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Applied new MSR to ARA & Cyanobacteria Results

+ started building '_Main' analysis script as control center to batch-execute other analyses.
+ Re-ran ARA & Cyanobacteria with new MSD method.
  - MSD is NaN for Time ?!
- Removed old Heterocyst results (to reflect the fact that they are essentially deprecated).
  • Loading branch information...
commit 0f1f52cef570ccfd3a12f69eba6926f69b7021c0 1 parent 5fcd8af
Jonathan A. Whiteley authored
Showing with 79 additions and 920 deletions.
  1. +1 −1  ARA.R
  2. +7 −14 TODO
  3. +15 −4 _Main.R
  4. BIN  graphs/Results - ARA.m - 1.pdf
  5. BIN  graphs/Results - ARA.m - 123.pdf
  6. BIN  graphs/Results - ARA.m - 2.pdf
  7. BIN  graphs/Results - ARA.m - 3.pdf
  8. BIN  graphs/Results - Cells.m - 1.pdf
  9. BIN  graphs/Results - Cells.m - 123.pdf
  10. BIN  graphs/Results - Cells.m - 2.pdf
  11. BIN  graphs/Results - Cells.m - 3.pdf
  12. BIN  graphs/Results - Hcells.m - 1.pdf
  13. BIN  graphs/Results - Hcells.m - 123.pdf
  14. BIN  graphs/Results - Hcells.m - 2.pdf
  15. BIN  graphs/Results - Hcells.m - 3.pdf
  16. +6 −6 output/Results - ARA.m - 1.txt
  17. +10 −10 output/Results - ARA.m - 123.txt
  18. +6 −6 output/Results - ARA.m - 2.txt
  19. +6 −6 output/Results - ARA.m - 3.txt
  20. +6 −6 output/Results - Cells.m - 1.txt
  21. +10 −10 output/Results - Cells.m - 123.txt
  22. +6 −6 output/Results - Cells.m - 2.txt
  23. +6 −6 output/Results - Cells.m - 3.txt
  24. +0 −151 output/Results - Hcells.m - 1.txt
  25. +0 −396 output/Results - Hcells.m - 123.txt
  26. +0 −149 output/Results - Hcells.m - 2.txt
  27. +0 −149 output/Results - Hcells.m - 3.txt
View
2  ARA.R
@@ -41,7 +41,7 @@ Chamber.use <- levels(SECC$Chamber)[c(1, 3)] # Chamber treatments to include
Y.units <- bquote( sqrt(.(Y.units)) ) # store as quote(expression) *****
## Output Results?
-Save.results <- FALSE
+Save.results <- TRUE
##================================================
View
21 TODO
@@ -1,4 +1,3 @@
-- Check LSD calculations
- allow plotMeans to accept a single value for error, and create appropriate matrix automatically?
- Load Moisture Data
@@ -13,7 +12,7 @@
- Replace print() calls in error messages with cat() (fun.R). Don't forget to add \n at the end of each line.
- Or, concatenate all output together to include in the stop() message.
-- Separate Patch & Meta-Community scale analyses
+- Separate Patch & Meta-Community scale analyses (& output)
- inside a for loop to do the same thing on each scale of data...
- collect results for output?
- can I turn major operations of Nested ANOVA script into functions?
@@ -25,16 +24,10 @@
Current Changes:
================
-LSD -> MSD for full 'aovlist'
-
-+ LSD() changed to MSD() to be more generic
- + specify method = "LSD" or "planned" for LSD
- + specify method = "MSR" or "unplanned" for MSRs (Tukey HSD)
-+ MSD() uses MSE from nested model level for each comparison
- + but df are calculated according to number of comparisons in each treatment group.
-+ new MSD() applied to main ANOVA script.
-- Am I using the correct degrees of freedom and/or n?
- Welcome to friggin' nested (i.e. hierarchical) models. Oy!
- - n = # of observations in each group, or # of groups?
- - df depends on whether you think the comparisons are planned (LSD for any 2 comparisons) or unplanned (MSD / Tukey's HSD).
+Applied new MSR to ARA & Cyanobacteria Results
+
++ started building '_Main' analysis script as control center to batch-execute other analyses.
++ Re-ran ARA & Cyanobacteria with new MSD method.
+ - MSD is NaN for Time ?!
+- Removed old Heterocyst results (to reflect the fact that they are essentially deprecated).
View
19 _Main.R
@@ -5,14 +5,25 @@
##################################################
## INITIALIZE
rm(list=ls()) # clear memory
-setwd("./ SECC/") # Project Directory.
+## Project Directory
+if (FALSE) { # do not run automatically
+ ## Set Working Directory: path in quotes "".
