Skip to content

Commit

Permalink
cca-object-tests.Rout.save needs upgrading
Browse files Browse the repository at this point in the history
  • Loading branch information
@jarioksa
jarioksa committed Aug 21, 2024
1 parent 8f516ce commit aab4307
Showing 1 changed file with 135 additions and 27 deletions.
162 changes: 135 additions & 27 deletions tests/cca-object-tests.Rout.save
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand All @@ -23,16 +23,37 @@ Type 'q()' to quit R.
> ## models
> data(dune, dune.env)
> mcca <- cca(dune ~ Condition(Management) + Manure + A1, dune.env)

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mrda <- rda(dune ~ Condition(Management) + Manure + A1, dune.env)

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mrda1 <- rda(dune ~ Condition(Management) + Manure + A1, dune.env, scale=TRUE)

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mcap <- capscale(dune ~ Condition(Management) + Manure + A1, dune.env,
+ dist = "bray")

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mdb <- dbrda(dune ~ Condition(Management) + Manure + A1, dune.env,
+ dist = "bray")

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mancap <- capscale(dune ~ Condition(Management) + Manure + A1, dune.env,
+ dist = "manhattan")

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mandb <- dbrda(dune ~ Condition(Management) + Manure + A1, dune.env,
+ dist = "manhattan")

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> ## 0-rank constraints
> m0cca <- cca(dune ~ Condition(Management) + Management, dune.env)
> ## univariate model, rank-1 constraint
Expand All @@ -44,13 +65,22 @@ Type 'q()' to quit R.
Call: cca(formula = dune ~ Condition(Management) + Manure + A1, data =
dune.env)

-- Model Summary --

Inertia Proportion Rank
Total 2.115 1.000
Conditional 0.604 0.285 3
Constrained 0.450 0.213 4
Unconstrained 1.062 0.502 12
Inertia is scaled Chi-square
Some constraints or conditions were aliased because they were redundant

Inertia is scaled Chi-square

-- Note --

Some constraints or conditions were aliased because they were redundant.
This can happen if terms are linearly dependent (collinear): 'Manure^4'

-- Eigenvalues --

Eigenvalues for constrained axes:
CCA1 CCA2 CCA3 CCA4
Expand All @@ -64,13 +94,22 @@ Eigenvalues for unconstrained axes:
Call: rda(formula = dune ~ Condition(Management) + Manure + A1, data =
dune.env)

-- Model Summary --

Inertia Proportion Rank
Total 84.124 1.000
Conditional 29.231 0.347 3
Constrained 16.791 0.200 4
Unconstrained 38.102 0.453 12
Inertia is variance
Some constraints or conditions were aliased because they were redundant

Inertia is variance

-- Note --

Some constraints or conditions were aliased because they were redundant.
This can happen if terms are linearly dependent (collinear): 'Manure^4'

-- Eigenvalues --

Eigenvalues for constrained axes:
RDA1 RDA2 RDA3 RDA4
Expand All @@ -81,8 +120,10 @@ Eigenvalues for unconstrained axes:
10.25 8.21 4.95 3.36 3.12 2.49 1.87 1.26 1.02 0.74 0.48 0.35

> mcap
Call: capscale(formula = dune ~ Condition(Management) + Manure + A1,
data = dune.env, distance = "bray")
Call: capscale(formula = dune ~ Condition(Management) + Manure + A1, data =
dune.env, distance = "bray")

-- Model Summary --

Inertia Proportion Rank
Total 4.299
Expand All @@ -91,9 +132,17 @@ Conditional 1.500 0.327 3
Constrained 1.073 0.233 4
Unconstrained 2.021 0.440 12
Imaginary -0.295
Inertia is squared Bray distance
Species scores projected from 'dune'
Some constraints or conditions were aliased because they were redundant

Inertia is squared Bray distance

-- Note --

Species scores projected from 'dune'

Some constraints or conditions were aliased because they were redundant.
This can happen if terms are linearly dependent (collinear): 'Manure^4'

-- Eigenvalues --

Eigenvalues for constrained axes:
CAP1 CAP2 CAP3 CAP4
Expand All @@ -104,16 +153,25 @@ Eigenvalues for unconstrained axes:
0.749 0.338 0.308 0.213 0.137 0.136 0.062 0.039 0.017 0.011 0.006 0.004

> mdb
Call: dbrda(formula = dune ~ Condition(Management) + Manure + A1, data
= dune.env, distance = "bray")
Call: dbrda(formula = dune ~ Condition(Management) + Manure + A1, data =
dune.env, distance = "bray")

-- Model Summary --

Inertia Proportion Rank RealDims
Total 4.299 1.000
Conditional 1.469 0.342 3
Constrained 1.035 0.241 4 4
Unconstrained 1.796 0.418 12 9
Inertia is squared Bray distance
Some constraints or conditions were aliased because they were redundant

