Merge pull request #28 from msrosenberg/dev-branch

Publication Bias Reorg

MetaWin_mac.spec

@@ -97,6 +97,12 @@ added_files = [("resources/images/[email protected]", "resources/images"),
 			   ("resources/images/analysis_regression1.png", "resources/images"),
 			   ("resources/images/analysis_regression2.png", "resources/images"),
 			   ("resources/images/metacalc.png", "resources/images"),
+			   ("resources/images/example_egger.png", "resources/images"),
+			   ("resources/images/pubbias_egger.png", "resources/images"),
+			   ("resources/images/example_funnel1.png", "resources/images"),
+			   ("resources/images/example_funnel2.png", "resources/images"),
+			   ("resources/images/example_funnel3.png", "resources/images"),
+			   ("resources/images/pubbias_funnel.png", "resources/images"),
 
 			   ("resources/metawin.css", "resources"),
 			   ("resources/metacalc_help.html", "resources"),

MetaWin_windows.spec

@@ -97,6 +97,12 @@ added_files = [("resources/images/[email protected]", "resources/images"),
 			   ("resources/images/analysis_regression1.png", "resources/images"),
 			   ("resources/images/analysis_regression2.png", "resources/images"),
 			   ("resources/images/metacalc.png", "resources/images"),
+			   ("resources/images/example_egger.png", "resources/images"),
+			   ("resources/images/pubbias_egger.png", "resources/images"),
+			   ("resources/images/example_funnel1.png", "resources/images"),
+			   ("resources/images/example_funnel2.png", "resources/images"),
+			   ("resources/images/example_funnel3.png", "resources/images"),
+			   ("resources/images/pubbias_funnel.png", "resources/images"),
 
 			   ("resources/metawin.css", "resources"),
 			   ("resources/metacalc_help.html", "resources"),

src/MetaWinConstants.py

@@ -13,7 +13,7 @@
 
 MAJOR_VERSION = 3
 MINOR_VERSION = 0
-PATCH_VERSION = 13
+PATCH_VERSION = 14
 
 # validity check when fetching value from data matrix
 VALUE_NUMBER = 0
@@ -87,8 +87,7 @@ def resource_path(relative_path: str, inc_file: bool = False) -> str:
 english_icon = resource_path(icon_path + "[email protected]")
 spanish_icon = resource_path(icon_path + "[email protected]")
 color_swatch_icon = resource_path(icon_path + "[email protected]")
-# in anticipation of a new section
-# pub_bias_icon = resource_path(icon_path + "[email protected]")
+pub_bias_icon = resource_path(icon_path + "[email protected]")
 
 metawin_icon = resource_path(icon_path + "metawin3toolbar_icon.png")
 metawin_splash = resource_path(icon_path + "metawin3splash_square.png")
@@ -103,8 +102,10 @@ def resource_path(relative_path: str, inc_file: bool = False) -> str:
     "basic_analysis": resource_path(doc_path + "metawin_help.html#basic_analysis", True),
     "cumulative_analysis": resource_path(doc_path + "metawin_help.html#cumulative_analysis", True),
     "effect_sizes": resource_path(doc_path + "metawin_help.html#effect_sizes", True),
+    "egger_regression": resource_path(doc_path + "metawin_help.html#egger_regression", True),
     "filtering_data": resource_path(doc_path + "metawin_help.html#filtering_data", True),
     "forest_plot": resource_path(doc_path + "metawin_help.html#forest_plot", True),
+    "funnel_plot": resource_path(doc_path + "metawin_help.html#funnel_plot", True),
     "galbraith_plot": resource_path(doc_path + "metawin_help.html#galbraith_plot", True),
     "glm_analysis": resource_path(doc_path + "metawin_help.html#glm_analysis", True),
     "graph_edit": resource_path(doc_path + "metawin_help.html#graph_edit", True),
@@ -213,6 +214,10 @@ def resource_path(relative_path: str, inc_file: bool = False) -> str:
     "Kendall_1938": ["Kendall, M. (1938) A new measure of rank correlation. <em>Biometrika</em>. "
                      "30(1&ndash;2):81&ndash;89.", "Kendall (1938)", "10.1093/biomet/30.1-2.81"],
 
+    "Kossmeier_et_2020": ["Kossmeier, M., U.S. Tran, and M. Voracek (2020) Power-enhanced funnel plots for "
+                          "meta-analysis: The sunset funnel plot. <em>Zeitschrift für Psychologie</em> "
+                          "228(1):43&ndash;49.", "Kossmeier <em>et al.</em> (2020)", "10.1027/2151-2604/a000392"],
+
     "LAbbe_et_1987": ["L&rsquo;Abbé, K.A., A.S. Detsky, and K. O&rsquo;Rourke (1987) Meta-analysis in clinical "
                       "research. <em>Annals of Internal Medicine</em> 107:224&ndash;233.",
                       "L&rsquo;Abbé <em>et al.</em> (1987)", "10.7326/0003-4819-107-2-224"],
@@ -226,6 +231,12 @@ def resource_path(relative_path: str, inc_file: bool = False) -> str:
                            "Press: Princeton, NJ.</span></li>", "Lajeunesse <em>et al.</em> (2013)",
                            "10.23943/princeton/9780691137285.003.0017"],
 
