def setup_pages(self, model, last_analysis):
self.choose_effect_size_page = ChooseEffectSizePage(
add_generic_effect=True,
data_type=last_analysis['data_type'],
metric=last_analysis['metric'],
var_groups = model.get_variable_groups())
self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page)
self.data_location_page = DataLocationPage(model=model)
self.setPage(Page_DataLocation, self.data_location_page)
self.refine_studies_page = RefineStudiesPage(model=model)
self.setPage(Page_RefineStudies, self.refine_studies_page)
self.meta_reg_details_page = MetaRegDetailsPage(
fixed_effects=last_analysis['fixed_effects'],
random_effects_method=last_analysis['random_effects_method'],
analysis_type=last_analysis['analysis_type'], # PARAMETRIC or BOOTSTRAP
conf_level=last_analysis['conf_level'],
phylogen=last_analysis['phylogen'],
disable_analysis_type_groupbox=True,
disable_output_type_groupbox=True)
self.setPage(Page_MetaRegDetails, self.meta_reg_details_page)
self.ma_details_page = MADetailsPage()
self.setPage(Page_MADetails, self.ma_details_page)
self.perm_pg = PermuationPage()
self.setPage(Page_Permutation, self.perm_pg)
self.select_covariates_page = SelectCovariatesPage(
model=model,
previously_included_covs=last_analysis['included_covariates'],
disable_require_categorical=True)
self.setPage(Page_SelectCovariates, self.select_covariates_page)
self.reference_value_page = ReferenceValuePage(
model=model,
prev_cov_to_ref_level=last_analysis['cov_2_ref_values'])
self.setPage(Page_ReferenceValues, self.reference_value_page)
self.summary_page = SummaryPage()
self.setPage(Page_Summary, self.summary_page)
class MetaRegressionWizard(QtGui.QWizard):
def __init__(self, model, parent=None):
super(MetaRegressionWizard, self).__init__(parent)
self.model = model
last_analysis=model.get_last_analysis_selections()
self.analysis_label = "Meta-Regression"
self.setWindowTitle(self.analysis_label)
self.setup_pages(model=model, last_analysis=last_analysis)
self.setWizardStyle(QWizard.ClassicStyle)
# Automatically resize wizard on each page flip
self.currentIdChanged.connect(self._change_size)
def _change_size(self, pageid):
print("changing size")
self.adjustSize()
def setup_pages(self, model, last_analysis):
self.choose_effect_size_page = ChooseEffectSizePage(add_generic_effect=True,
data_type=last_analysis['data_type'],
metric=last_analysis['metric'],
var_groups = model.get_variable_groups())
self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page)
self.data_location_page = DataLocationPage(model=model)
self.setPage(Page_DataLocation, self.data_location_page)
self.refine_studies_page = RefineStudiesPage(model=model)
self.setPage(Page_RefineStudies, self.refine_studies_page)
self.meta_reg_details_page = MetaRegDetailsPage(
fixed_effects=last_analysis['fixed_effects'],
random_effects_method = last_analysis['random_effects_method'],
analysis_type=last_analysis['analysis_type'], # PARAMETRIC or BOOTSTRAP
conf_level=last_analysis['conf_level'],
phylogen=last_analysis['phylogen'])
self.setPage(Page_MetaRegDetails, self.meta_reg_details_page)
self.select_covariates_page = SelectCovariatesPage(
model=model,
previously_included_covs=last_analysis['included_covariates'])
self.setPage(Page_SelectCovariates, self.select_covariates_page)
self.reference_value_page = ReferenceValuePage(
model=model,
prev_cov_to_ref_level=last_analysis['cov_2_ref_values'])
self.setPage(Page_ReferenceValues, self.reference_value_page)
self.summary_page = SummaryPage()
self.setPage(Page_Summary, self.summary_page)
# weird stuff
self.cond_means_pg = CondMeansPage(model=model)
self.setPage(Page_CondMeans, self.cond_means_pg)
self.bootstrap_page = BootstrapPage(model=model)
self.setPage(Page_Bootstrap, self.bootstrap_page)
def _require_categorical(self):
return self.meta_reg_details_page.get_output_type() == CONDITIONAL_MEANS
def nextId(self):
current_id = self.currentId()
return self.nextId_helper(current_id)
def nextId_helper(self, page_id):
