summary.TRAMP: Create Presence/Absence Matrices from TRAMP Objects
In TRAMPR: 'TRFLP' Analysis and Matching Package for R
Description
Usage
Arguments
Value
Examples
Description
Generate a summary of a TRAMP object, by producing a
presence/absence matrix. This is the preferred way of extracting the
presence/absence matrix from a TRAMP object, and allows for
grouping, naming knowns, and ignoring matches (specified by
remove.TRAMP.match).
Usage
1
2
Arguments
object
A TRAMP object.
name
Logical: Should the knowns be named?
grouped
Logical: Should the knowns be grouped?
ignore
Logical: Should matches marked as ignored be excluded?
...
Further arguments passed to or from other methods.
Value
A presence/absence matrix, with samples as rows
and knowns as columns. If name is TRUE, then names of
knowns (or groups of knowns) are used, otherwise the knowns.fk
is used (group.strict if grouped). If grouped is
TRUE, then the knowns are collapsed by group (using
group.strict; see group.knowns). A group is
present if any of the knowns belonging to it are present. If
ignore is TRUE, then any matches marked by
remove.TRAMP.match are excluded.
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
data(demo.knowns)
data(demo.samples)
res <- TRAMP(demo.samples, demo.knowns)
head(summary(res))
head(summary(res, name=TRUE))
head(summary(res, name=TRUE, grouped=TRUE))
## Extract the species richness for each sample (i.e. the number of
## knowns present in each sample)
rowSums(summary(res, grouped=TRUE))
## Extract species frequencies and plot a rank abundance diagram:
## (i.e. the number of times each known was recorded)
sp.freq <- colSums(summary(res, name=TRUE, grouped=TRUE))
sp.freq <- sort(sp.freq[sp.freq > 0], decreasing=TRUE)
plot(sp.freq, xlab="Species rank", ylab="Species frequency", log="y")
text(1:2, sp.freq[1:2], names(sp.freq[1:2]), cex=.7, pos=4, font=3)
Example output
known
sample 674 733 734 735 737 739 741 1042 2265 2295 2299 2301
101 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
102 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
110 TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
111 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
117 FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
118 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
known
sample 2601 2635 2656 2667 2682 2686 2688 2690 2697 2699 2701 2702
101 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
102 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
110 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
111 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
117 FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
118 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
known
sample 2703 2709 2712 2718 2719 2722 2725 2732 2734 2736 2739 2740
101 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
102 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
110 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
111 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
117 TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE
118 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE
known
sample Cenococcum geophillum Amanita muscaria Collybia/Calocybe sp
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 TRUE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE TRUE
118 FALSE FALSE FALSE
known
sample Suillus luteus Scleroderma verrucosum Amanita muscaria
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Cortinarius sp. (DA406) Russula tawai Rhizopogon rubescens
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 TRUE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Suillus sp. (DA430) Suillus sp. (DA430) Russula acrolamellata Suillus
101 FALSE FALSE FALSE FALSE
102 FALSE FALSE FALSE FALSE
110 FALSE FALSE FALSE FALSE
111 FALSE FALSE FALSE FALSE
117 FALSE FALSE FALSE FALSE
118 FALSE FALSE FALSE FALSE
known
sample Amanita mumura Cortinarius dulciolens Cortinarius singularis
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Cuphocybe alborosea Cortinarius porphyrophaeus Cortinarius
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE TRUE
118 FALSE FALSE FALSE
known
sample Cortinarius pholiotellus Cortinarius alienatus Cortinarius achrous
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Austropaxillus macnabbii Tricholoma elegans Cortinarius
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE TRUE
118 FALSE FALSE FALSE
known
sample Cortinarius laquellus Cortinarius peraureus Thelephora terrestris
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Cortinarius cycneus Dermocybe canaria Russula tawai
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 TRUE TRUE FALSE
118 FALSE FALSE FALSE
known