+    "Light_Pillemer_1984": ["Light, R.J., and D.B. Pillemer (1984) <em>Summing Up: The Science of Reviewing "
+                            "Research</em>. Harvard University Press: Cambridge.", "Light and Pillemer (1984)", ""],
+
+    "Lin_Chu_2018": ["Lin, L., and H. Chu (2018) Quantifying publication bias in meta-analysis. <em>Biometrics</em> "
+                     "74(3):785&ndash;794.", "Lin and Chu (2018)", "10.1111/biom.12817"],
+
     "Mantel_and_Haenszel_1959": ["Mantel, N., and W. Haenszel (1959) Statistical aspects of the analysis of data "
                                  "from retrospective studies of disease. <em>Journal of the National Cancer "
                                  "Institute</em> 22:719&ndash;748.", "Mantel and Haenszel (1959)",
@@ -237,13 +248,23 @@ def resource_path(relative_path: str, inc_file: bool = False) -> str:
                                  "Princeton University Press: Princeton, NJ.", "Mengersen and Gurevitch (2013)",
                                  "10.23943/princeton/9780691137285.003.0007"],
 
+    "Nakagawa_et_2022": ["Nakagawa, S., M. Lagisz, M.D. Jennions, J. Koricheva, D.W.A. Noble, T.H. Parker, A. "
+                         "Sánchez-Tójar, Y. Yang, and R.E. O'Dea (2022) Methods for testing publication bias in "
+                         "ecological and evolutionary meta-analyses. <em>Methods in Ecology and Evolution</em> "
+                         "13(1):4&ndash;21.", "Nakagawa <em>et al.</em> (2022)", "10.1111/2041-210X.13724"],
+
     "Normand_1999": ["Normand, S.-L.T. (1999) Meta-analysis: Formulating, evaluating, combining, and reporting. "
                      "<em>Statistics in Medicine</em> 18:321&mdash;359.", "Normand (1999)",
                      "10.1002/(SICI)1097-0258(19990215)18:3<321::AID-SIM28>3.0.CO;2-P"],
 
     "Orwin_1983": ["Orwin, R.G. (1983) A fail-safe <em>N</em> for effect size in meta-analysis. <em>Journal of "
                    "Educational Statistics</em> 8(2):157&ndash;159.", "Orwin (1983)", "10.2307/1164923"],
 
+    "Peters_et_2008": ["Peters, J.L., A.J. Sutton, D.R. Jones, K.R. Abrams, and L. Rushton (2008) Contour-enhanced "
+                       "meta-analysis funnel plots help distinguish publication bias from other causes of asymmetry. "
+                       "<em>Journal of Clinical Epidemiology</em> 61(10):991&ndash;996.",
+                       "Peters <em>et al.</em> (2008)", "10.1016/j.jclinepi.2007.11.010"],
+
     "Rosenberg_et_2000": ["Rosenberg, M.S., D.C. Adams, and J. Gurevitch (2000) <em>MetaWin: Statistical Software "
                           "for Meta-analysis</em>. Sinauer Associates, Sunderland, MA.",
                           "Rosenberg <em>et al.</em> (2000)", ""],
@@ -270,6 +291,10 @@ def resource_path(relative_path: str, inc_file: bool = False) -> str:
     "Spearman_1904": ["Spearman C. (1904) The proof and measurement of association between two things. <em>American "
                       "Journal of Psychology</em>. 15(1):72&ndash;101.", "Spearman (1904)", "10.2307/1412159"],
 
+    "Sterne_Egger_2001": ["Sterne, J.A.C., and M. Egger (2001) Funnel plots for detecting bias in meta-analysis: "
+                          "Guidelines on choice of axis. <em>Journal of Clinical Epidemiology</em> "
+                          "54(10):1045&ndash;1055.", "Sterne and Egger (2001)", "10.1016/S0895-4356(01)00377-8"],
+
     "Wang_and_Bushman_1998": ["Wang, M.C., and B.J. Bushman (1998) Using the normal quantile plot to explore "
                               "meta-analytic data sets. <em>Psychological Methods</em> 3:46&ndash;54.",
                               "Wang and Bushman (1998)", "10.1037/1082-989X.3.1.46"]

src/MetaWinDraw.py

@@ -9,7 +9,6 @@
 """
 import webbrowser
 import math
-from typing import Tuple
 
 from PyQt6.QtWidgets import QDialog, QLabel, QVBoxLayout, QFrame, QComboBox, QGroupBox, QLineEdit, QRadioButton, \
     QGridLayout
@@ -24,6 +23,7 @@
 from MetaWinWidgets import add_ok_cancel_help_button_layout, add_effect_choice_to_dialog
 import MetaWinCharts
 from MetaWinLanguage import get_text
+from MetaWinUtils import calculate_regression
 
 
 class MetaAnalysisDrawScatterDialog(QDialog):
@@ -38,7 +38,7 @@ def __init__(self, data: MetaWinData):
     def init_ui(self, data: MetaWinData):
         button_layout, _ = add_ok_cancel_help_button_layout(self)
 
