREDICTION EXECUTABLE TYPES
#
#####################################


[docs]class PredictionExecutableLMER(PredictionExecutable):
    MANIP = 'predict-lmer'
    STATIC_PREREQ_TYPES = ['scripts/predict-lmer.sh', 'scripts/lmer-tools.R', 'scripts/predict-lmer.R']
    DESCR_SHORT = 'LMER prediction executable'
    DESCR_LONG = "Exectuable for prediction from a linear mixed-effects (LMER) regression model"

    def body(self):
        out = 'cp %s %s' % (
            self.static_prereqs()[0].path,
            self.path
        )

        return out





#####################################
#
# SIGNIF EXECUTABLE TYPES
#
#####################################


[docs]class SignifExecutableLRT(SignifExecutable):
    MANIP = 'signif-lrt'
    STATIC_PREREQ_TYPES = ['scripts/signif-lrt.sh', 'scripts/lmer-tools.R', 'scripts/signif-lrt.R', 'scripts/signif.py']
    DESCR_SHORT = 'LRT signif executable'
    DESCR_LONG = "Exectuable for computing likelihood ratio test (LRT)"

    def body(self):
        out = 'cp %s %s' % (
            self.static_prereqs()[0].path,
            self.path
        )

        return out





#####################################
#
# REGRESSION TYPES
#
#####################################


[docs]class RegressionLMER(Regression):
    REGRESSION_TYPE = 'lmer'
    DESCR_SHORT = 'LMER regression'
    DESCR_LONG = "Run linear mixed-effects (LMER) regression"





#####################################
#
# PREDICTION TYPES
#
#####################################


[docs]class PredictionLMER(Prediction):
    REGRESSION_TYPE = 'lmer'
    DESCR_SHORT = 'LMER prediction'
    DESCR_LONG = "Predict from linear mixed-effects (LMER) regression"





#####################################
#
# SIGNIF TYPES
#
#####################################


[docs]class SignifLRT(Signif):
    STEM_PREREQ_TYPES = [PredictionLMER]
    SIGNIF_TYPE = 'lrt'
    DESCR_SHORT = 'LRT signif'
    DESCR_LONG = "Likelihood ratio significance test(s). Only available for LMER models."