sample Cortinarius sp. (DA892) Cortinarius anisodorus Laccaria sp. (DA2996)
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE TRUE
118 FALSE FALSE TRUE
known
sample Laccaria sp. (DA2999) Laccaria sp. (DA3000)
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 TRUE TRUE
118 TRUE TRUE
sample Cenococcum geophillum Amanita muscaria
101 FALSE FALSE
102 FALSE FALSE
110 TRUE FALSE
111 FALSE FALSE
117 FALSE FALSE
118 FALSE FALSE
sample Collybia/Calocybe sp, Laccaria sp. (DA2996), Laccaria sp. (DA2999), Laccaria sp. (DA3000)
101 FALSE
102 FALSE
110 FALSE
111 FALSE
117 TRUE
118 TRUE
sample Suillus, Suillus luteus, Suillus sp. (DA430) Scleroderma verrucosum
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 FALSE FALSE
118 FALSE FALSE
sample Cortinarius sp. (DA406), Dermocybe canaria Russula tawai
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 TRUE FALSE
118 FALSE FALSE
sample Rhizopogon rubescens Russula acrolamellata Amanita mumura
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
sample Cortinarius dulciolens Cortinarius singularis Cuphocybe alborosea
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
sample Cortinarius porphyrophaeus Cortinarius, Cortinarius cycneus
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 FALSE TRUE
118 FALSE FALSE
sample Cortinarius pholiotellus Cortinarius alienatus, Cortinarius sp. (DA892)
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 FALSE FALSE
118 FALSE FALSE
sample Cortinarius achrous Austropaxillus macnabbii Tricholoma elegans
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
sample Cortinarius laquellus Cortinarius peraureus Thelephora terrestris
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
sample Cortinarius anisodorus
101 FALSE
102 FALSE
110 FALSE
111 FALSE
117 FALSE
118 FALSE
101 102 110 111 117 118 125 126 134 135 141 172 173 182 183 185 186 188 189 192
0 0 1 0 3 1 0 0 0 0 0 0 0 3 1 1 1 0 1 1
193 220 221 223 224 227 228 230 231 233 234 237 238 240 241 243 244 246 247 279
1 0 1 0 0 0 0 1 2 1 0 0 1 1 1 0 0 2 2 0
280 303 304 307 308 310 311 314 315 334 335 339 340 342 343 345 346 348 349 351
0 0 0 0 0 1 1 0 0 1 1 0 0 1 1 0 0 0 0 0
352 564 565 567 568 571 572 579 580 582 583 585 586 589 590 661 662 664 665 667
0 0 3 2 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0
668 670 671 675 676 678 681 682
0 0 0 1 2 0 1 0
TRAMPR documentation built on Feb. 8, 2022, 1:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Examples
Description
Generate a summary of a TRAMP object, by producing a
presence/absence matrix. This is the preferred way of extracting the
presence/absence matrix from a TRAMP object, and allows for
grouping, naming knowns, and ignoring matches (specified by
remove.TRAMP.match).
Usage
1 2 |
Arguments
object |
A |
name |
Logical: Should the knowns be named? |
grouped |
Logical: Should the knowns be grouped? |
ignore |
Logical: Should matches marked as ignored be excluded? |
... |
Further arguments passed to or from other methods. |
Value
A presence/absence matrix, with samples as rows
and knowns as columns. If name is TRUE, then names of
knowns (or groups of knowns) are used, otherwise the knowns.fk
is used (group.strict if grouped). If grouped is
TRUE, then the knowns are collapsed by group (using
group.strict; see group.knowns). A group is
present if any of the knowns belonging to it are present. If
ignore is TRUE, then any matches marked by
remove.TRAMP.match are excluded.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | data(demo.knowns)
data(demo.samples)
res <- TRAMP(demo.samples, demo.knowns)
head(summary(res))
head(summary(res, name=TRUE))
head(summary(res, name=TRUE, grouped=TRUE))
## Extract the species richness for each sample (i.e. the number of
## knowns present in each sample)
rowSums(summary(res, grouped=TRUE))
## Extract species frequencies and plot a rank abundance diagram:
## (i.e. the number of times each known was recorded)
sp.freq <- colSums(summary(res, name=TRUE, grouped=TRUE))
sp.freq <- sort(sp.freq[sp.freq > 0], decreasing=TRUE)
plot(sp.freq, xlab="Species rank", ylab="Species frequency", log="y")
text(1:2, sp.freq[1:2], names(sp.freq[1:2]), cex=.7, pos=4, font=3)
|
Example output
known
sample 674 733 734 735 737 739 741 1042 2265 2295 2299 2301
101 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
102 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
110 TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
111 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
117 FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
118 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
known
sample 2601 2635 2656 2667 2682 2686 2688 2690 2697 2699 2701 2702
101 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
102 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
