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Added test data directory for compare_distance_matrices.py.

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1 parent bd546c8 commit 30bcf1d43dc59c0e5c9f61d77200a9b17d719598 @jairideout jairideout committed Oct 16, 2012
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+ PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+PC.636 0.0 36.7287353444 49.9599839872 48.3528696149 58.7792480387 56.4003546088 53.2634959423 50.3884907494 46.7332857822
+PC.635 36.7287353444 0.0 32.3264597505 29.7825452237 44.4747119159 42.3792402008 36.7967389859 31.5594676761 29.6141857899
+PC.356 49.9599839872 32.3264597505 0.0 30.8220700148 30.8382878902 38.3536178215 36.5102725271 37.0270171631 39.9749921826
+PC.481 48.3528696149 29.7825452237 30.8220700148 0.0 41.3400532172 40.5832477754 33.8378486314 32.8785644455 37.8153408024
+PC.354 58.7792480387 44.4747119159 30.8382878902 41.3400532172 0.0 48.6415460281 45.9347363114 47.6235235992 49.6487663492
+PC.593 56.4003546088 42.3792402008 38.3536178215 40.5832477754 48.6415460281 0.0 48.1456124688 38.2883794382 48.3632091574
+PC.355 53.2634959423 36.7967389859 36.5102725271 33.8378486314 45.9347363114 48.1456124688 0.0 42.8719022205 34.7419055321
+PC.607 50.3884907494 31.5594676761 37.0270171631 32.8785644455 47.6235235992 38.2883794382 42.8719022205 0.0 40.3360880602
+PC.634 46.7332857822 29.6141857899 39.9749921826 37.8153408024 49.6487663492 48.3632091574 34.7419055321 40.3360880602 0.0
@@ -0,0 +1,15 @@
+# Number of entries refers to the number of rows (or cols) retained in each
+# distance matrix after filtering the distance matrices to include only those
+# samples that were in both distance matrices. p-value contains the correct
+# number of significant digits.
+# Distance classes with values of None were in the second half of the distance
+# classes and not all samples could be included in the distance class, so
+# calculations were not performed.
+DM1 DM2 Number of entries Number of permutations Class index Number of distances Mantel r statistic p-value p-value (Bonferroni corrected) Tail type
+unweighted_unifrac_dm.txt PH_dm.txt 9 999 31.697404522 12 0.319710665547 0.025 0.075 greater
+ 35.8638419861 14 0.130482940829 0.241 0.723 greater
+ 40.0302794502 12 0.0605954868263 0.360 1.000 greater
+ 44.1967169143 8 None None None None
+ 48.3631543784 18 None None None None
+ 52.5295918425 2 None None None None
+ 56.6960293066 4 None None None None
@@ -0,0 +1,11 @@
+# Number of entries refers to the number of rows (or cols) retained in each
+# distance matrix after filtering the distance matrices to include only those
+# samples that were in both distance matrices. p-value contains the correct
+# number of significant digits.
+DM1 DM2 Number of entries Mantel r statistic p-value Number of permutations Tail type
+weighted_unifrac_dm.txt unweighted_unifrac_dm.txt 9 1.00000 0.001 999 two sided
+weighted_unifrac_dm.txt weighted_unifrac_even100_dm.txt 9 1.00000 0.001 999 two sided
+weighted_unifrac_dm.txt unweighted_unifrac_even100_dm.txt 9 1.00000 0.001 999 two sided
+unweighted_unifrac_dm.txt weighted_unifrac_even100_dm.txt 9 1.00000 0.001 999 two sided
+unweighted_unifrac_dm.txt unweighted_unifrac_even100_dm.txt 9 1.00000 0.001 999 two sided
+weighted_unifrac_even100_dm.txt unweighted_unifrac_even100_dm.txt 9 1.00000 0.001 999 two sided
@@ -0,0 +1,6 @@
+# Number of entries refers to the number of rows (or cols) retained in each
+# distance matrix after filtering the distance matrices to include only those
+# samples that were in both distance matrices. p-value contains the correct
+# number of significant digits.