+ setwd("/Users/jonathan/Documents/ My Documents/PhD/Analysis/ SECC/") # iMac@McGill
+ setwd("/Users/jaw/Documents/ My Documents/ Academic/McGill/PhD/Analysis/ SECC/") # JAW-MBP
+ setwd("./ SECC/") # relative to my usual default wd in R GUI (Mac).
+ getwd() # Check that we're in the right place
+}
+
#source("./lib/load.R") # (re-)load data
#source("./lib/init.R") # Initialize - all analysis scripts should start with this.
-## GO
+## DO
source("./SECC-Data-Template.R") # Generate Template Data Frame & files.
-source("./do.R") # Perform Analyses
+source("do.R") # Perform Analyses
+
+source("ARA.R") # Acetylene Reduction Assay (N-fixation) Analysis
+source("Cyanobacteria.R") # Cyanobcateria density Analysis
## OUTPUT
-source("./lib/out.R") # Produce Outputs: graphs, reports, export.
+source("lib/out.R") # Produce Outputs: graphs, reports, export.
View
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BIN  graphs/Results - Cells.m - 1.pdf
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BIN  graphs/Results - Hcells.m - 1.pdf
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BIN  graphs/Results - Hcells.m - 123.pdf
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BIN  graphs/Results - Hcells.m - 2.pdf
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12 output/Results - ARA.m - 1.txt
@@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, other, Outer
-Mon Mar 28 18:47:21 2011
+Tue Mar 29 14:04:58 2011
================================================================
================ Patch scale Results =========================
@@ -103,11 +103,11 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Full Chamber 3.090 0.000 0.000 0.698
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Position Chamber:Frag
- 1.551744 2.208955 1.906697 3.167000
+ 2.341968 5.288539 2.533198 8.670254
Chamber:Position Frag:Position Chamber:Frag:Position
- 2.723730 3.935375 5.844825
+ 4.255076 6.817509 10.664052
================================================================
@@ -154,9 +154,9 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Ambient 9.711 12.442 10.365 10.994
Full Chamber 6.252 7.686 7.222 8.169
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Chamber:Frag
- 2.750229 3.973662 5.901690
+ 2.021658 5.673492 9.379260
<============================= END ============================>
View
20 output/Results - ARA.m - 123.txt
@@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, other, Outer
-Mon Mar 28 18:47:23 2011
+Tue Mar 29 14:05:02 2011
================================================================
================ Patch scale Results =========================
@@ -324,17 +324,17 @@ Time Ambient Full Chamber
2009-08 14.676 0.000
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Time Chamber Frag
- 0.9018618 0.7355851 1.0424924
+ NaN 1.683026 2.060138
Position Time:Chamber Time:Frag
- 0.9018618 1.2795343 1.8214562
+ 1.198133 2.008533 3.210886
Chamber:Frag Time:Position Chamber:Position
- 1.4806869 1.5722214 1.2795343
+ 3.370561 2.652873 2.008533
Frag:Position Time:Chamber:Frag Time:Chamber:Position
- 1.8214562 2.6114395 2.2459287
+ 3.210886 5.007347 4.173507
Time:Frag:Position Chamber:Frag:Position Time:Chamber:Frag:Position
- 3.2450249 2.6114395 4.8195163
+ 6.444563 5.007347 9.828822
================================================================
@@ -443,11 +443,11 @@ Time Ambient Full Chamber
2009-08 16.122 11.354
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Time Chamber Frag Time:Chamber Time:Frag
- 1.307340 1.063963 1.514585 1.867544 2.698316
+ NaN 1.774241 2.172564 2.917521 4.674471
Chamber:Frag Time:Chamber:Frag
- 2.171475 4.007543
+ 3.561793 7.311879
<============================= END ============================>
View
12 output/Results - ARA.m - 2.txt
@@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, other, Outer
-Mon Mar 28 18:47:22 2011
+Tue Mar 29 14:05:00 2011
================================================================
================ Patch scale Results =========================
@@ -101,11 +101,11 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Full Chamber 0.000 0.000 0.788 1.185
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Position Chamber:Frag
- 0.8067316 1.1484072 0.9912675 1.6464825
+ 3.598753 1.212279 1.316977 1.987461
Chamber:Position Frag:Position Chamber:Frag:Position
- 1.4160321 2.0459508 3.0386495
+ 2.212159 3.544335 5.544104
================================================================
@@ -150,9 +150,9 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Ambient 0.852 1.639 2.010 1.424
Full Chamber 2.954 3.219 3.589 2.383
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Chamber:Frag
- 0.6339410 0.9159482 1.3603678
+ 4.186189 1.307767 2.161964
<============================= END ============================>
View
12 output/Results - ARA.m - 3.txt
@@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, other, Outer
-Mon Mar 28 18:47:23 2011
