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README: use twinspan(..., cutlevels=1:6)
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jarioksa authored Nov 22, 2024
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Expand Up @@ -30,9 +30,9 @@ you need **C** and **Fortran** compilers.
If you cannot install a source package, you can install **twinspan** from R-Universe:

```r
install.packages('twinspan', repos = c('https://jarioksa.r-universe.dev', 'https://cloud.r-project.org'))
install.packages('twinspan', repos = c('https://jarioksa.r-universe.dev',
'https://cloud.r-project.org'))
```


## What you can do with twinspan?

Expand All @@ -41,7 +41,7 @@ The basic command to run twinspan is – unsurprisingly – `twinspan`:
> library(twinspan)
> library(natto) # for data
> data(spurn)
> tw <- twinspan(spurn, cutlevels = 0:6)
> tw <- twinspan(spurn, cutlevels = 1:6)
```
The example uses Spurn Point dune scrub data (Shimwell 1971).
TWINSPAN uses basically binary data, and quantitative data are broken into
Expand All @@ -55,14 +55,14 @@ The pseudospecies data can be generated with `twinsform` transformation:
[1] "Elaerham1" "Jacovulg1" "Soladulc1" "Rubufrut1" "UrtidioiA1"
[6] "Rumecris1" "ClayperfB1" "StelmediB1" "FestrubrC1" "ElymrepeC1"
... cut ...
[111] "ElymrepeC4" "AmmoarenC4" "Epilangu4" "Elaerham5" "UrtidioiA5"
[116] "ClayperfB5" "StelmediB5" "FestrubrC5" "ElymrepeC5" "AmmoarenC5"
[121] "Elaerham6" "ClayperfB6" "AmmoarenC6" "Elaerham7"
[71] "ElymrepeC3" "AmmoarenC3" "Epilangu3" "Elaerham4" "UrtidioiA4"
[76] "ClayperfB4" "StelmediB4" "FestrubrC4" "ElymrepeC4" "AmmoarenC4"
[81] "Elaerham5" "ClayperfB5" "AmmoarenC5" "Elaerham6"
```
The original data of 40 species are extended to a matrix of 124 pseudospecies.
The original data of 40 species are extended to a matrix of 84 pseudospecies.
The names of pseudospecies are formed appending an integer for the cut level
after the species name. Level `1` means that the taxon occurs in the data,
and `7` that it occurs at least the seventh cut level.
and `6` that it occurs at least the seventh cut level.

The `twinspan` result can be inspected with support functions of the package.
The hierarchy of groups can be displayed as a cluster tree with
Expand All @@ -86,21 +86,17 @@ The summary of division process can be inspected with `summary` (with argument
`binname = TRUE` binary labels are used instead of numeric):
```r
> summary(tw)
1) eig=0.56: +ElymrepeC1 < 1
2) eig=0.399: -UrtidioiA1 < 0
4) eig=0.355: -Soncarve1 < 0
1) eig=0.561: +ElymrepeC1 < 1
2) eig=0.4: -UrtidioiA1 < 0
4) eig=0.361: -Soncarve1 < 0
8) N=1: A19
9) N=4: A1 A2 A3 A20
5) eig=0.263: +Inulcony1 < 1
10) eig=0.229: -Rumecris1 < 0
20) N=1: B16
21) N=4: B4 B5 B10 B12
11) N=2: B17 B18
3) eig=0.23: +AmmoarenC5 +Jacovulg1 -Galiveru1 < 1
6) N=3: C6 C8 X14
7) eig=0.226: -Calysold1 < 0
14) N=3: C7 C9 C15
15) N=2: C11 C13
5) eig=0.258: -ClayperfB4 < 0
10) N=4: B4 B5 B10 B16
11) N=3: B12 B17 B18
3) eig=0.248: +AmmoarenC4 +Jacovulg1 -Rumecris1 -Soncarve1 < 0
6) N=4: C6 C8 C9 X14
7) N=4: C7 C11 C13 C15
```
`twinspan` is divisive: it splits data into two parts at each step, and these steps are
described here. The splits are based on the first correspondence analysis axis of the
Expand All @@ -111,7 +107,7 @@ These are used to calculate indicator scores for each quadrat, adding or subtrac
one for each pseudospecies in the quadrat. If the quadrat score is less than the critical
score, we proceed from group $k$ to $2k$, and if the condition is false (quadrat score is
equal or greater than the critical score), we proceed to its opposite $2k+1$.
The first split is made at eigenvalue 0.56, and the pseudospecies best indicating this division
The first split is made at eigenvalue 0.561, and the pseudospecies best indicating this division
is `ElymrepeC1` (_Elymus repens_ at class value 1). The quadrat score will be 1 for quadrats
with _Elymys repens_ and 0 without, and with condition $< 1$ we continue from 2 with quadrats
without the species, and from 3 with quadrats with the indicator species.
Expand Down Expand Up @@ -154,9 +150,9 @@ You can extract the classification of each quadrat with `cut` either for termina
groups or for a certain level:
```r
> cut(tw)
[1] 9 9 9 21 21 6 14 6 14 21 15 21 15 6 14 20 11 11 8 9
[1] 9 9 9 10 10 6 7 6 6 10 7 11 7 6 7 10 11 11 8 9
> cut(tw, level=2)
[1] 4 4 4 5 5 6 7 6 7 5 7 5 7 6 7 5 5 5 4 4
[1] 4 4 4 5 5 6 7 6 6 5 7 5 7 6 7 5 5 5 4 4
```
The Roleček groups respecting heterogeneity can be extracted with `cuth` ("cut height")
where you must specify the number of groups:
Expand All @@ -170,11 +166,11 @@ and threshold score. This can also be done with argument `newdata` using data se
contains same species, but is not used in developing the classification.
```r
> predict(tw, level=2)
[1] 4 4 4 5 5 6 7 6 7 5 7 5 7 6 7 5 5 5 4 4
[1] 4 4 4 5 5 6 7 6 6 5 6 5 7 6 7 5 5 5 4 4
```
Care is needed with `newdata`: TWINSPAN will predict a class also when the
`newdata` is completely unrelated to the original data. If there are no indicator
species, the predicted class will be the one with indicator scores always 0, or group 21
species, the predicted class will be the one with indicator scores always 0, or group 11
in this example.