if page_id in [Page_MetaRegDetails, Page_Bootstrap, Page_ReferenceValues]:
analysis_type = self.get_analysis_type() # PARAMETRIC or BOOTSTRAP
output_type = self.get_output_type() # NORMAL or CONDITIONAL_MEANS
if page_id == Page_ChooseEffectSize:
return Page_DataLocation
elif page_id == Page_DataLocation:
return Page_RefineStudies
elif page_id == Page_RefineStudies:
return Page_SelectCovariates
elif page_id == Page_SelectCovariates:
return Page_MetaRegDetails
elif page_id == Page_MetaRegDetails:
if self._categorical_covariates_selected():
return Page_ReferenceValues
else:
if analysis_type == BOOTSTRAP:
return Page_Bootstrap
elif output_type == CONDITIONAL_MEANS:
return Page_CondMeans
else:
return Page_Summary
elif page_id == Page_Bootstrap:
if output_type == CONDITIONAL_MEANS:
return Page_CondMeans
else:
return Page_Summary
elif page_id == Page_CondMeans:
return Page_Summary
elif page_id == Page_ReferenceValues:
if analysis_type == BOOTSTRAP:
return Page_Bootstrap
elif output_type == CONDITIONAL_MEANS:
return Page_CondMeans
else:
return Page_Summary
elif page_id == Page_Summary:
return -1
def _categorical_covariates_selected(self):
'''are categorical variables selected?'''
included_covariates = self.get_included_covariates()
categorical_covariates = [cov for cov in included_covariates if cov.get_type()==CATEGORICAL]
return len(categorical_covariates) > 0
################ Getters to get data from wizard #########################
# Effect Size Page
def get_data_type_and_metric(self):
''' returns tuple (data_type, metric) '''
return self.choose_effect_size_page.get_data_type_and_metric()
# Data location page
def get_data_location(self):
return self.data_location_page.get_data_locations()
# Refine studies page
def get_included_studies_in_proper_order(self):
all_studies = self.model.get_studies_in_current_order()
included_studies = self.refine_studies_page.get_included_studies()
included_studies_in_order = [study for study in all_studies if study in included_studies]
return included_studies_in_order
# Select covariates Page
def get_included_covariates(self):
return self.select_covariates_page.get_included_covariates()
def get_included_interactions(self):
return self.select_covariates_page.get_interactions()
# Meta regression details page
def using_fixed_effects(self):
return self.meta_reg_details_page.get_using_fixed_effects()
def get_conf_level(self):
return self.meta_reg_details_page.get_confidence_level()
def get_random_effects_method(self):
return self.meta_reg_details_page.get_random_effects_method()
def get_phylogen(self):
return self.meta_reg_details_page.get_phylogen()
def get_analysis_type(self): # NORMAL or BOOTSTRAP
return self.meta_reg_details_page.get_analysis_type()
def get_output_type(self): # PARAMETRIC or CONDITIONAL_MEANS
return self.meta_reg_details_page.get_output_type()
def get_btt(self): # (a var or interaction, None, 'covariate', 'interaction' i.e. the type)
return self.meta_reg_details_page.get_btt()
# Reference Values page
def get_covariate_reference_levels(self):
return self.reference_value_page.get_covariate_reference_levels()
# Conditional Means page
def get_meta_reg_cond_means_info(self):
# returns a tuple (cat. cov to stratify over, the values for the other covariates)
return self.cond_means_pg.get_meta_reg_cond_means_data()
# Bootstrap page
def get_bootstrap_params(self):
return self.bootstrap_page.get_bootstrap_params()
# Summary page
def save_selections(self):
return self.summary_page.save_selections()
######################### end of getters #################################
# Summary Page
def get_summary(self):
''' Make a summary string to show the user at the end of the wizard summarizing most of the user selections '''
summary = wizard_summary(
wizard=self,
next_id_helper=self.nextId_helper,
summary_page_id=Page_Summary,
analysis_label=self.analysis_label
)
return summary
def __init__(self, model, parent=None):
super(MiMaWizard, self).__init__(parent)