+Tue Mar 29 14:05:01 2011
================================================================
================ Patch scale Results =========================
@@ -105,11 +105,11 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Full Chamber 2.546 0.000 0.000 0.000
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Position Chamber:Frag
- 1.361213 1.937728 1.672583 2.778139
+ 2.707484 3.053627 2.222159 5.006245
Chamber:Position Frag:Position Chamber:Frag:Position
- 2.389296 3.452169 5.127167
+ 3.732616 5.980420 9.354665
================================================================
@@ -158,9 +158,9 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Ambient 13.724 17.210 17.833 16.122
Full Chamber 10.411 12.195 12.803 11.354
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Chamber:Frag
- 1.580353 2.283369 3.391264
+ 2.770739 3.260135 5.389566
<============================= END ============================>
View
12 output/Results - Cells.m - 1.txt
@@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, Outer
-Mon Mar 28 18:51:54 2011
+Tue Mar 29 14:05:44 2011
================================================================
================ Patch scale Results =========================
@@ -94,11 +94,11 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Full Chamber 99.49 121.37 114.94 95.30
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Position Chamber:Frag
- 22.01271 31.44531 22.01271 45.43368
+ 29.21489 44.70007 25.23328 73.41196
Chamber:Position Frag:Position Chamber:Frag:Position
- 31.44531 45.43368 67.47817
+ 45.05723 73.99852 117.47377
================================================================
@@ -143,9 +143,9 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Ambient 109.81 142.94 117.48 143.09
Full Chamber 137.21 138.46 147.13 134.51
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Chamber:Frag
- 24.78080 35.80449 53.17688
+ 31.21841 51.12072 84.51135
<============================= END ============================>
View
20 output/Results - Cells.m - 123.txt
@@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, Outer
-Mon Mar 28 18:51:56 2011
+Tue Mar 29 14:05:47 2011
================================================================
================ Patch scale Results =========================
@@ -269,17 +269,17 @@ Time Ambient Full Chamber
2009-08 136.06 114.19
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Time Chamber Frag
- 15.84932 12.92019 18.33078
+ NaN 25.72807 28.86003
Position Time:Chamber Time:Frag
- 12.92019 22.52385 32.17548
+ 14.78693 35.31531 56.48460
Chamber:Frag Time:Position Chamber:Position
- 26.09443 22.52385 18.33078
+ 47.24028 35.31531 26.32142
Frag:Position Time:Chamber:Frag Time:Chamber:Position
- 26.09443 46.48866 32.17548
+ 43.08489 88.14176 56.48460
Time:Frag:Position Chamber:Frag:Position Time:Chamber:Frag:Position
- 46.48866 37.41183 69.04504
+ 88.14176 68.09918 135.45247
================================================================
@@ -386,11 +386,11 @@ Time Ambient Full Chamber
2009-08 141.72 148.64
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Time Chamber Frag Time:Chamber Time:Frag
- 18.63042 15.16215 21.58379 26.61368 38.45271
+ NaN 25.35604 30.96041 41.57652 66.61416
Chamber:Frag Time:Chamber:Frag
- 30.94489 57.11003
+ 50.75780 104.19890
<============================= END ============================>
View
12 output/Results - Cells.m - 2.txt
@@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, Outer
-Mon Mar 28 18:51:54 2011
+Tue Mar 29 14:05:45 2011
================================================================
================ Patch scale Results =========================
@@ -92,11 +92,11 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Full Chamber 139.49 124.45 110.42 138.34
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Position Chamber:Frag
- 23.08083 32.97113 23.08083 47.63825
+ 58.92732 61.02001 26.45767 100.21456
Chamber:Position Frag:Position Chamber:Frag:Position
- 32.97113 47.63825 70.75241
+ 47.24354 77.58915 123.17394
================================================================
@@ -141,9 +141,9 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Ambient 100.58 89.52 132.42 90.75
Full Chamber 174.66 144.11 148.52 123.29
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Chamber:Frag
- 31.22485 45.11516 67.00511
+ 59.02144 64.41425 106.48786
<============================= END ============================>
View
12 output/Results - Cells.m - 3.txt
@@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, Outer
-Mon Mar 28 18:51:55 2011
+Tue Mar 29 14:05:46 2011
================================================================
================ Patch scale Results =========================
@@ -92,11 +92,11 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Full Chamber 122.21 141.79 135.04 114.19
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Position Chamber:Frag
- 22.46525 32.09176 22.46525 46.36771
