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Merge pull request #27 from msrosenberg/dev-branch
Dev branch 3.0.13 release
2 parents f7aacfd + 6deaf10 commit 79d82e7

16 files changed

Lines changed: 438 additions & 336 deletions

‎MetaWin_mac.spec‎

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@@ -44,6 +44,8 @@ added_files = [("resources/images/exit@256px.png", "resources/images"),
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("resources/images/flag-spain@256px.png", "resources/images"),
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("resources/images/letter-t@256px.png", "resources/images"),
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("resources/images/sum-gear-filled@256px.png", "resources/images"),
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("resources/images/color-swatches@256px.png", "resources/images"),
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("resources/images/waste-bin-full-filled-browse@256px.png", "resources/images"),
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("resources/images/metawin3icon.png", "resources/images"),
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("resources/images/draw_forest.png", "resources/images"),

‎MetaWin_windows.spec‎

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@@ -44,6 +44,8 @@ added_files = [("resources/images/exit@256px.png", "resources/images"),
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("resources/images/flag-spain@256px.png", "resources/images"),
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("resources/images/letter-t@256px.png", "resources/images"),
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("resources/images/sum-gear-filled@256px.png", "resources/images"),
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("resources/images/color-swatches@256px.png", "resources/images"),
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("resources/images/waste-bin-full-filled-browse@256px.png", "resources/images"),
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("resources/images/metawin3icon.png", "resources/images"),
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("resources/images/draw_forest.png", "resources/images"),

‎resources/images/color-swatches@256px.png‎

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‎resources/images/waste-bin-full-filled-browse@256px.png‎

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‎resources/metawin_help.html‎

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‎src/MetaWinAnalysis.py‎

Lines changed: 13 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1798,62 +1798,58 @@ def do_meta_analysis(data, options, decimal_places: int = 4, alpha: float = 0.05
17981798
output, all_citations = options.report_choices()
17991799
output_blocks.extend(output)
18001800
if options.structure == SIMPLE_MA:
1801-
(output, figure, chart_data, analysis_values,
1801+
(output, chart_data, analysis_values,
18021802
citations) = MetaWinAnalysisFunctions.simple_meta_analysis(data, options, decimal_places, alpha, norm_ci,
18031803
sender=sender)
18041804
elif options.structure == GROUPED_MA:
1805-
(output, figure, chart_data, analysis_values,
1805+
(output, chart_data, analysis_values,
18061806
citations) = MetaWinAnalysisFunctions.grouped_meta_analysis(data, options, decimal_places, alpha, norm_ci,
18071807
sender=sender)
18081808
elif options.structure == CUMULATIVE_MA:
1809-
output, figure, chart_data = MetaWinAnalysisFunctions.cumulative_meta_analysis(data, options, decimal_places,
1810-
alpha, norm_ci, sender=sender)
1809+
output, chart_data = MetaWinAnalysisFunctions.cumulative_meta_analysis(data, options, decimal_places, alpha,
1810+
norm_ci, sender=sender)
18111811
analysis_values = None
18121812
citations = []
18131813
elif options.structure == REGRESSION_MA:
1814-
(output, figure, chart_data, analysis_values,
1814+
(output, chart_data, analysis_values,
18151815
citations) = MetaWinAnalysisFunctions.regression_meta_analysis(data, options, decimal_places, alpha, norm_ci,
18161816
sender=sender)
18171817
elif options.structure == COMPLEX_MA:
18181818
output, analysis_values, citations = MetaWinAnalysisFunctions.complex_meta_analysis(data, options,
18191819
decimal_places, alpha,
18201820
norm_ci, sender=sender)
1821-
figure = None
18221821
chart_data = None
18231822
elif options.structure == NESTED_MA:
1824-
(output, figure, chart_data, analysis_values,
1823+
(output, chart_data, analysis_values,
18251824
citations) = MetaWinAnalysisFunctions.nested_meta_analysis(data, options, decimal_places, alpha, norm_ci,
18261825
sender=sender)
18271826
elif options.structure == TRIM_FILL:
1828-
(output, figure, chart_data, analysis_values,
1827+
(output, chart_data, analysis_values,
18291828
citations) = MetaWinAnalysisFunctions.trim_and_fill_analysis(data, options, decimal_places, alpha, norm_ci)
18301829
elif options.structure == JACKKNIFE:
1831-
(output, figure, chart_data,
1830+
(output, chart_data,
18321831
citations) = MetaWinAnalysisFunctions.jackknife_meta_analysis(data, options, decimal_places, alpha, norm_ci,
18331832
sender=sender)
18341833
analysis_values = None
18351834
elif options.structure == PHYLOGENETIC_MA:
18361835
output, citations = MetaWinAnalysisFunctions.phylogenetic_meta_analysis(data, options, tree, decimal_places,
18371836
alpha, norm_ci, sender=sender)
18381837
analysis_values = None
1839-
figure = None
18401838
chart_data = None
18411839
elif options.structure == RANKCOR:
18421840
output, citations = MetaWinAnalysisFunctions.rank_correlation_analysis(data, options, decimal_places,
18431841
sender=sender)
1844-
figure = None
18451842
chart_data = None
18461843
analysis_values = None
18471844
else:
18481845
output = []
18491846
analysis_values = None
1850-
figure = None
18511847
chart_data = None
18521848
citations = []
18531849
all_citations.extend(citations)
18541850
output_blocks.extend(output)
18551851
output_blocks.extend(create_reference_list(all_citations))
1856-
return output_blocks, figure, chart_data, analysis_values
1852+
return output_blocks, chart_data, analysis_values
18571853