self.analysis_label = "Multiply-Imputed Meta Analysis/Regression"
self.model = model
self.imp_results = None
last_analysis = model.get_last_analysis_selections() # selections from last analysis of whatever type
# Initialize pages that we will need to access later
self.parameters_page = MetaAnalysisParametersPage(method="FE" if last_analysis['fixed_effects'] else last_analysis['random_effects_method'],
level=model.get_conf_level(),
digits=model.get_precision(),
knha=last_analysis['knha'])
self.setPage(Page_Parameters, self.parameters_page)
# choose effect size
self.choose_effect_size_page = ChooseEffectSizePage(add_generic_effect=True,
data_type=last_analysis['data_type'],
metric=last_analysis['metric'],
var_groups = model.get_variable_groups())
self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page)
# data location page
self.data_location_page = DataLocationPage(model=model)
self.setPage(Page_DataLocation, self.data_location_page)
# refine studies page
self.refine_studies_page = RefineStudiesPage(model=model)
self.setPage(Page_RefineStudies, self.refine_studies_page)
# summary page
self.summary_page = SummaryPage()
self.setPage(Page_Summary, self.summary_page)
# Mice Parameters Page
self.mice_params_page = MiceParametersPage()
self.setPage(Page_MiceParameters, self.mice_params_page)
# Covariate Select Page (for choosing covariates to impute with)
self.cov_select_page = CovariateSelectPage(model = self.model)
self.setPage(Page_CovariateSelect, self.cov_select_page)
# Select Covariates page (for choosing covariates to do with regression with)
self.select_covariates_page = SelectCovariatesPage(
model=model,
previously_included_covs=last_analysis['included_covariates'],
min_covariates=0,
allow_covs_with_missing_data=True)
self.setPage(Page_SelectCovariates, self.select_covariates_page)
# Reference Value Page
self.reference_value_page = ReferenceValuePage(
model=model,
prev_cov_to_ref_level=last_analysis['cov_2_ref_values'])
self.setPage(Page_ReferenceValues, self.reference_value_page)
# Mice Output page
self.mice_output_page = MiceOutputPage()
self.setPage(Page_MiceOutput, self.mice_output_page)
self.setWizardStyle(QWizard.ClassicStyle)
self.setStartId(Page_ChooseEffectSize)
self.setOption(QWizard.HaveFinishButtonOnEarlyPages,True)
QObject.connect(self, SIGNAL("currentIdChanged(int)"), self._change_size)
self.setWindowTitle("Multiply-Imputed Meta-Analysis")
class PermutationWizard(QtGui.QWizard):
# if meta_reg mode is True, the wizard will do a permutation
# test for a meta-regression, otherwise it does a standard
# meta-analysis
def __init__(self, model, meta_reg_mode=False, parent=None):
super(PermutationWizard, self).__init__(parent)
self.model = model
last_analysis = model.get_last_analysis_selections()
self.meta_reg_mode = meta_reg_mode
# Set window title
if meta_reg_mode:
self.analysis_label = "Permuted Meta-Regression"
else:
self.analysis_label = "Permuted Meta-Analysis"
self.setWindowTitle(self.analysis_label)
self.setup_pages(model=model, last_analysis=last_analysis)
self.setWizardStyle(QWizard.ClassicStyle)
# Automatically resize wizard on each page flip
self.currentIdChanged.connect(self.adjustSize)
def setup_pages(self, model, last_analysis):
self.choose_effect_size_page = ChooseEffectSizePage(
add_generic_effect=True,
data_type=last_analysis['data_type'],
metric=last_analysis['metric'],
var_groups = model.get_variable_groups())
self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page)
self.data_location_page = DataLocationPage(model=model)
self.setPage(Page_DataLocation, self.data_location_page)
self.refine_studies_page = RefineStudiesPage(model=model)
self.setPage(Page_RefineStudies, self.refine_studies_page)
self.meta_reg_details_page = MetaRegDetailsPage(
fixed_effects=last_analysis['fixed_effects'],
random_effects_method=last_analysis['random_effects_method'],
analysis_type=last_analysis['analysis_type'], # PARAMETRIC or BOOTSTRAP