+ 41.57382 44.09494 25.75203 72.41814
Chamber:Position Frag:Position Chamber:Frag:Position
- 32.09176 46.36771 68.86540
+ 45.98352 75.51980 119.88881
================================================================
@@ -141,9 +141,9 @@ Chamber Continuous Full Corridors Pseudo-Corridors Isolated
Ambient 118.24 137.97 149.72 141.72
Full Chamber 128.83 158.03 154.62 148.64
-95% Least Significant Differences (LSD):
+95% Minimum Significant Ranges (MSR):
Chamber Frag Chamber:Frag
- 23.14700 33.44389 49.67092
+ 39.03425 47.75032 78.93951
<============================= END ============================>
View
151 output/Results - Hcells.m - 1.txt
@@ -1,151 +0,0 @@
-Nested ANOVA Results for: Heterocyst Cell Density ( Hcells.m )
-Transformation used: Y.4rt
-Sample Time: 2008-08
-Chamber: Ambient, Full Chamber
-Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
-Patches: Inner, Outer
-
-Mon Mar 28 16:48:38 2011
-
-================================================================
-================ Patch scale Results =========================
-
-Y.trans ~ Chamber * Frag * Position + Error(Block/Chamber/Frag)
-
-Error: Block
- Df Sum Sq Mean Sq F value Pr(>F)
-Residuals 7 73640 10520
-
-Error: Block:Chamber
- Df Sum Sq Mean Sq F value Pr(>F)
-Chamber 1 298 297.6 0.0561 0.8196
-Residuals 7 37152 5307.4
-
-Error: Block:Chamber:Frag
- Df Sum Sq Mean Sq F value Pr(>F)
-Frag 3 11759 3919.6 1.0059 0.3997
-Chamber:Frag 3 7120 2373.3 0.6090 0.6129
-Residuals 42 163665 3896.8
-
-Error: Within
- Df Sum Sq Mean Sq F value Pr(>F)
-Position 1 11333 11333.1 2.8624 0.09623 .
-Chamber:Position 1 1054 1053.6 0.2661 0.60798
-Frag:Position 3 3412 1137.5 0.2873 0.83437
-Chamber:Frag:Position 3 8741 2913.7 0.7359 0.53501
-Residuals 56 221721 3959.3
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-
-
-Tables of means
-Grand mean
-
-118.5282
-
- Chamber
-Chamber
- Ambient Full Chamber
- 117.00 120.05
-
- Frag
-Frag
- Continuous Full Corridors Pseudo-Corridors Isolated
- 102.58 126.92 119.64 124.98
-
- Position
-Position
- Inner Outer
-127.94 109.12
-
- Chamber:Frag
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 101.15 127.79 106.53 132.54
- Full Chamber 104.02 126.04 132.74 117.41
-
- Chamber:Position
- Position
-Chamber Inner Outer
- Ambient 123.54 110.46
- Full Chamber 132.33 107.77
-
- Frag:Position
- Position
-Frag Inner Outer
- Continuous 116.17 88.99
- Full Corridors 131.09 122.74
- Pseudo-Corridors 124.04 115.23
- Isolated 140.45 109.51
-
- Chamber:Frag:Position
-, , Position = Inner
-
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 123.80 131.47 97.53 141.37
- Full Chamber 108.54 130.72 150.55 139.52
-
-, , Position = Outer
-
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 78.50 124.11 115.53 123.72
- Full Chamber 99.49 121.37 114.94 95.30
-
-
-95% Least Significant Differences (LSD):
- Chamber Frag Position Chamber:Frag
- 22.01271 31.44531 22.01271 45.43368
- Chamber:Position Frag:Position Chamber:Frag:Position
- 31.44531 45.43368 67.47817
-
-
-================================================================
-================ Meta-Community scale Results ================
-================================================================
-Y.trans ~ Chamber * Frag + Error(Block/Chamber)
-
-Error: Block
- Df Sum Sq Mean Sq F value Pr(>F)
-Residuals 7 38680 5525.7
-
-Error: Block:Chamber
- Df Sum Sq Mean Sq F value Pr(>F)
-Chamber 1 1935.5 1935.5 0.655 0.445
-Residuals 7 20685.4 2955.1
-
-Error: Within
- Df Sum Sq Mean Sq F value Pr(>F)
-Frag 3 2892 964.1 0.3921 0.7593
-Chamber:Frag 3 4959 1653.2 0.6723 0.5738
-Residuals 42 103273 2458.9
-
-
-Tables of means
-Grand mean
-
-133.8295
-
- Chamber
-Chamber
- Ambient Full Chamber
- 128.33 139.33
-
- Frag
-Frag
- Continuous Full Corridors Pseudo-Corridors Isolated
- 123.51 140.70 132.31 138.80
-
- Chamber:Frag
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 109.81 142.94 117.48 143.09
- Full Chamber 137.21 138.46 147.13 134.51
-
-95% Least Significant Differences (LSD):
- Chamber Frag Chamber:Frag
- 24.78080 35.80449 53.17688
-
-
-<============================= END ============================>
View
396 output/Results - Hcells.m - 123.txt
@@ -1,396 +0,0 @@
-Nested ANOVA Results for: Heterocyst Cell Density ( Hcells.m )
-Transformation used: Y.4rt
-Sample Time: 2008-08, 2009-06, 2009-08
-Chamber: Ambient, Full Chamber
-Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
-Patches: Inner, Outer
-
-Mon Mar 28 16:48:40 2011
-
-================================================================
-================ Patch scale Results =========================
-
-Y.trans ~ Time * Chamber * Frag * Position + Error(Time/Block/Chamber/Frag)
-
-Error: Time
- Df Sum Sq Mean Sq
-Time 2 25859 12930
-
-Error: Time:Block
- Df Sum Sq Mean Sq F value Pr(>F)
-Residuals 21 402682 19175
-
-Error: Time:Block:Chamber
- Df Sum Sq Mean Sq F value Pr(>F)
-Chamber 1 46726 46726 3.7234 0.06727 .