18581854

18591855
def meta_analysis(sender, data, last_effect, last_var, decimal_places: int = 4, alpha: float = 0.05,
@@ -1909,9 +1905,9 @@ def meta_analysis(sender, data, last_effect, last_var, decimal_places: int = 4,
19091905
meta_analysis_options.structure = None
19101906

19111907
if meta_analysis_options.structure is not None:
1912-
output, figure, chart_data, _ = do_meta_analysis(data, meta_analysis_options, decimal_places, alpha, tree,
1913-
norm_ci, sender=sender)
1908+
output, chart_data, _ = do_meta_analysis(data, meta_analysis_options, decimal_places, alpha, tree, norm_ci,
1909+
sender=sender)
19141910
sender.last_effect = meta_analysis_options.effect_data
19151911
sender.last_var = meta_analysis_options.effect_vars
1916-
return output, figure, chart_data
1917-
return None, None, None
1912+
return output, chart_data
1913+
return None, None

‎src/MetaWinAnalysisFunctions.py‎

Lines changed: 22 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -601,7 +601,6 @@ def simple_meta_analysis(data, options, decimal_places: int = 4, alpha: float =
601601

602602
output_blocks = output_filtered_bad(filtered, bad_data)
603603

604-
figure = None
605604
chart_data = None
606605
n = len(e_data)
607606
citations = []
@@ -670,15 +669,15 @@ def simple_meta_analysis(data, options, decimal_places: int = 4, alpha: float =
670669
citations.extend(new_cites)
671670

672671
if options.create_graph:
673-
figure, chart_data = MetaWinCharts.chart_forest_plot("basic analysis", effect_sizes.label, forest_data,
674-
alpha, options.bootstrap_mean, normal_ci=norm_ci)
672+
chart_data = MetaWinCharts.chart_forest_plot("basic analysis", effect_sizes.label, forest_data,
673+
alpha, options.bootstrap_mean, normal_ci=norm_ci)
675674

676675
else:
677676
output_blocks.append([get_text("Fewer than two studies were valid for analysis")])
678677
qt, df, p, pooled_var, i2 = None, None, None, None, None
679678
mean_data = None
680679

681-
return output_blocks, figure, chart_data, simple_ma_values(mean_data, pooled_var, qt, df, p, i2), citations
680+
return output_blocks, chart_data, simple_ma_values(mean_data, pooled_var, qt, df, p, i2), citations
682681

