From 87c793b8789ea3dc3ed2a2de70930743b949f470 Mon Sep 17 00:00:00 2001 From: "Jonathan A. Whiteley" Date: Thu, 13 Dec 2012 18:05:42 -0500 Subject: [PATCH] Moss Growth - Productivity: updated graphs - added clearer panel labels for thesis. Signed-off-by: Jonathan A. Whiteley --- Moss-Prod-Decomp.R | 6 +++--- Moss-growth.R | 19 +++++++++--------- output/Results - Decompositng - 3.txt | 18 ++++++++--------- output/Results - PD.bal - 3.txt | 18 ++++++++--------- output/Results - Productivity - 3.txt | 4 ++-- output/Results - Productivity - Years 1-2.txt | 20 +++++++++---------- output/Results - grow01 - 12.txt | 4 ++-- output/Results - grow12 - 12.txt | 6 +++--- output/Results - grow13 - 12.txt | 10 +++++----- output/Results - grow23 - 12.txt | 10 +++++----- 10 files changed, 58 insertions(+), 57 deletions(-) diff --git a/Moss-Prod-Decomp.R b/Moss-Prod-Decomp.R index 6c9cb7e..b895488 100644 --- a/Moss-Prod-Decomp.R +++ b/Moss-Prod-Decomp.R @@ -503,7 +503,7 @@ if (Save.results == TRUE && is.null(Save.text) == FALSE) { } if (Save.results == TRUE && is.null(Save.final) == FALSE) { Save.final <- paste(SaveDir.plots(), "Figure - ", "PD-balance", sep="") - ggsave(file = paste(Save.final, "- PD.eps" ), plot = PD.CP.plot, width = 4, height = 5, scale = 1) - ggsave(file = paste(Save.final, "- CxP.eps"), plot = CxP.plot, width = 4, height = 5, scale = 1) - ggsave(file = paste(Save.final, "- CFP.eps"), plot = CFP.plot, width = 6, height = 5, scale = 1) + ggsave(file = paste(Save.final, "- PD.eps" ), plot = PD.CP.plot, width = 4, height = 5, scale = 1) # to accommodate Y-axis label + ggsave(file = paste(Save.final, "- CxP.eps"), plot = CxP.plot, width = 4, height = 4, scale = 1) + ggsave(file = paste(Save.final, "- CFP.eps"), plot = CFP.plot, width = 6, height = 4, scale = 1) } diff --git a/Moss-growth.R b/Moss-growth.R index 7051058..40653f5 100644 --- a/Moss-growth.R +++ b/Moss-growth.R @@ -80,8 +80,8 @@ SECC <- within( SECC, ) Time[is.na(Time)] <- levels(Time)[1] Position <- recode(Pos, - "1='Inner'; 0='Outer'; 'c'='corridor'; 'c2'='corridor'; else='other'", - levels=c( "Inner", "other", "Outer", "corridor"), + "1='Inner'; 0='Outer'; 'c'='corridor'; 'c2'='corridor'; else='intermediate'", # **** non-standard! + levels=c( "Inner", "intermediate", "Outer", "corridor"), as.factor.result=TRUE ) } @@ -126,7 +126,7 @@ for (Y.col in Ycols) ## delete lines to use the defaults. ## Specify which treatment levels to include (by index is probably easiest) - ## Including "other" patches throws errors when fitting models (for grow01)? + ## Including "intermediate" patches throws errors when fitting models (for grow01)? ## Include Partial Chambers throws errors when doing post-hoc multiple tests (grow01)? Time.use <- levels(SECC$Time) # samples collected from t3 AND t4 (t3 not normally included in SECC) Chamber.use <- levels(SECC$Chamber)[c(1, 3)] # Chamber treatments to include @@ -214,9 +214,9 @@ rownames(CxP.data) <- NULL CxP.labels <- attr(SECC, "labels")[which(names(attr(SECC, "labels")) %in% unique(CxP.data$Var) )] CxP.TimeP <- substring(CxP.labels, gregexpr("[0-9-]+ months", CxP.labels) ) -Months <- c("August", "June", "August") -Months <- c(Months, rep( "", len = length(CxP.TimeP) - length(Months) ) ) -CxP.data$Panel <- factor(CxP.data$Var, labels = paste(Months, CxP.TimeP, sep="\n") ) +Season <- c("Year 1", "Winter 2", "Summer 2", "Year 2") +Season <- c(Season, rep( "", len = length(CxP.TimeP) - length(Season) ) ) # fill panels with blank months? +CxP.data$Panel <- factor(CxP.data$Var, labels = paste(Season, CxP.TimeP, sep="\n") ) CxP.data$Chamber <- factor(CxP.data$Chamber, labels = c("Ambient", "Chamber")) @@ -246,7 +246,7 @@ Y.labels <- gsub("\\s+[0-9-]+ months", "", CxP.labels) Y.plotlab <- bquote( .(Y.labels[1]) * " (" * .(Y.units) * ")" ) Plot.Title <- bquote("Patch means " %+-% "95% Confidence Intervals") Position.label <- "Patch\nPosition" # attr(SECC, "labels")[["Pos"]] -Position.map <- plotMap( factor = "Position", labels = c("Inner", "other", "Outer") ) +Position.map <- plotMap( factor = "Position", labels = levels(SECC.full$Position) ) Position.map <- Position.map[ levels(SECC$Position) %in% Position.use, ] PositionPts <- ggPts.SECC(Position.map, Position.label) @@ -290,7 +290,7 @@ if (F) { ## Specify which treatment levels to include (optional: hide to use same as previous analyses) Time.use <- levels(SECC$Time) # samples collected from t3 AND t4 (t3 not normally included in SECC) Chamber.use <- levels(SECC$Chamber)[c(1, 3)] # Chamber treatments to include (No Productivity measurements from Partial; no Moss_Biomass data for these treatments). - Position.use <- levels(SECC$Position)[c(1:3)] # Position treatments to include: other patches normally excluded for consistency, but they are kind of interesting here ... + Position.use <- levels(SECC$Position)[c(1:3)] # Position treatments to include: intermediate patches normally excluded for consistency, but they are kind of interesting here ... } @@ -520,6 +520,7 @@ if (T) ##================================================ CPY.data <- effect.to.df(CPY.eff) CPY.data$Chamber <- factor(CPY.data$Chamber, labels = c("Ambient", "Chamber")) +CPY.data$Year <- factor(CPY.data$Year, labels = c("Year 1", "Year 2")) @@ -530,7 +531,7 @@ Y.lim <- range(c(CPY.data$lower, CPY.data$upper)) Y.plotlab <- bquote( .(attr(SECC, "labels")[["Prod"]]) * " (" * .(attr(SECC, "units")[["Prod"]]) * ")" ) Plot.Title <- bquote("Patch means " %+-% "95% Confidence Intervals") Position.label <- "Patch\nPosition" # attr(SECC, "labels")[["Pos"]] -Position.map <- plotMap( factor = "Position", labels = c("Inner", "other", "Outer") ) +Position.map <- plotMap( factor = "Position", labels = levels(SECC.full$Position) ) Position.map <- Position.map[ levels(SECC$Position) %in% Position.use, ] PositionPts <- ggPts.SECC(Position.map, Position.label) diff --git a/output/Results - Decompositng - 3.txt b/output/Results - Decompositng - 3.txt index 343f1b1..612e7db 100644 --- a/output/Results - Decompositng - 3.txt +++ b/output/Results - Decompositng - 3.txt @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber Fragmentation: Contiguous, Full Corridors, Pseudo-Corridors, Isolated Patches: Inner, Outer -Sun Nov 4 23:56:42 2012 +Thu Dec 13 15:47:06 2012 ================================================================ ================ Patch scale Results ========================= @@ -24,7 +24,7 @@ Chamber:Frag:Position 3 56 0.39868 0.7545 % latex table