-Time:Chamber 2 29728 14864 1.1845 0.32554
-Residuals 21 263533 12549
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-
-Error: Time:Block:Chamber:Frag
- Df Sum Sq Mean Sq F value Pr(>F)
-Frag 3 16240 5413.3 1.0863 0.3575
-Time:Frag 6 45991 7665.2 1.5381 0.1710
-Chamber:Frag 3 7036 2345.2 0.4706 0.7033
-Time:Chamber:Frag 6 11802 1967.0 0.3947 0.8813
-Residuals 126 627917 4983.5
-
-Error: Within
- Df Sum Sq Mean Sq F value Pr(>F)
-Position 1 9763 9763.3 2.3553 0.1267
-Time:Position 2 3976 1988.2 0.4796 0.6199
-Chamber:Position 1 364 363.7 0.0877 0.7674
-Frag:Position 3 10681 3560.5 0.8589 0.4637
-Time:Chamber:Position 2 4725 2362.6 0.5699 0.5666
-Time:Frag:Position 6 33469 5578.1 1.3456 0.2396
-Chamber:Frag:Position 3 3746 1248.7 0.3012 0.8245
-Time:Chamber:Frag:Position 6 45326 7554.3 1.8224 0.0975 .
-Residuals 168 696412 4145.3
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-
-
-Tables of means
-Grand mean
-
-116.4034
-
- Time
-Time
-2008-08 2009-06 2009-08
- 118.53 105.46 125.22
-
- Chamber
-Chamber
- Ambient Full Chamber
- 105.37 127.43
-
- Frag
-Frag
- Continuous Full Corridors Pseudo-Corridors Isolated
- 110.80 120.14 125.15 109.53
-
- Position
-Position
- Inner Outer
-121.45 111.36
-
- Time:Chamber
- Chamber
-Time Ambient Full Chamber
- 2008-08 117.00 120.05
- 2009-06 82.72 128.20
- 2009-08 116.39 134.05
-
- Time:Frag
- Frag
-Time Continuous Full Corridors Pseudo-Corridors Isolated
- 2008-08 102.58 126.92 119.64 124.98
- 2009-06 122.79 98.64 116.14 84.27
- 2009-08 107.02 134.88 139.66 119.33
-
- Chamber:Frag
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 94.13 108.71 113.73 104.92
- Full Chamber 127.46 131.58 136.56 114.13
-
- Time:Position
- Position
-Time Inner Outer
- 2008-08 127.94 109.12
- 2009-06 109.43 101.49
- 2009-08 126.97 123.47
-
- Chamber:Position
- Position
-Chamber Inner Outer
- Ambient 109.44 101.30
- Full Chamber 133.45 121.42
-
- Frag:Position
- Position
-Frag Inner Outer
- Continuous 113.09 108.51
- Full Corridors 125.60 114.69
- Pseudo-Corridors 138.46 111.83
- Isolated 108.64 110.41
-
- Time:Chamber:Frag
-, , Frag = Continuous
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 101.15 104.02
- 2009-06 85.50 160.07
- 2009-08 95.75 118.30
-
-, , Frag = Full Corridors
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 127.79 126.04
- 2009-06 77.30 119.98
- 2009-08 121.03 148.72
-
-, , Frag = Pseudo-Corridors
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 106.53 132.74
- 2009-06 98.68 133.60
- 2009-08 135.98 143.34
-
-, , Frag = Isolated
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 132.54 117.41
- 2009-06 69.40 99.14
- 2009-08 112.80 125.85
-
-
- Time:Chamber:Position
-, , Position = Inner
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 123.54 132.33
- 2009-06 90.63 128.22
- 2009-08 114.15 139.80
-
-, , Position = Outer
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 110.46 107.77
- 2009-06 74.81 128.18
- 2009-08 118.64 128.31
-
-
- Time:Frag:Position
-, , Position = Inner
-
- Frag
-Time Continuous Full Corridors Pseudo-Corridors Isolated
- 2008-08 116.17 131.09 124.04 140.45
- 2009-06 130.70 96.47 138.60 71.95
- 2009-08 92.39 149.23 152.74 113.53
-
-, , Position = Outer
-
- Frag
-Time Continuous Full Corridors Pseudo-Corridors Isolated
- 2008-08 88.99 122.74 115.23 109.51
- 2009-06 114.87 100.82 93.69 96.60
- 2009-08 121.66 120.52 126.58 125.13
-
-
- Chamber:Frag:Position
-, , Position = Inner
-
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 91.65 117.23 123.93 104.96
- Full Chamber 134.52 133.96 152.99 112.32
-
-, , Position = Outer
-
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 96.62 100.18 103.54 104.88
- Full Chamber 120.40 129.20 120.13 115.94
-
-