Inertia is squared Bray distance

-- Note --

Some constraints or conditions were aliased because they were redundant.
This can happen if terms are linearly dependent (collinear): 'Manure^4'

-- Eigenvalues --

Eigenvalues for constrained axes:
dbRDA1 dbRDA2 dbRDA3 dbRDA4
Expand All @@ -126,8 +184,10 @@ Eigenvalues for unconstrained axes:
-0.059

> mancap
Call: capscale(formula = dune ~ Condition(Management) + Manure + A1,
data = dune.env, distance = "manhattan")
Call: capscale(formula = dune ~ Condition(Management) + Manure + A1, data =
dune.env, distance = "manhattan")

-- Model Summary --

Inertia Proportion Rank
Total 994.092
Expand All @@ -136,9 +196,17 @@ Conditional 412.304 0.383 3
Constrained 213.079 0.198 4
Unconstrained 452.264 0.420 12
Imaginary -83.555
Inertia is mean squared Manhattan distance
Species scores projected from 'dune'
Some constraints or conditions were aliased because they were redundant

Inertia is mean squared Manhattan distance

-- Note --

Species scores projected from 'dune'

Some constraints or conditions were aliased because they were redundant.
This can happen if terms are linearly dependent (collinear): 'Manure^4'

-- Eigenvalues --

Eigenvalues for constrained axes:
CAP1 CAP2 CAP3 CAP4
Expand All @@ -149,16 +217,25 @@ Eigenvalues for unconstrained axes:
163.7 97.1 59.0 40.2 34.9 24.9 12.7 10.9 4.7 1.9 1.5 0.8

> mandb
Call: dbrda(formula = dune ~ Condition(Management) + Manure + A1, data
= dune.env, distance = "manhattan")
Call: dbrda(formula = dune ~ Condition(Management) + Manure + A1, data =
dune.env, distance = "manhattan")

-- Model Summary --

Inertia Proportion Rank RealDims
Total 994.092 1.000
Conditional 404.069 0.406 3
Constrained 202.576 0.204 4 4
Unconstrained 387.447 0.390 12 8
Inertia is mean squared Manhattan distance
Some constraints or conditions were aliased because they were redundant

Inertia is mean squared Manhattan distance

-- Note --

Some constraints or conditions were aliased because they were redundant.
This can happen if terms are linearly dependent (collinear): 'Manure^4'

-- Eigenvalues --

Eigenvalues for constrained axes:
dbRDA1 dbRDA2 dbRDA3 dbRDA4
Expand All @@ -172,11 +249,16 @@ Eigenvalues for unconstrained axes:
Call: cca(formula = dune ~ Condition(Management) + Management, data =
dune.env)

-- Model Summary --

Inertia Proportion Rank
Total 2.115 1.000
Conditional 0.604 0.285 3
Unconstrained 1.511 0.715 16
Inertia is scaled Chi-square

Inertia is scaled Chi-square

-- Eigenvalues --

Eigenvalues for unconstrained axes:
CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 CA11 CA12 CA13
Expand All @@ -187,11 +269,16 @@ Eigenvalues for unconstrained axes:
> m1rda
Call: rda(formula = H ~ A1, data = dune.env)

-- Model Summary --

Inertia Proportion Rank
Total 0.07321 1.00000
Constrained 0.00294 0.04020 1
Unconstrained 0.07027 0.95980 1
Inertia is variance

Inertia is variance

-- Eigenvalues --

Eigenvalues for constrained axes:
RDA1
Expand Down Expand Up @@ -1952,12 +2039,33 @@ Residual 18 0.0703
> ## the following do not all work with partial models
>
> mcca <- cca(dune ~ Management + Manure + A1, dune.env)

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mrda <- rda(dune ~ Management + Manure + A1, dune.env)

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mrda1 <- rda(dune ~ Management + Manure + A1, dune.env, scale = TRUE)

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mcap <- capscale(dune ~ Management + Manure + A1, dune.env, dist = "bray")

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mdb <- dbrda(dune ~ Management + Manure + A1, dune.env, dist = "bray")

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mancap <- capscale(dune ~ Management + Manure + A1, dune.env, dist = "man")

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
> mandb <- dbrda(dune ~ Management + Manure + A1, dune.env, dist = "man")

Some constraints or conditions were aliased because they were redundant. This
can happen if terms are linearly dependent (collinear): 'Manure^4'
>
> head(calibrate(mcca))
ManagementHF ManagementNM ManagementSF Manure.L Manure.Q Manure.C A1
Expand Down Expand Up @@ -2229,4 +2337,4 @@ Alopgeni 0.031859 0.35291 0.051066 0.12889917 0.190337 0.197400 0.181314
>
> proc.time()
user system elapsed
0.921 0.068 1.614
0.864 0.077 1.501

0 comments on commit aab4307

Please sign in to comment.