conf_level=last_analysis['conf_level'],
phylogen=last_analysis['phylogen'],
disable_analysis_type_groupbox=True,
disable_output_type_groupbox=True)
self.setPage(Page_MetaRegDetails, self.meta_reg_details_page)
self.ma_details_page = MADetailsPage()
self.setPage(Page_MADetails, self.ma_details_page)
self.perm_pg = PermuationPage()
self.setPage(Page_Permutation, self.perm_pg)
self.select_covariates_page = SelectCovariatesPage(
model=model,
previously_included_covs=last_analysis['included_covariates'],
disable_require_categorical=True)
self.setPage(Page_SelectCovariates, self.select_covariates_page)
self.reference_value_page = ReferenceValuePage(
model=model,
prev_cov_to_ref_level=last_analysis['cov_2_ref_values'])
self.setPage(Page_ReferenceValues, self.reference_value_page)
self.summary_page = SummaryPage()
self.setPage(Page_Summary, self.summary_page)
def nextId(self):
current_id = self.currentId()
return self.nextId_helper(current_id)
def nextId_helper(self, page_id):
if self.meta_reg_mode:
if page_id == Page_ChooseEffectSize:
return Page_DataLocation
elif page_id == Page_DataLocation:
return Page_RefineStudies
elif page_id == Page_RefineStudies:
return Page_SelectCovariates
elif page_id == Page_SelectCovariates:
return Page_MetaRegDetails
elif page_id == Page_MetaRegDetails:
if self._categorical_covariates_selected():
return Page_ReferenceValues
else:
return Page_Permutation
elif page_id == Page_ReferenceValues:
return Page_Permutation
elif page_id == Page_Permutation:
return Page_Summary
elif page_id == Page_Summary:
return -1
else: # non-meta regression mode (no moderators)
if page_id == Page_ChooseEffectSize:
return Page_DataLocation
elif page_id == Page_DataLocation:
return Page_RefineStudies
elif page_id == Page_RefineStudies:
return Page_MADetails
elif page_id == Page_MADetails:
return Page_Permutation
elif page_id == Page_ReferenceValues:
return Page_Permutation
elif page_id == Page_Permutation:
return Page_Summary
elif page_id == Page_Summary:
return -1
def _categorical_covariates_selected(self):
'''are categorical variables selected?'''
included_covariates = self.get_included_covariates()
categorical_covariates = [cov for cov in included_covariates if cov.get_type()==CATEGORICAL]
return len(categorical_covariates) > 0
################# getters #########################
def get_parameters(self):
data_type_and_metric = self.choose_effect_size_page.get_data_type_and_metric()
data_location = self.data_location_page.get_data_locations()
studies = self.refine_studies_page.get_included_studies_in_proper_order()
parameters = {
'data_type_and_metric': data_type_and_metric,
'data_location': data_location,
'studies': studies,
}
parameters.update(self.perm_pg.get_choices())
# meta-regression specific
if self.meta_reg_mode:
covariates = self.select_covariates_page.get_included_covariates()
interactions = self.select_covariates_page.get_interactions()
_fixed_effects = self.meta_reg_details_page.get_using_fixed_effects()
level = self.meta_reg_details_page.get_confidence_level()
_random_effects_method = self.meta_reg_details_page.get_random_effects_method()
method = _random_effects_method if not _fixed_effects else FIXED_EFFECTS_METHOD_STR
phylogen = self.meta_reg_details_page.get_phylogen()
btt = self.meta_reg_details_page.get_btt()
reference_values = self.reference_value_page.get_covariate_reference_levels()
parameters.update({
'covariates': covariates,
'interactions': interactions,
'level': level,
'method': method,
'phylogen': phylogen,
'btt': btt,
'reference_values': reference_values,
})
else:
# ma specific (no moderators)
method = self.ma_details_page.get_method()
intercept = self.ma_details_page.get_intercept()
weighted = self.ma_details_page.get_weighted_least_squares()
knha = self.ma_details_page.get_knha()
level = self.ma_details_page.get_confidence_level()
digits = self.ma_details_page.get_digits()
parameters.update({
'method':method,
'intercept':intercept,
'weighted':weighted,