- Time:Chamber:Frag:Position
-, , Frag = Continuous, Position = Inner
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 123.80 108.54
- 2009-06 80.75 180.65
- 2009-08 70.40 114.38
-
-, , Frag = Full Corridors, Position = Inner
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 131.47 130.72
- 2009-06 77.42 115.51
- 2009-08 142.80 155.65
-
-, , Frag = Pseudo-Corridors, Position = Inner
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 97.53 150.55
- 2009-06 120.41 156.79
- 2009-08 153.83 151.64
-
-, , Frag = Isolated, Position = Inner
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 141.37 139.52
- 2009-06 83.96 59.94
- 2009-08 89.55 137.52
-
-, , Frag = Continuous, Position = Outer
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 78.50 99.49
- 2009-06 90.26 139.49
- 2009-08 121.10 122.21
-
-, , Frag = Full Corridors, Position = Outer
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 124.11 121.37
- 2009-06 77.18 124.45
- 2009-08 99.26 141.79
-
-, , Frag = Pseudo-Corridors, Position = Outer
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 115.53 114.94
- 2009-06 76.95 110.42
- 2009-08 118.12 135.04
-
-, , Frag = Isolated, Position = Outer
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 123.72 95.30
- 2009-06 54.85 138.34
- 2009-08 136.06 114.19
-
-
-95% Least Significant Differences (LSD):
- Time Chamber Frag
- 15.84932 12.92019 18.33078
- Position Time:Chamber Time:Frag
- 12.92019 22.52385 32.17548
- Chamber:Frag Time:Position Chamber:Position
- 26.09443 22.52385 18.33078
- Frag:Position Time:Chamber:Frag Time:Chamber:Position
- 26.09443 46.48866 32.17548
- Time:Frag:Position Chamber:Frag:Position Time:Chamber:Frag:Position
- 46.48866 37.41183 69.04504
-
-
-================================================================
-================ Meta-Community scale Results ================
-================================================================
-Y.trans ~ Time * Chamber * Frag + Error(Time/Block/Chamber)
-
-Error: Time
- Df Sum Sq Mean Sq
-Time 2 8967.3 4483.6
-
-Error: Time:Block
- Df Sum Sq Mean Sq F value Pr(>F)
-Residuals 21 203790 9704.3
-
-Error: Time:Block:Chamber
- Df Sum Sq Mean Sq F value Pr(>F)
-Chamber 1 23191 23190.6 3.8358 0.06358 .
-Time:Chamber 2 11984 5992.0 0.9911 0.38787
-Residuals 21 126962 6045.8
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-
-Error: Within
- Df Sum Sq Mean Sq F value Pr(>F)
-Frag 3 5117 1705.7 0.6014 0.6152
-Time:Frag 6 18230 3038.3 1.0713 0.3833
-Chamber:Frag 3 4810 1603.4 0.5654 0.6388
-Time:Chamber:Frag 6 8394 1399.0 0.4933 0.8124
-Residuals 126 357344 2836.1
-
-
-Tables of means
-Grand mean
-
-133.8441
-
- Time
-Time
-2008-08 2009-06 2009-08
- 133.83 125.48 142.22
-
- Chamber
-Chamber
- Ambient Full Chamber
- 122.85 144.83
-
- Frag
-Frag
- Continuous Full Corridors Pseudo-Corridors Isolated
- 128.22 135.17 141.65 130.33
-
- Time:Chamber
- Chamber
-Time Ambient Full Chamber
- 2008-08 128.33 139.33
- 2009-06 103.32 147.64
- 2009-08 136.91 147.53
-
- Time:Frag
- Frag
-Time Continuous Full Corridors Pseudo-Corridors Isolated
- 2008-08 123.51 140.70 132.31 138.80
- 2009-06 137.62 116.82 140.47 107.02
- 2009-08 123.53 148.00 152.17 145.18
-
- Chamber:Frag
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 109.54 123.48 133.21 125.19
- Full Chamber 146.90 146.87 150.09 135.48
-
- Time:Chamber:Frag
-, , Frag = Continuous
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 109.81 137.21
- 2009-06 100.58 174.66
- 2009-08 118.24 128.83
-
-, , Frag = Full Corridors
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 142.94 138.46
- 2009-06 89.52 144.11
- 2009-08 137.97 158.03
-
-, , Frag = Pseudo-Corridors
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 117.48 147.13