TWINSPAN classification is based
Expand All @@ -189,53 +185,52 @@ The data can be tabulated with:
> twintable(tw)

00000000000011111111
00000111111100011111
011110000011 00011
01111
00000111111100001111
011110000111

A AB BBBB X CCC
1AAA21BB1111CC1CC111
91230645027868479513
00000 ClayperfB -----6566443--------
00000 StelmediB -----2322543--------
00000 GeasfornB ------22-222--------
00001 CerafontB -----2--2233--------
00001 CirsvulgB -----2----2---------
00001 Heraspho ----------2---------
00001 CardhirsB ----------22--------
0001 Inulcony ----2-----23--------
0001 Bracruta --23--2-2222--------
001000 Hyporadi 2-------------------
001000 Arrhelat 3-------------------
001001 UrtidioiA 25334---------------
001001 Soncaspe ----2---------------
001001 EurhpraeA 33233---------------
001001 Lophhete ----2---------------
00101 Sambnigr ----22--------------
0011 Soladulc 2442332232-22-22--2-
0011 Rubufrut 223-4223222---2-----
0011 Epilangu 4---22--23----2-----
0011 Hypncupr -222---22-----2-----
01 Elaerham 77777777777756644555
01 Jacovulg 33232222---2--222322
01 Rumecris 322222-----2222-2-22
10 Soncarve 2-------2---222-223-
10 Calysold --------22-2-33222--
10 Agrostol ----2-----2--22-22--
10 Verocham 2-------2-----2-2---
11000 FestrubrC -------2----33322345
11000 BracalbiC ------------2-2-3-2-
11001 ElymrepeC ------------22445222
11001 AmmoarenC ------------44262653
11001 PoapratC -------------22-2232
1101 RanubulbC --------------2-2-22
1101 PlanlancC --------------2-2323
1101 Cladranf -------------------2
111 Ononspin ------------3-------
111 Galiveru ------------2-2-----
111 Bryuincl ------------2-2-----
111 Syntrura -------------22-----
111 Bovinigr --------------2-----
A A BBBBB X CCC
1AAA2BB11111CCC1C111
91230450627868947135
11111 Bovinigr ---------------1----
11111 Syntrura -------------1-1----
11111 Bryuincl ------------1--1----
11111 Galiveru ------------1--1----
11111 Ononspin ------------2-------
11110 BracalbiC ------------1-21-1--
11101 RanubulbC --------------11-11-
11101 PoapratC -------------111-211
11101 ElymrepeC ------------11433111
11101 FestrubrC ------1-----22121342
11100 Cladranf ------------------1-
11100 PlanlancC --------------11-122
11100 AmmoarenC ------------33115425
110 Agrostol ----1-----1--111---1
110 Calysold -------1-1-1-2121--1
110 Soncarve 1------1----1111-2-1
10 Verocham 1------1------11----
01 Rumecris 21111---1--11111-11-
01 Jacovulg 2212111-1--1--111112
01 Elaerham 66666666666645353444
0011 Hypncupr -111--11-------1----
0011 Epilangu 3---1--112-----1----
0011 Soladulc 1331211221-11--111--
00101 Sambnigr ----1---1-----------
00101 Rubufrut 112-3121111----1----
001001 Lophhete ----1---------------
001001 EurhpraeA 22122---------------
001001 Soncaspe ----1---------------
001001 UrtidioiA 14223---------------
001000 Arrhelat 2-------------------
001000 Hyporadi 1-------------------
0001 Bracruta --12-1-1-111--------
0001 Inulcony ----1-----12--------
000011 CardhirsB ----------11--------
000011 Heraspho ----------1---------
000011 CerafontB -------11122--------
000010 GeasfornB -----11--111--------
000010 CirsvulgB --------1-1---------
000010 StelmediB -----2111432--------
00000 ClayperfB -----4555332--------
20 sites, 40 species
```
The binary labels before species and above quadrats specify the
Expand Down

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