683682

684683
# ---------- grouped meta-analysis ----------
@@ -740,7 +739,6 @@ def grouped_meta_analysis(data, options, decimal_places: int = 4, alpha: float =
740739

741740
output_blocks = output_filtered_bad(filtered, bad_data)
742741

743-
figure = None
744742
chart_data = None
745743
n = len(e_data)
746744
g_cnt = len(group_names)
@@ -905,9 +903,8 @@ def grouped_meta_analysis(data, options, decimal_places: int = 4, alpha: float =
905903
citations.extend(new_cites)
906904

907905
if options.create_graph:
908-
figure, chart_data = MetaWinCharts.chart_forest_plot("grouped analysis", effect_sizes.label, forest_data,
909-
alpha, options.bootstrap_mean, groups.label,
910-
normal_ci=norm_ci)
906+
chart_data = MetaWinCharts.chart_forest_plot("grouped analysis", effect_sizes.label, forest_data, alpha,
907+
options.bootstrap_mean, groups.label, normal_ci=norm_ci)
911908

912909
global_values = simple_ma_values(global_mean_data, pooled_var, qt, df, pqt, i2)
913910
else:
@@ -917,7 +914,7 @@ def grouped_meta_analysis(data, options, decimal_places: int = 4, alpha: float =
917914
model_het = None
918915
error_het = None
919916

920-
return (output_blocks, figure, chart_data,
917+
return (output_blocks, chart_data,
921918
group_ma_values(global_values, group_mean_values, group_het_values, model_het, error_het), citations)
922919

923920

@@ -945,7 +942,6 @@ def cumulative_meta_analysis(data, options, decimal_places: int = 4, alpha: floa
945942

946943
output_blocks = output_filtered_bad(filtered, bad_data)
947944

948-
figure = None
949945
chart_data = None
950946
n = len(tmp_data)
951947
if n > 1:
@@ -1016,14 +1012,14 @@ def cumulative_meta_analysis(data, options, decimal_places: int = 4, alpha: floa
10161012
decimal_places, alpha, options.log_transformed))
10171013

10181014
if options.create_graph:
1019-
figure, chart_data = MetaWinCharts.chart_forest_plot("cumulative analysis", effect_sizes.label,
1020-
cumulative_means, alpha, options.bootstrap_mean,
1021-
order.label, normal_ci=norm_ci)
1015+
chart_data = MetaWinCharts.chart_forest_plot("cumulative analysis", effect_sizes.label,
1016+
cumulative_means, alpha, options.bootstrap_mean, order.label,
1017+
normal_ci=norm_ci)
10221018

10231019
else:
10241020
output_blocks.append([get_text("Fewer than two studies were valid for analysis")])
10251021

1026-
return output_blocks, figure, chart_data
1022+
return output_blocks, chart_data
10271023

10281024

10291025
# ---------- simple regression meta-analysis ----------
@@ -1076,7 +1072,6 @@ def regression_meta_analysis(data, options, decimal_places: int = 4, alpha: floa
10761072

10771073
output_blocks = output_filtered_bad(filtered, bad_data)
10781074

1079-
figure = None
10801075
chart_data = None
10811076
model_het = None
10821077
error_het = None
@@ -1205,14 +1200,13 @@ def regression_meta_analysis(data, options, decimal_places: int = 4, alpha: floa
12051200
get_citation("Greenland_1987"))
12061201
model = get_text("fixed effects")
12071202
fig_citations = ["Hedges_Olkin_1985", "Greenland_1987"]
1208-
figure, chart_data = MetaWinCharts.chart_regression(options.independent_variable.label, effect_sizes.label,
1209-
x_data, e_data, b1_slope, b0_intercept, model,
1210-
ref_list, fig_citations)
1203+
chart_data = MetaWinCharts.chart_regression(options.independent_variable.label, effect_sizes.label, x_data,
1204+
e_data, b1_slope, b0_intercept, model, ref_list, fig_citations)
12111205

12121206
else:
12131207
output_blocks.append([get_text("Fewer than two studies were valid for analysis")])
12141208