- 2009-06 132.42 148.52
- 2009-08 149.72 154.62
-
-, , Frag = Isolated
-
- Chamber
-Time Ambient Full Chamber
- 2008-08 143.09 134.51
- 2009-06 90.75 123.29
- 2009-08 141.72 148.64
-
-
-95% Least Significant Differences (LSD):
- Time Chamber Frag Time:Chamber Time:Frag
- 18.63042 15.16215 21.58379 26.61368 38.45271
- Chamber:Frag Time:Chamber:Frag
- 30.94489 57.11003
-
-
-<============================= END ============================>
View
149 output/Results - Hcells.m - 2.txt
@@ -1,149 +0,0 @@
-Nested ANOVA Results for: Heterocyst Cell Density ( Hcells.m )
-Transformation used: Y.4rt
-Sample Time: 2009-06
-Chamber: Ambient, Full Chamber
-Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
-Patches: Inner, Outer
-
-Mon Mar 28 16:48:38 2011
-
-================================================================
-================ Patch scale Results =========================
-
-Y.trans ~ Chamber * Frag * Position + Error(Block/Chamber/Frag)
-
-Error: Block
- Df Sum Sq Mean Sq F value Pr(>F)
-Residuals 7 94498 13500
-
-Error: Block:Chamber
- Df Sum Sq Mean Sq F value Pr(>F)
-Chamber 1 66175 66175 3.0647 0.1235
-Residuals 7 151148 21593
-
-Error: Block:Chamber:Frag
- Df Sum Sq Mean Sq F value Pr(>F)
-Frag 3 29112 9704.0 1.3363 0.2754
-Chamber:Frag 3 9704 3234.5 0.4454 0.7218
-Residuals 42 304988 7261.6
-
-Error: Within
- Df Sum Sq Mean Sq F value Pr(>F)
-Position 1 2014 2014.5 0.4628 0.4991
-Chamber:Position 1 1992 1991.9 0.4576 0.5015
-Frag:Position 3 21138 7046.0 1.6187 0.1953
-Chamber:Frag:Position 3 26448 8815.9 2.0253 0.1208
-Residuals 56 243760 4352.9
-
-
-Tables of means
-Grand mean
-
-105.4604
-
- Chamber
-Chamber
- Ambient Full Chamber
- 82.72 128.20
-
- Frag
-Frag
- Continuous Full Corridors Pseudo-Corridors Isolated
- 122.79 98.64 116.14 84.27
-
- Position
-Position
- Inner Outer
-109.43 101.49
-
- Chamber:Frag
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 85.50 77.30 98.68 69.40
- Full Chamber 160.07 119.98 133.60 99.14
-
- Chamber:Position
- Position
-Chamber Inner Outer
- Ambient 90.63 74.81
- Full Chamber 128.22 128.18
-
- Frag:Position
- Position
-Frag Inner Outer
- Continuous 130.70 114.87
- Full Corridors 96.47 100.82
- Pseudo-Corridors 138.60 93.69
- Isolated 71.95 96.60
-
- Chamber:Frag:Position
-, , Position = Inner
-
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 80.75 77.42 120.41 83.96
- Full Chamber 180.65 115.51 156.79 59.94
-
-, , Position = Outer
-
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 90.26 77.18 76.95 54.85
- Full Chamber 139.49 124.45 110.42 138.34
-
-
-95% Least Significant Differences (LSD):
- Chamber Frag Position Chamber:Frag
- 23.08083 32.97113 23.08083 47.63825
- Chamber:Position Frag:Position Chamber:Frag:Position
- 32.97113 47.63825 70.75241
-
-
-================================================================
-================ Meta-Community scale Results ================
-================================================================
-Y.trans ~ Chamber * Frag + Error(Block/Chamber)
-
-Error: Block
- Df Sum Sq Mean Sq F value Pr(>F)
-Residuals 7 53703 7671.9
-
-Error: Block:Chamber
- Df Sum Sq Mean Sq F value Pr(>F)
-Chamber 1 31435 31435 2.9762 0.1282
-Residuals 7 73937 10562
-
-Error: Within
- Df Sum Sq Mean Sq F value Pr(>F)
-Frag 3 12610 4203.2 1.0766 0.3693
-Chamber:Frag 3 7704 2567.8 0.6578 0.5827
-Residuals 42 163967 3904.0
-
-
-Tables of means
-Grand mean
-
-125.4814
-
- Chamber
-Chamber
- Ambient Full Chamber
- 103.32 147.64
-
- Frag
-Frag
- Continuous Full Corridors Pseudo-Corridors Isolated
- 137.62 116.82 140.47 107.02
-
- Chamber:Frag
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 100.58 89.52 132.42 90.75
- Full Chamber 174.66 144.11 148.52 123.29