110 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
111 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
117 FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
118 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
known
sample 2703 2709 2712 2718 2719 2722 2725 2732 2734 2736 2739 2740
101 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
102 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
110 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
111 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
117 TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE
118 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE
known
sample Cenococcum geophillum Amanita muscaria Collybia/Calocybe sp
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 TRUE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE TRUE
118 FALSE FALSE FALSE
known
sample Suillus luteus Scleroderma verrucosum Amanita muscaria
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Cortinarius sp. (DA406) Russula tawai Rhizopogon rubescens
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 TRUE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Suillus sp. (DA430) Suillus sp. (DA430) Russula acrolamellata Suillus
101 FALSE FALSE FALSE FALSE
102 FALSE FALSE FALSE FALSE
110 FALSE FALSE FALSE FALSE
111 FALSE FALSE FALSE FALSE
117 FALSE FALSE FALSE FALSE
118 FALSE FALSE FALSE FALSE
known
sample Amanita mumura Cortinarius dulciolens Cortinarius singularis
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Cuphocybe alborosea Cortinarius porphyrophaeus Cortinarius
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE TRUE
118 FALSE FALSE FALSE
known
sample Cortinarius pholiotellus Cortinarius alienatus Cortinarius achrous
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Austropaxillus macnabbii Tricholoma elegans Cortinarius
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE TRUE
118 FALSE FALSE FALSE
known
sample Cortinarius laquellus Cortinarius peraureus Thelephora terrestris
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
known
sample Cortinarius cycneus Dermocybe canaria Russula tawai
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 TRUE TRUE FALSE
118 FALSE FALSE FALSE
known
sample Cortinarius sp. (DA892) Cortinarius anisodorus Laccaria sp. (DA2996)
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE TRUE
118 FALSE FALSE TRUE
known
sample Laccaria sp. (DA2999) Laccaria sp. (DA3000)
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 TRUE TRUE
118 TRUE TRUE
sample Cenococcum geophillum Amanita muscaria
101 FALSE FALSE
102 FALSE FALSE
110 TRUE FALSE
111 FALSE FALSE
117 FALSE FALSE
118 FALSE FALSE
sample Collybia/Calocybe sp, Laccaria sp. (DA2996), Laccaria sp. (DA2999), Laccaria sp. (DA3000)
101 FALSE
102 FALSE
110 FALSE
111 FALSE
117 TRUE
118 TRUE
sample Suillus, Suillus luteus, Suillus sp. (DA430) Scleroderma verrucosum
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 FALSE FALSE
118 FALSE FALSE
sample Cortinarius sp. (DA406), Dermocybe canaria Russula tawai
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 TRUE FALSE
118 FALSE FALSE
sample Rhizopogon rubescens Russula acrolamellata Amanita mumura
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
sample Cortinarius dulciolens Cortinarius singularis Cuphocybe alborosea
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
sample Cortinarius porphyrophaeus Cortinarius, Cortinarius cycneus
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 FALSE TRUE
118 FALSE FALSE
sample Cortinarius pholiotellus Cortinarius alienatus, Cortinarius sp. (DA892)
101 FALSE FALSE
102 FALSE FALSE
110 FALSE FALSE
111 FALSE FALSE
117 FALSE FALSE
118 FALSE FALSE
sample Cortinarius achrous Austropaxillus macnabbii Tricholoma elegans
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
sample Cortinarius laquellus Cortinarius peraureus Thelephora terrestris
101 FALSE FALSE FALSE
102 FALSE FALSE FALSE
110 FALSE FALSE FALSE
111 FALSE FALSE FALSE
117 FALSE FALSE FALSE
118 FALSE FALSE FALSE
sample Cortinarius anisodorus
101 FALSE
102 FALSE
110 FALSE
111 FALSE
117 FALSE
118 FALSE
101 102 110 111 117 118 125 126 134 135 141 172 173 182 183 185 186 188 189 192
0 0 1 0 3 1 0 0 0 0 0 0 0 3 1 1 1 0 1 1
193 220 221 223 224 227 228 230 231 233 234 237 238 240 241 243 244 246 247 279
1 0 1 0 0 0 0 1 2 1 0 0 1 1 1 0 0 2 2 0
280 303 304 307 308 310 311 314 315 334 335 339 340 342 343 345 346 348 349 351
0 0 0 0 0 1 1 0 0 1 1 0 0 1 1 0 0 0 0 0
352 564 565 567 568 571 572 579 580 582 583 585 586 589 590 661 662 664 665 667
0 0 3 2 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0
668 670 671 675 676 678 681 682
0 0 0 1 2 0 1 0
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.