-        draw_label = QLabel(get_text("Scatter/Funnel Plot"))
+        draw_label = QLabel(get_text("Scatter Plot"))
         draw_label.setStyleSheet(MetaWinConstants.title_label_style)
 
         self.columns = data.cols
@@ -50,7 +50,7 @@ def init_ui(self, data: MetaWinData):
             self.y_box.addItem(col.label)
         x_label = QLabel(get_text("Data for X-axis"))
         y_label = QLabel(get_text("Data for Y-axis"))
-        info_label = QLabel(get_text("note_funnel_plot"))
+        # info_label = QLabel(get_text("note_funnel_plot"))
 
         options_layout = QVBoxLayout()
         options_layout.addWidget(x_label)
@@ -66,12 +66,12 @@ def init_ui(self, data: MetaWinData):
         main_layout = QVBoxLayout()
         main_layout.addWidget(draw_label)
         main_layout.addWidget(main_frame)
-        main_layout.addWidget(info_label)
+        # main_layout.addWidget(info_label)
         main_layout.addLayout(button_layout)
 
         self.setLayout(main_layout)
         self.setWindowIcon(QIcon(MetaWinConstants.metawin_icon))
-        self.setWindowTitle(get_text("Scatter/Funnel Plot"))
+        self.setWindowTitle(get_text("Scatter Plot"))
 
     def show_help(self):
         webbrowser.open(self.help)
@@ -342,11 +342,13 @@ def ok_clicked(self):
         if not self.chart_data.suppress_y:
             self.chart_data.y_label = self.y_box.text()
         for edit_panel in self.panel_list:
-            if edit_panel.isChecked():
-                edit_panel.data.visible = True
-                edit_panel.data.update_style()
-            else:
-                edit_panel.data.visible = False
+            edit_panel.data.visible = edit_panel.isChecked()
+            edit_panel.data.update_style()
+            # if edit_panel.isChecked():
+            #     edit_panel.data.visible = True
+            #     edit_panel.data.update_style()
+            # else:
+            #     edit_panel.data.visible = False
         self.accept()
 
 
@@ -387,20 +389,20 @@ def draw_scatter_dialog(sender, data):
     return None
 
 
-def calculate_regression(x: numpy.array, y: numpy.array) -> Tuple[float, float]:
-    """
-    Basic linear regression of y vs x, returning slope and intercept
-    """
-    n = len(x)
-    sum_y = numpy.sum(y)
-    sum_x = numpy.sum(x)
-    mean_y = sum_y/n
-    mean_x = sum_x/n
-    sum_x2 = numpy.sum(numpy.square(x))
-    sum_xy = numpy.sum(x*y)
-    slope = (n*sum_xy - sum_x*sum_y)/(n*sum_x2 - sum_x**2)
-    intercept = mean_y - slope*mean_x
-    return slope, intercept
+# def calculate_regression(x: numpy.array, y: numpy.array) -> Tuple[float, float]:
+#     """
+#     Basic linear regression of y vs x, returning slope and intercept
+#     """
+#     n = len(x)
+#     sum_y = numpy.sum(y)
+#     sum_x = numpy.sum(x)
+#     mean_y = sum_y/n
+#     mean_x = sum_x/n
+#     sum_x2 = numpy.sum(numpy.square(x))
+#     sum_xy = numpy.sum(x*y)
+#     slope = (n*sum_xy - sum_x*sum_y)/(n*sum_x2 - sum_x**2)
+#     intercept = mean_y - slope*mean_x
+#     return slope, intercept
 
 
 def draw_normal_quantile_plot(data, e_data_col, v_data_col, alpha: float = 0.05):
@@ -425,7 +427,7 @@ def draw_normal_quantile_plot(data, e_data_col, v_data_col, alpha: float = 0.05)
 
         x_data = numpy.array(x_data)
         y_data = numpy.array(y_data)
-        slope, intercept = calculate_regression(x_data, y_data)
+        slope, intercept, _, _ = calculate_regression(x_data, y_data)
 
         return MetaWinCharts.chart_normal_quantile(get_text("Normal Quantile"), get_text("Standardized Effect Size"),
                                                    x_data, y_data, slope, intercept, alpha)