-
-95% Least Significant Differences (LSD):
- Chamber Frag Chamber:Frag
- 31.22485 45.11516 67.00511
-
-
-<============================= END ============================>
View
149 output/Results - Hcells.m - 3.txt
@@ -1,149 +0,0 @@
-Nested ANOVA Results for: Heterocyst Cell Density ( Hcells.m )
-Transformation used: Y.4rt
-Sample Time: 2009-08
-Chamber: Ambient, Full Chamber
-Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
-Patches: Inner, Outer
-
-Mon Mar 28 16:48:39 2011
-
-================================================================
-================ Patch scale Results =========================
-
-Y.trans ~ Chamber * Frag * Position + Error(Block/Chamber/Frag)
-
-Error: Block
- Df Sum Sq Mean Sq F value Pr(>F)
-Residuals 7 234544 33506
-
-Error: Block:Chamber
- Df Sum Sq Mean Sq F value Pr(>F)
-Chamber 1 9981 9981.2 0.9287 0.3673
-Residuals 7 75233 10747.6
-
-Error: Block:Chamber:Frag
- Df Sum Sq Mean Sq F value Pr(>F)
-Frag 3 21360 7120.1 1.8777 0.1480
-Chamber:Frag 3 2014 671.4 0.1771 0.9113
-Residuals 42 159264 3792.0
-
-Error: Within
- Df Sum Sq Mean Sq F value Pr(>F)
-Position 1 392 392.2 0.0951 0.7589
-Chamber:Position 1 2043 2043.4 0.4955 0.4844
-Frag:Position 3 19600 6533.3 1.5843 0.2034
-Chamber:Frag:Position 3 13883 4627.6 1.1222 0.3479
-Residuals 56 230931 4123.8
-
-
-Tables of means
-Grand mean
-
-125.2217
-
- Chamber
-Chamber
- Ambient Full Chamber
- 116.39 134.05
-
- Frag
-Frag
- Continuous Full Corridors Pseudo-Corridors Isolated
- 107.02 134.88 139.66 119.33
-
- Position
-Position
- Inner Outer
-126.97 123.47
-
- Chamber:Frag
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 95.75 121.03 135.98 112.80
- Full Chamber 118.30 148.72 143.34 125.85
-
- Chamber:Position
- Position
-Chamber Inner Outer
- Ambient 114.15 118.64
- Full Chamber 139.80 128.31
-
- Frag:Position
- Position
-Frag Inner Outer
- Continuous 92.39 121.66
- Full Corridors 149.23 120.52
- Pseudo-Corridors 152.74 126.58
- Isolated 113.53 125.13
-
- Chamber:Frag:Position
-, , Position = Inner
-
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 70.40 142.80 153.83 89.55
- Full Chamber 114.38 155.65 151.64 137.52
-
-, , Position = Outer
-
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 121.10 99.26 118.12 136.06
- Full Chamber 122.21 141.79 135.04 114.19
-
-
-95% Least Significant Differences (LSD):
- Chamber Frag Position Chamber:Frag
- 22.46525 32.09176 22.46525 46.36771
- Chamber:Position Frag:Position Chamber:Frag:Position
- 32.09176 46.36771 68.86540
-
-
-================================================================
-================ Meta-Community scale Results ================
-================================================================
-Y.trans ~ Chamber * Frag + Error(Block/Chamber)
-
-Error: Block
- Df Sum Sq Mean Sq F value Pr(>F)
-Residuals 7 111407 15915
-
-Error: Block:Chamber
- Df Sum Sq Mean Sq F value Pr(>F)
-Chamber 1 1804 1803.7 0.3904 0.5519
-Residuals 7 32340 4619.9
-
-Error: Within
- Df Sum Sq Mean Sq F value Pr(>F)
-Frag 3 7845 2615.06 1.2190 0.3147
-Chamber:Frag 3 542 180.53 0.0841 0.9683
-Residuals 42 90104 2145.34
-
-
-Tables of means
-Grand mean
-
-142.2214
-
- Chamber
-Chamber
- Ambient Full Chamber
- 136.91 147.53
-
- Frag
-Frag
- Continuous Full Corridors Pseudo-Corridors Isolated
- 123.53 148.00 152.17 145.18
-
- Chamber:Frag
- Frag
-Chamber Continuous Full Corridors Pseudo-Corridors Isolated
- Ambient 118.24 137.97 149.72 141.72
- Full Chamber 128.83 158.03 154.62 148.64
-
-95% Least Significant Differences (LSD):
- Chamber Frag Chamber:Frag
- 23.14700 33.44389 49.67092
-
-
-<============================= END ============================>
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