1215-
return output_blocks, figure, chart_data, reg_ma_values(global_values, model_het, error_het, predictors), citations
1209+
return output_blocks, chart_data, reg_ma_values(global_values, model_het, error_het, predictors), citations
12161210

12171211

12181212
# ---------- complex (glm) meta-analysis ----------
@@ -1665,7 +1659,6 @@ def nested_meta_analysis(data, options, decimal_places: int = 4, alpha: float =
16651659

16661660
n = len(e_data)
16671661

1668-
figure = None
16691662
chart_data = None
16701663
group_het_values = None
16711664
group_mean_values = None
@@ -1810,11 +1803,11 @@ def nested_meta_analysis(data, options, decimal_places: int = 4, alpha: float =
18101803
citations.extend(new_cites)
18111804

18121805
if options.create_graph:
1813-
figure, chart_data = MetaWinCharts.chart_forest_plot("nested analysis", effect_sizes.label, forest_data,
1814-
alpha, options.bootstrap_mean, normal_ci=norm_ci)
1806+
chart_data = MetaWinCharts.chart_forest_plot("nested analysis", effect_sizes.label, forest_data, alpha,
1807+
options.bootstrap_mean, normal_ci=norm_ci)
18151808

1816-
return (output_blocks, figure, chart_data, group_ma_values(global_values, group_mean_values, group_het_values,
1817-
model_het_values, error_het_values), citations)
1809+
return (output_blocks, chart_data, group_ma_values(global_values, group_mean_values, group_het_values,
1810+
model_het_values, error_het_values), citations)
18181811

18191812

18201813
# ---------- trim-and-fill analysis ----------
@@ -1847,7 +1840,6 @@ def trim_and_fill_analysis(data, options, decimal_places: int = 4, alpha: float
18471840

18481841
output_blocks = output_filtered_bad(filtered, bad_data)
18491842

1850-
figure = None
18511843
chart_data = None
18521844
n = len(e_data)
18531845
citations = []
@@ -1969,13 +1961,12 @@ def trim_and_fill_analysis(data, options, decimal_places: int = 4, alpha: float
19691961
decimal_places, alpha, options.log_transformed))
19701962

19711963
if options.create_graph:
1972-
figure, chart_data = MetaWinCharts.chart_trim_fill_plot(effect_sizes.label, tmp_data, n, original_mean,
1973-
mean_e)
1964+
chart_data = MetaWinCharts.chart_trim_fill_plot(effect_sizes.label, tmp_data, n, original_mean, mean_e)
19741965

19751966
else:
19761967
output_blocks.append([get_text("Fewer than two studies were valid for analysis")])
19771968

1978-
return output_blocks, figure, chart_data, None, citations
1969+
return output_blocks, chart_data, None, citations
19791970

19801971

19811972
# ---------- phylogenetic meta-analysis ----------
@@ -2275,7 +2266,6 @@ def jackknife_meta_analysis(data, options, decimal_places: int = 4, alpha: float
22752266

22762267
output_blocks = output_filtered_bad(filtered, bad_data)
22772268

2278-
figure = None
22792269
chart_data = None
22802270
n = len(e_data)
22812271
citations = []
@@ -2380,12 +2370,12 @@ def jackknife_meta_analysis(data, options, decimal_places: int = 4, alpha: float
23802370
citations.extend(new_cites)
23812371

23822372
if options.create_graph:
2383-
figure, chart_data = MetaWinCharts.chart_forest_plot("jackknife analysis", effect_sizes.label, forest_data,
2384-
alpha, options.bootstrap_mean, normal_ci=norm_ci)
2373+
chart_data = MetaWinCharts.chart_forest_plot("jackknife analysis", effect_sizes.label, forest_data, alpha,
2374+
options.bootstrap_mean, normal_ci=norm_ci)
23852375
else:
23862376
output_blocks.append([get_text("Fewer than two studies were valid for analysis")])
23872377

2388-
return output_blocks, figure, chart_data, citations
2378+
return output_blocks, chart_data, citations
23892379

23902380

23912381
# ---------- rank correlation analysis ----------

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