generated in R 2.12.0 by xtable 1.5-6 package -% Sun Nov 4 23:56:53 2012 +% Thu Dec 13 15:47:18 2012 \begin{table}[ht] \begin{center} \begin{tabular}{rrrrr} @@ -56,11 +56,11 @@ Fit: lme.formula(fixed = Y.trans ~ CxP, data = SECCp, random = Yp.random) Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) Full Chamber.Inner - Ambient.Inner == 0 1.798 10.460 0.172 0.9980 -Ambient.Outer - Ambient.Inner == 0 6.140 6.347 0.967 0.7533 -Full Chamber.Outer - Ambient.Inner == 0 -23.725 10.460 -2.268 0.0964 . +Ambient.Outer - Ambient.Inner == 0 6.140 6.347 0.967 0.7532 +Full Chamber.Outer - Ambient.Inner == 0 -23.725 10.460 -2.268 0.0965 . Ambient.Outer - Full Chamber.Inner == 0 4.342 10.460 0.415 0.9738 Full Chamber.Outer - Full Chamber.Inner == 0 -25.524 6.347 -4.021 <0.001 *** -Full Chamber.Outer - Ambient.Outer == 0 -29.866 10.460 -2.855 0.0199 * +Full Chamber.Outer - Ambient.Outer == 0 -29.866 10.460 -2.855 0.0202 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Adjusted p values reported -- single-step method) @@ -75,10 +75,10 @@ Fit: lme.formula(fixed = Y.trans ~ Chamber * Position, data = SECCp, Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) -Ambient:Inner == 0 50.867 7.395 6.878 <0.001 *** -Full Chamber:Inner == 0 52.665 7.395 7.122 <0.001 *** -Ambient:Outer == 0 57.007 7.395 7.709 <0.001 *** -Full Chamber:Outer == 0 27.141 7.395 3.670 <0.001 *** +Ambient:Inner == 0 50.867 7.395 6.878 < 1e-04 *** +Full Chamber:Inner == 0 52.665 7.395 7.122 < 1e-04 *** +Ambient:Outer == 0 57.007 7.395 7.709 < 1e-04 *** +Full Chamber:Outer == 0 27.141 7.395 3.670 0.000895 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Adjusted p values reported -- single-step method) diff --git a/output/Results - PD.bal - 3.txt b/output/Results - PD.bal - 3.txt index 6a8107d..beece1b 100644 --- a/output/Results - PD.bal - 3.txt +++ b/output/Results - PD.bal - 3.txt @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber Fragmentation: Contiguous, Full Corridors, Pseudo-Corridors, Isolated Patches: Inner, Outer -Sun Nov 4 23:56:57 2012 +Thu Dec 13 15:47:22 2012 ================================================================ ================ Patch scale Results ========================= @@ -24,7 +24,7 @@ Chamber:Frag:Position 3 43 2.417197 0.0793 % latex table generated in R 2.12.0 by xtable 1.5-6 package -% Sun Nov 4 23:57:08 2012 +% Thu Dec 13 15:47:33 2012 \begin{table}[ht] \begin{center} \begin{tabular}{rrrrr} @@ -57,10 +57,10 @@ Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) Full Chamber.Inner - Ambient.Inner == 0 -11.884 21.887 -0.543 0.948 Ambient.Outer - Ambient.Inner == 0 -5.559 21.310 -0.261 0.994 -Full Chamber.Outer - Ambient.Inner == 0 -148.060 21.126 -7.008 <1e-05 *** +Full Chamber.Outer - Ambient.Inner == 0 -148.060 21.126 -7.008 <1e-04 *** Ambient.Outer - Full Chamber.Inner == 0 6.325 22.469 0.282 0.992 -Full Chamber.Outer - Full Chamber.Inner == 0 -136.175 21.135 -6.443 <1e-05 *** -Full Chamber.Outer - Ambient.Outer == 0 -142.501 21.721 -6.561 <1e-05 *** +Full Chamber.Outer - Full Chamber.Inner == 0 -136.175 21.135 -6.443 <1e-04 *** +Full Chamber.Outer - Ambient.Outer == 0 -142.501 21.721 -6.561 <1e-04 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Adjusted p values reported -- single-step method) @@ -75,10 +75,10 @@ Fit: lme.formula(fixed = Y.trans ~ Chamber * Position, data = SECCp, Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) -Ambient:Inner == 0 108.41 17.32 6.258 <1e-04 *** -Full Chamber:Inner == 0 96.53 18.04 5.351 <1e-04 *** -Ambient:Outer == 0 102.85 18.04 5.702 <1e-04 *** -Full Chamber:Outer == 0 -39.66 17.11 -2.318 0.0766 . +Ambient:Inner == 0 108.41 17.32 6.258 <0.001 *** +Full Chamber:Inner == 0 96.53 18.04 5.351 <0.001 *** +Ambient:Outer == 0 102.85 18.04 5.702 <0.001 *** +Full Chamber:Outer == 0 -39.66 17.11 -2.318 0.0765 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Adjusted p values reported -- single-step method) diff --git a/output/Results - Productivity - 3.txt b/output/Results - Productivity - 3.txt index fd5ecd4..bd12227 100644 --- a/output/Results - Productivity - 3.txt +++ b/output/Results - Productivity - 3.txt @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber Fragmentation: Contiguous, Full Corridors, Pseudo-Corridors, Isolated Patches: Inner, Outer -Sun Nov 4 23:56:31 2012 +Thu Dec 13 15:46:50 2012 ================================================================ ================ Patch scale Results ========================= @@ -24,7 +24,7 @@ Chamber:Frag:Position 3 43 2.89987 0.0458 % latex table generated in R 2.12.0 by xtable 1.5-6 package -% Sun Nov 4 23:56:42 2012 +% Thu Dec 13 15:47:05 2012 \begin{table}[ht] \begin{center} \begin{tabular}{rrrrr} diff --git a/output/Results - Productivity - Years 1-2.txt b/output/Results - Productivity - Years 1-2.txt index 3252bb9..924bcee 100644 --- a/output/Results - Productivity - Years 1-2.txt +++ b/output/Results - Productivity - Years 1-2.txt @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber Fragmentation: Contiguous, Full Corridors, Pseudo-Corridors, Isolated Patches: Inner, Outer -Sun Nov 4 23:55:52 2012 +Thu Dec 13 18:01:21 2012 ================================================================ numDF denDF F-value p-value @@ -26,7 +26,7 @@ Chamber:Position:Year 1 106 11.15488 0.0012 % latex table generated in R 2.12.0 by xtable 1.5-6 package -% Sun Nov 4 23:55:52 2012 +% Thu Dec 13 18:01:21 2012 \begin{table}[ht] \begin{center} \begin{tabular}{rrrrr} @@ -68,24 +68,24 @@ Full Chamber.Inner.1 - Ambient.Inner.1 == 0 0.03721 0.31672 0.117 1. Ambient.Outer.1 - Ambient.Inner.1 == 0 0.08702 0.31341 0.278 0.99999 Full Chamber.Outer.1 - Ambient.Inner.1 == 0 -1.64066 0.31672 -5.180 < 0.001 *** Ambient.Inner.2 - Ambient.Inner.1 == 0 1.03153 0.24990 4.128 < 0.001 *** -Full Chamber.Inner.2 - Ambient.Inner.1 == 0 1.05499 0.32337 3.262 0.02356 * -Ambient.Outer.2 - Ambient.Inner.1 == 0 1.23629 0.32532 3.800 0.00358 ** +Full Chamber.Inner.2 - Ambient.Inner.1 == 0 1.05499 0.32337 3.262 0.02333 * +Ambient.Outer.2 - Ambient.Inner.1 == 0 1.23629 0.32532 3.800 0.00349 ** Full Chamber.Outer.2 - Ambient.Inner.1 == 0 -2.21719 0.31882 -6.954 < 0.001 *** Ambient.Outer.1 - Full Chamber.Inner.1 == 0 0.04981 0.31462 0.158 1.00000 Full Chamber.Outer.1 - Full Chamber.Inner.1 == 0 -1.67787 0.31129 -5.390 < 0.001 *** -Ambient.Inner.2 - Full Chamber.Inner.1 == 0 0.99432 0.31895 3.118 0.03689 * -Full Chamber.Inner.2 - Full Chamber.Inner.1 == 0 1.01778 0.25009 4.070 0.00112 ** -Ambient.Outer.2 - Full Chamber.Inner.1 == 0 1.19908 0.32645 3.673 0.00570 ** +Ambient.Inner.2 - Full Chamber.Inner.1 == 0 0.99432 0.31895 3.118 0.03706 * +Full Chamber.Inner.2 - Full Chamber.Inner.1 == 0 1.01778 0.25009 4.070 0.00123 ** +Ambient.Outer.2 - Full Chamber.Inner.1 == 0 1.19908 0.32645 3.673 0.00580 ** Full Chamber.Outer.2 - Full Chamber.Inner.1 == 0 -2.25440 0.31341 -7.193 < 0.001 *** Full Chamber.Outer.1 - Ambient.Outer.1 == 0 -1.72768 0.31462 -5.491 < 0.001 *** -Ambient.Inner.2 - Ambient.Outer.1 == 0 0.94451 0.31566 2.992 0.05378 . -Full Chamber.Inner.2 - Ambient.Outer.1 == 0 0.96797 0.32130 3.013 0.05050 . +Ambient.Inner.2 - Ambient.Outer.1 == 0 0.94451 0.31566 2.992 0.05338 . +Full Chamber.Inner.2 - Ambient.Outer.1 == 0 0.96797 0.32130 3.013 0.05104 . Ambient.Outer.2 - Ambient.Outer.1 == 0 1.14927 0.25668 4.477 < 0.001 *** Full Chamber.Outer.2 - Ambient.Outer.1 == 0 -2.30421 0.31672 -7.275 < 0.001 *** Ambient.Inner.2 - Full Chamber.Outer.1 == 0 2.67220 0.31895 8.378 < 0.001 *** Full Chamber.Inner.2 - Full Chamber.Outer.1 == 0 2.69565 0.31804 8.476 < 0.001 *** Ambient.Outer.2 - Full Chamber.Outer.1 == 0 2.87695 0.32645 8.813 < 0.001 *** -Full Chamber.Outer.2 - Full Chamber.Outer.1 == 0 -0.57653 0.24419 -2.361 0.25209 +Full Chamber.Outer.2 - Full Chamber.Outer.1 == 0 -0.57653 0.24419 -2.361 0.25183 Full Chamber.Inner.2 - Ambient.Inner.2 == 0 0.02346 0.32553 0.072 1.00000 Ambient.Outer.2 - Ambient.Inner.2 == 0 0.20475 0.32741 0.625 0.99841 Full Chamber.Outer.2 - Ambient.Inner.2 == 0 -3.24872 0.32099 -10.121 < 0.001 *** diff --git a/output/Results - grow01 - 12.txt b/output/Results - grow01 - 12.txt index 0b10a8c..6c9fef8 100644 --- a/output/Results - grow01 - 12.txt +++ b/output/Results - grow01 - 12.txt @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber Fragmentation: Contiguous, Full Corridors, Pseudo-Corridors, Isolated Patches: Inner, Outer -Sun Nov 4 23:51:28 2012 +Thu Dec 13 17:56:52 2012 ================================================================ ================ Patch scale Results ========================= @@ -24,7 +24,7 @@ Chamber:Frag:Position 3 55 0.39866 0.7545 % latex table generated in R 2.12.0 by xtable 1.5-6 package -% Sun Nov 4 23:51:40 2012 +% Thu Dec 13 17:57:03 2012 \begin{table}[ht] \begin{center} \begin{tabular}{rrrrr} diff --git a/output/Results - grow12 - 12.txt b/output/Results - grow12 - 12.txt index 94b3813..95ff1d9 100644 --- a/output/Results - grow12 - 12.txt +++ b/output/Results - grow12 - 12.txt @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber Fragmentation: Contiguous, Full Corridors, Pseudo-Corridors, Isolated Patches: Inner, Outer -Sun Nov 4 23:51:41 2012 +Thu Dec 13 17:57:04 2012 ================================================================ ================ Patch scale Results ========================= @@ -32,7 +32,7 @@ Time:Chamber:Frag:Position 3 103 0.49111 0.6892 % latex table generated in R 2.12.0 by xtable 1.5-6 package -% Sun Nov 4 23:52:11 2012 +% Thu Dec 13 17:57:36 2012 \begin{table}[ht] \begin{center} \begin{tabular}{rrrrr} @@ -71,7 +71,7 @@ Fit: lme.formula(fixed = Y.trans ~ CxP, data = SECCp, random = Yp.random) Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) -Full Chamber.Inner - Ambient.Inner == 0 0.65167 0.61869 1.053 0.717 +Full Chamber.Inner - Ambient.Inner == 0 0.65167 0.61869 1.053 0.718 Ambient.Outer - Ambient.Inner == 0 0.04474 0.59398 0.075 1.000 Full Chamber.Outer - Ambient.Inner == 0 -4.34179 0.61621 -7.046 <1e-04 *** Ambient.Outer - Full Chamber.Inner == 0 -0.60693 0.62339 -0.974 0.764 diff --git a/output/Results - grow13 - 12.txt b/output/Results - grow13 - 12.txt index b676fc1..7e81dd9 100644 --- a/output/Results - grow13 - 12.txt +++ b/output/Results - grow13 - 12.txt @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber Fragmentation: Contiguous, Full Corridors, Pseudo-Corridors, Isolated Patches: Inner, Outer -Sun Nov 4 23:52:43 2012 +Thu Dec 13 17:58:06 2012 ================================================================ ================ Patch scale Results ========================= @@ -32,7 +32,7 @@ Time:Chamber:Frag:Position 3 98 0.74191 0.5296 % latex table generated in R 2.12.0 by xtable 1.5-6 package -% Sun Nov 4 23:53:13 2012 +% Thu Dec 13 17:58:36 2012 \begin{table}[ht] \begin{center} \begin{tabular}{rrrrr} @@ -91,9 +91,9 @@ Fit: lme.formula(fixed = Y.trans ~ Chamber * Position, data = SECCp, Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) -Ambient:Inner == 0 8.6235 0.7761 11.111 <1e-07 *** -Full Chamber:Inner == 0 9.0126 0.7795 11.562 <1e-07 *** -Ambient:Outer == 0 8.7577 0.7942 11.027 <1e-07 *** +Ambient:Inner == 0 8.6235 0.7761 11.111 <1e-08 *** +Full Chamber:Inner == 0 9.0126 0.7795 11.562 <1e-08 *** +Ambient:Outer == 0 8.7577 0.7942 11.027 <1e-08 *** Full Chamber:Outer == 0 0.1668 0.7763 0.215 0.999 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 diff --git a/output/Results - grow23 - 12.txt b/output/Results - grow23 - 12.txt index 5e97b7f..ce639dc 100644 --- a/output/Results - grow23 - 12.txt +++ b/output/Results - grow23 - 12.txt @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber Fragmentation: Contiguous, Full Corridors, Pseudo-Corridors, Isolated Patches: Inner, Outer -Sun Nov 4 23:52:12 2012 +Thu Dec 13 17:57:36 2012 ================================================================ ================ Patch scale Results ========================= @@ -32,7 +32,7 @@ Time:Chamber:Frag:Position 3 107 0.87640 0.4558 % latex table generated in R 2.12.0 by xtable 1.5-6 package -% Sun Nov 4 23:52:43 2012 +% Thu Dec 13 17:58:06 2012 \begin{table}[ht] \begin{center} \begin{tabular}{rrrrr} @@ -73,10 +73,10 @@ Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) Full Chamber.Inner - Ambient.Inner == 0 -0.09365 0.43049 -0.218 0.996 Ambient.Outer - Ambient.Inner == 0 0.19180 0.43418 0.442 0.971 -Full Chamber.Outer - Ambient.Inner == 0 -4.05488 0.43050 -9.419 <1e-05 *** +Full Chamber.Outer - Ambient.Inner == 0 -4.05488 0.43050 -9.419 <1e-06 *** Ambient.Outer - Full Chamber.Inner == 0 0.28545 0.43593 0.655 0.914 -Full Chamber.Outer - Full Chamber.Inner == 0 -3.96123 0.43224 -9.164 <1e-05 *** -Full Chamber.Outer - Ambient.Outer == 0 -4.24668 0.43575 -9.746 <1e-05 *** +Full Chamber.Outer - Full Chamber.Inner == 0 -3.96123 0.43224 -9.164 <1e-06 *** +Full Chamber.Outer - Ambient.Outer == 0 -4.24668 0.43575 -9.746 <1e-06 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Adjusted p values reported -- single-step method)