'knha':knha,
'level':level,
'digits':digits,
})
return parameters
# Summary page
def save_selections(self):
return self.summary_page.save_selections()
# Effect Size Page
def get_data_type_and_metric(self):
''' returns tuple (data_type, metric) '''
return self.choose_effect_size_page.get_data_type_and_metric()
# Data location page
def get_data_location(self):
return self.data_location_page.get_data_locations()
# Refine studies page
def get_included_studies_in_proper_order(self):
all_studies = self.model.get_studies_in_current_order()
included_studies = self.refine_studies_page.get_included_studies()
included_studies_in_order = [study for study in all_studies if study in included_studies]
return included_studies_in_order
# Select covariates Page
def get_included_covariates(self):
return self.select_covariates_page.get_included_covariates()
def get_included_interactions(self):
return self.select_covariates_page.get_interactions()
######################### end of getters #################################
# Summary Page
def get_summary(self):
''' Make a summary string to show the user at the end of the wizard summarizing most of the user selections '''
summary = wizard_summary(
wizard=self,
next_id_helper=self.nextId_helper,
summary_page_id=Page_Summary,
analysis_label=self.analysis_label
)
return summary
class MiMaWizard(QtGui.QWizard):
def __init__(self, model, parent=None):
super(MiMaWizard, self).__init__(parent)
self.analysis_label = "Multiply-Imputed Meta Analysis/Regression"
self.model = model
self.imp_results = None
last_analysis = model.get_last_analysis_selections() # selections from last analysis of whatever type
# Initialize pages that we will need to access later
self.parameters_page = MetaAnalysisParametersPage(method="FE" if last_analysis['fixed_effects'] else last_analysis['random_effects_method'],
level=model.get_conf_level(),
digits=model.get_precision(),
knha=last_analysis['knha'])
self.setPage(Page_Parameters, self.parameters_page)
# choose effect size
self.choose_effect_size_page = ChooseEffectSizePage(add_generic_effect=True,
data_type=last_analysis['data_type'],
metric=last_analysis['metric'],
var_groups = model.get_variable_groups())
self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page)
# data location page
self.data_location_page = DataLocationPage(model=model)
self.setPage(Page_DataLocation, self.data_location_page)
# refine studies page
self.refine_studies_page = RefineStudiesPage(model=model)
self.setPage(Page_RefineStudies, self.refine_studies_page)
# summary page
self.summary_page = SummaryPage()
self.setPage(Page_Summary, self.summary_page)
# Mice Parameters Page
self.mice_params_page = MiceParametersPage()
self.setPage(Page_MiceParameters, self.mice_params_page)
# Covariate Select Page (for choosing covariates to impute with)
self.cov_select_page = CovariateSelectPage(model = self.model)
self.setPage(Page_CovariateSelect, self.cov_select_page)
# Select Covariates page (for choosing covariates to do with regression with)
self.select_covariates_page = SelectCovariatesPage(
model=model,
previously_included_covs=last_analysis['included_covariates'],
min_covariates=0,
allow_covs_with_missing_data=True)
self.setPage(Page_SelectCovariates, self.select_covariates_page)
# Reference Value Page
self.reference_value_page = ReferenceValuePage(
model=model,
prev_cov_to_ref_level=last_analysis['cov_2_ref_values'])
self.setPage(Page_ReferenceValues, self.reference_value_page)
# Mice Output page
self.mice_output_page = MiceOutputPage()
self.setPage(Page_MiceOutput, self.mice_output_page)
self.setWizardStyle(QWizard.ClassicStyle)
self.setStartId(Page_ChooseEffectSize)
self.setOption(QWizard.HaveFinishButtonOnEarlyPages,True)
QObject.connect(self, SIGNAL("currentIdChanged(int)"), self._change_size)
self.setWindowTitle("Multiply-Imputed Meta-Analysis")
# Meta analysis nextID
def nextId_helper(self, page_id):
if page_id == Page_ChooseEffectSize:
return Page_DataLocation