+DM1 DM2 CDM Number of entries Mantel r statistic p-value Number of permutations Tail type
+weighted_unifrac_dm.txt unweighted_unifrac_dm.txt PH_dm.txt 9 1.00000 0.01 99 greater
@@ -0,0 +1,10 @@
+ PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+PC.636 0.0 0.275683407854 0.453169793694 0.463169006849 0.530075154635 0.316693638219 0.367507936661 0.367668532106 0.207390851351
+PC.635 0.275683407854 0.0 0.332995003579 0.341452795348 0.411631543624 0.262879798658 0.301005982286 0.221100536913 0.240434181208
+PC.356 0.453169793694 0.332995003579 0.0 0.154091373516 0.144798193736 0.332624051454 0.186403568707 0.322076019239 0.443208
+PC.481 0.463169006849 0.341452795348 0.154091373516 0.0 0.168675520364 0.329334425393 0.192866592582 0.318716145536 0.433075579909
+PC.354 0.530075154635 0.411631543624 0.144798193736 0.168675520364 0.0 0.395430805369 0.237877518605 0.396216241611 0.510311668456
+PC.593 0.316693638219 0.262879798658 0.332624051454 0.329334425393 0.395430805369 0.0 0.322882191481 0.220838053691 0.340061936913
+PC.355 0.367507936661 0.301005982286 0.186403568707 0.192866592582 0.237877518605 0.322882191481 0.0 0.324959266311 0.360463247619
+PC.607 0.367668532106 0.221100536913 0.322076019239 0.318716145536 0.396216241611 0.220838053691 0.324959266311 0.0 0.356951809843
+PC.634 0.207390851351 0.240434181208 0.443208 0.433075579909 0.510311668456 0.340061936913 0.360463247619 0.356951809843 0.0
@@ -0,0 +1,10 @@
+ PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+PC.636 0.0 0.275683407854 0.453169793694 0.463169006849 0.530075154635 0.316693638219 0.367507936661 0.367668532106 0.207390851351
+PC.635 0.275683407854 0.0 0.332995003579 0.341452795348 0.411631543624 0.262879798658 0.301005982286 0.221100536913 0.240434181208
+PC.356 0.453169793694 0.332995003579 0.0 0.154091373516 0.144798193736 0.332624051454 0.186403568707 0.322076019239 0.443208
+PC.481 0.463169006849 0.341452795348 0.154091373516 0.0 0.168675520364 0.329334425393 0.192866592582 0.318716145536 0.433075579909
+PC.354 0.530075154635 0.411631543624 0.144798193736 0.168675520364 0.0 0.395430805369 0.237877518605 0.396216241611 0.510311668456
+PC.593 0.316693638219 0.262879798658 0.332624051454 0.329334425393 0.395430805369 0.0 0.322882191481 0.220838053691 0.340061936913
+PC.355 0.367507936661 0.301005982286 0.186403568707 0.192866592582 0.237877518605 0.322882191481 0.0 0.324959266311 0.360463247619
+PC.607 0.367668532106 0.221100536913 0.322076019239 0.318716145536 0.396216241611 0.220838053691 0.324959266311 0.0 0.356951809843
+PC.634 0.207390851351 0.240434181208 0.443208 0.433075579909 0.510311668456 0.340061936913 0.360463247619 0.356951809843 0.0
@@ -0,0 +1,10 @@
+ PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+PC.636 0.0 0.275683407854 0.453169793694 0.463169006849 0.530075154635 0.316693638219 0.367507936661 0.367668532106 0.207390851351
+PC.635 0.275683407854 0.0 0.332995003579 0.341452795348 0.411631543624 0.262879798658 0.301005982286 0.221100536913 0.240434181208
+PC.356 0.453169793694 0.332995003579 0.0 0.154091373516 0.144798193736 0.332624051454 0.186403568707 0.322076019239 0.443208
+PC.481 0.463169006849 0.341452795348 0.154091373516 0.0 0.168675520364 0.329334425393 0.192866592582 0.318716145536 0.433075579909
+PC.354 0.530075154635 0.411631543624 0.144798193736 0.168675520364 0.0 0.395430805369 0.237877518605 0.396216241611 0.510311668456
+PC.593 0.316693638219 0.262879798658 0.332624051454 0.329334425393 0.395430805369 0.0 0.322882191481 0.220838053691 0.340061936913
+PC.355 0.367507936661 0.301005982286 0.186403568707 0.192866592582 0.237877518605 0.322882191481 0.0 0.324959266311 0.360463247619
+PC.607 0.367668532106 0.221100536913 0.322076019239 0.318716145536 0.396216241611 0.220838053691 0.324959266311 0.0 0.356951809843
+PC.634 0.207390851351 0.240434181208 0.443208 0.433075579909 0.510311668456 0.340061936913 0.360463247619 0.356951809843 0.0
@@ -0,0 +1,10 @@
+ PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+PC.636 0.0 0.275683407854 0.453169793694 0.463169006849 0.530075154635 0.316693638219 0.367507936661 0.367668532106 0.207390851351
+PC.635 0.275683407854 0.0 0.332995003579 0.341452795348 0.411631543624 0.262879798658 0.301005982286 0.221100536913 0.240434181208
+PC.356 0.453169793694 0.332995003579 0.0 0.154091373516 0.144798193736 0.332624051454 0.186403568707 0.322076019239 0.443208
+PC.481 0.463169006849 0.341452795348 0.154091373516 0.0 0.168675520364 0.329334425393 0.192866592582 0.318716145536 0.433075579909
+PC.354 0.530075154635 0.411631543624 0.144798193736 0.168675520364 0.0 0.395430805369 0.237877518605 0.396216241611 0.510311668456
+PC.593 0.316693638219 0.262879798658 0.332624051454 0.329334425393 0.395430805369 0.0 0.322882191481 0.220838053691 0.340061936913
+PC.355 0.367507936661 0.301005982286 0.186403568707 0.192866592582 0.237877518605 0.322882191481 0.0 0.324959266311 0.360463247619
+PC.607 0.367668532106 0.221100536913 0.322076019239 0.318716145536 0.396216241611 0.220838053691 0.324959266311 0.0 0.356951809843
+PC.634 0.207390851351 0.240434181208 0.443208 0.433075579909 0.510311668456 0.340061936913 0.360463247619 0.356951809843 0.0

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