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Moss Growth - Productivity: updated graphs
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- added clearer panel labels for thesis.

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
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jawhiteley committed Dec 13, 2012
1 parent bfa05dd commit 87c793b
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Showing 10 changed files with 58 additions and 57 deletions.
6 changes: 3 additions & 3 deletions Moss-Prod-Decomp.R
Expand Up @@ -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)
}
19 changes: 10 additions & 9 deletions Moss-growth.R
Expand Up @@ -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
)
}
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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"))


Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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 ...
}


Expand Down Expand Up @@ -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"))



Expand All @@ -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)

Expand Down
18 changes: 9 additions & 9 deletions output/Results - Decompositng - 3.txt
Expand Up @@ -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 =========================
Expand All @@ -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}
Expand Down Expand Up @@ -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)
Expand All @@ -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)
Expand Down
18 changes: 9 additions & 9 deletions output/Results - PD.bal - 3.txt
Expand Up @@ -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 =========================
Expand All @@ -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}
Expand Down Expand Up @@ -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)
Expand All @@ -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)
Expand Down
4 changes: 2 additions & 2 deletions output/Results - Productivity - 3.txt
Expand Up @@ -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 =========================
Expand All @@ -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}
Expand Down
20 changes: 10 additions & 10 deletions output/Results - Productivity - Years 1-2.txt
Expand Up @@ -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
Expand All @@ -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}
Expand Down Expand Up @@ -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 ***
Expand Down
4 changes: 2 additions & 2 deletions output/Results - grow01 - 12.txt
Expand Up @@ -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 =========================
Expand All @@ -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}
Expand Down
6 changes: 3 additions & 3 deletions output/Results - grow12 - 12.txt
Expand Up @@ -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 =========================
Expand All @@ -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}
Expand Down Expand Up @@ -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
Expand Down
10 changes: 5 additions & 5 deletions output/Results - grow13 - 12.txt
Expand Up @@ -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 =========================
Expand All @@ -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}
Expand Down Expand Up @@ -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
Expand Down
10 changes: 5 additions & 5 deletions output/Results - grow23 - 12.txt
Expand Up @@ -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 =========================
Expand All @@ -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}
Expand Down Expand Up @@ -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)
Expand Down

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