elif page_id == Page_DataLocation:
return Page_RefineStudies
elif page_id == Page_RefineStudies:
return Page_Parameters
elif page_id == Page_Parameters: # meta analysis parameters
return Page_MiceParameters
elif page_id == Page_MiceParameters: # mice parameters
return Page_CovariateSelect
elif page_id == Page_CovariateSelect:
return Page_MiceOutput
elif page_id == Page_MiceOutput:
return Page_SelectCovariates
elif page_id == Page_SelectCovariates:
if self._categorical_covariates_selected():
return Page_ReferenceValues
else:
return Page_Summary
elif page_id == Page_ReferenceValues:
return Page_Summary
elif page_id == Page_Summary:
return -1
def nextId(self):
next_id = self.nextId_helper(self.currentId())
return next_id
def _change_size(self, pageid):
print("changing size")
self.adjustSize()
def _require_categorical(self): # just to make select covariates page happy
return False
def _categorical_covariates_selected(self):
'''are categorical variables selected?'''
included_covariates = self.get_included_covariates()
categorical_covariates = [cov for cov in included_covariates if cov.get_type()==CATEGORICAL]
return len(categorical_covariates) > 0
# My details page
def get_analysis_parameters(self):
return self.parameters_page.get_parameters()
# refine studies page
def get_included_studies_in_proper_order(self):
all_studies = self.model.get_studies_in_current_order()
included_studies = self.refine_studies_page.get_included_studies()
included_studies_in_order = [study for study in all_studies if study in included_studies]
return included_studies_in_order
# data location page
def get_data_location(self):
return self.data_location_page.get_data_locations()
# choose effect size page
def get_data_type_and_metric(self):
''' returns tuple (data_type, metric) '''
return self.choose_effect_size_page.get_data_type_and_metric()
def _run_imputation(self):
imp_results = python_to_R.impute(model=self.model,
studies=self.get_included_studies_in_proper_order(),
covariates=self.get_covariates_for_imputation(),
m=self.get_m(),
maxit=self.get_maxit(),
defaultMethod_rstring=self.get_defaultMethod_rstring())
self.imp_results = imp_results
return imp_results
def get_imputation_summary(self):
return self.imp_results['summary']
# def get_imputation_choices(self):
# covariates = self.get_included_covariates() # covariates in original order
#
# imputation_choices = python_to_R.imputation_dataframes_to_pylist_of_ordered_dicts(
# self.imp_results['imputations'],
# covariates)
# return imputation_choices
def get_source_data(self):
# an ordered dict mapping covariates --> values to see which ones are
# none
return self.imp_results['source_data']
def get_imputations(self):
return self.imp_results['imputations'] # R list of imputations
######## getters ###########
### Covariate Select Page
def get_covariates_for_imputation(self):
return self.cov_select_page.get_included_covariates()
### Mice Parameters Page
def get_m(self): # number of multiple imputations
return self.mice_params_page.get_m()
def get_maxit(self): # number of iterations
return self.mice_params_page.get_maxit()
def get_defaultMethod_rstring(self):
return self.mice_params_page.get_defaultMethod_rstring()
### Reference values page
def get_covariate_reference_levels(self):
return self.reference_value_page.get_covariate_reference_levels()
# Select covariates Page
def get_included_covariates(self): # covariates for regression (not imputation)
return self.select_covariates_page.get_included_covariates()
def get_included_interactions(self):
return self.select_covariates_page.get_interactions()
# Summary page
def save_selections(self):
return self.summary_page.save_selections()
# Summary Page
def get_summary(self):
''' Make a summary string to show the user at the end of the wizard summarizing most of the user selections '''
return wizard_summary(wizard=self, next_id_helper=self.nextId_helper,
summary_page_id=Page_Summary,
analysis_label=self.analysis_label)