README.md
In EDiLD/restax: Resolving ambiguous taxa
restax
restax is a R package with implements the methods of Cuffney et al. (2007) to
resolve ambiguous taxa.
Methods
Currently the following functions are available:
- Remove parent, keep children (RPKC) :
rpkc_*()
- Merge children with parent (MCWP) :
mcwp_*()
- Remove parent or merge children (RPMC) :
rpmc_*()
- Distribute parent among children (DPAC) :
dpac_*()
Variants
All functions are available in two variants:
*_s : Resolve separately for each sample.*_g : Resolve for a group of samples.
Options
Moreover, some functions have additional options:
rpkc_g() and dpac_g()
option = 'C' : if the ambiguous parent has no child in a sample,
substitute the most frequently occurring child for the parent.option = 'L' : if the ambiguous parent has no child in a sample,
substitute all of the children associated with the parent in the grouped data.
mcwp_*()
level = 'Family' : remove all ambiguous parents above the specified level
(here family) before resolving ambiguous taxa.
Installation
restax is currently only available on github. To install restax use:
install.packages('devtools')
require(devtools)
install_github('restax', 'EDiLD')
require(restax)
Example
Let's say we have our data in the wide format (as commonly used in community ecology).
Here we have data of 5 samples (S1-S4, A) with 12 taxa:
require(restax)
data(samp)
samp
## Insecta Ephemeroptera Baetidae Acentrella Acentrella parvula
## S1 0 0 4 10 34
## S2 6 0 0 30 0
## S3 0 100 0 5 26
## S4 0 0 8 0 11
## A 6 100 12 45 71
## Acentrella turbida Baetis Baetis flavistriga Baetis intercalaris
## S1 3 0 54 78
## S2 0 44 0 21
## S3 0 35 0 0
## S4 9 100 6 0
## A 12 179 60 99
## Baetis pluto Zygoptera Argia
## S1 23 0 0
## S2 23 0 0
## S3 0 10 0
## S4 12 100 8
## A 58 110 8
restax currently accepts only the transposed wide format. So we need to reformat it
df <- data.frame(t(samp), stringsAsFactors = FALSE)
df[ , 'taxon'] <- rownames(df)
df
## S1 S2 S3 S4 A taxon
## Insecta 0 6 0 0 6 Insecta
## Ephemeroptera 0 0 100 0 100 Ephemeroptera
## Baetidae 4 0 0 8 12 Baetidae
## Acentrella 10 30 5 0 45 Acentrella
## Acentrella parvula 34 0 26 11 71 Acentrella parvula
## Acentrella turbida 3 0 0 9 12 Acentrella turbida
## Baetis 0 44 35 100 179 Baetis
## Baetis flavistriga 54 0 0 6 60 Baetis flavistriga
## Baetis intercalaris 78 21 0 0 99 Baetis intercalaris
## Baetis pluto 23 23 0 12 58 Baetis pluto
## Zygoptera 0 0 10 100 110 Zygoptera
## Argia 0 0 0 8 8 Argia
The first step is to retrieve taxonomic information about our taxa:
This is done via the get_hier() function,
which uses taxize to query ITIS:
df_w <- get_hier(df, taxa.var = 'taxon', db = 'itis')
df_w
## $comm
## S1 S2 S3 S4 A taxon
## 11 0 6 0 0 6 Insecta
## 10 0 0 100 0 100 Ephemeroptera
## 5 4 0 0 8 12 Baetidae
## 1 10 30 5 0 45 Acentrella
## 2 34 0 26 11 71 Acentrella parvula
## 3 3 0 0 9 12 Acentrella turbida
## 6 0 44 35 100 179 Baetis
## 7 54 0 0 6 60 Baetis flavistriga
## 8 78 21 0 0 99 Baetis intercalaris
## 9 23 23 0 12 58 Baetis pluto
## 12 0 0 10 100 110 Zygoptera
## 4 0 0 0 8 8 Argia
##
## $hier
## Kingdom Subkingdom Infrakingdom Superphylum Phylum Subphylum
## 11 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 10 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 5 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 1 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 2 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 3 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 6 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 7 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 8 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 9 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 12 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 4 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## Class Subclass Infraclass Order Suborder Family
## 11 Insecta <NA> <NA> <NA> <NA> <NA>
## 10 Insecta Pterygota Palaeoptera Ephemeroptera <NA> <NA>
## 5 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 1 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 2 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 3 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 6 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 7 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 8 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 9 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 12 Insecta Pterygota Palaeoptera Odonata Zygoptera <NA>
## 4 Insecta Pterygota Palaeoptera Odonata Zygoptera Coenagrionidae
## Genus Species taxon
## 11 <NA> <NA> Insecta
## 10 <NA> <NA> Ephemeroptera
## 5 <NA> <NA> Baetidae
## 1 Acentrella <NA> Acentrella
## 2 Acentrella Acentrella parvula Acentrella parvula
## 3 Acentrella Acentrella turbida Acentrella turbida
## 6 Baetis <NA> Baetis
## 7 Baetis Baetis flavistriga Baetis flavistriga
## 8 Baetis Baetis intercalaris Baetis intercalaris
## 9 Baetis Baetis pluto Baetis pluto
## 12 <NA> <NA> Zygoptera
## 4 Argia <NA> Argia
##
## $taxa.var
## [1] "taxon"
##
## attr(,"class")
## [1] "wide_class"
We need to specify the column containing the taxon names.
This function returns the original data and accompanying taxonomic information.
To resolve ambiguous taxa using the RPKC-S method (remove parents, keep childs - per sample) for sample A we use:
df_res <- rpkc_s(df_w, value.var = 'A')
df_res$comm
## taxon A
## 11 Insecta 0
## 10 Ephemeroptera 0
## 5 Baetidae 0
## 1 Acentrella 0
## 2 Acentrella parvula 71
## 3 Acentrella turbida 12
## 6 Baetis 0
## 7 Baetis flavistriga 60
## 8 Baetis intercalaris 99
## 9 Baetis pluto 58
## 12 Zygoptera 0
## 4 Argia 8
We see that only the 5 Baetidae species and Argia sp. are kept, all others (as they are parents) are set to zero.
Similarly, all samples can be resolved with on call by omitting value.var. However, this currently works only with group variants
*_g() . If group is ommited all samples are used as grouping variables.
Here we resolve all samples simultaneously using all samples as group using the RPMC-G variant:
# remove sample A
df <- data.frame(t(samp[1:4, ]), stringsAsFactors = FALSE)
df[ , 'taxon'] <- rownames(df)
# get hierachy
df_w <- get_hier(df, taxa.var = 'taxon', db = 'itis')
# resolve
df_rpmc <- rpmc_g(df_w)
# same as
# rpmc_g(df_w, group = group = c('S1', 'S2', 'S3', 'S4'))
df_rpmc$comm
## taxon S1 S2 S3 S4
## 11 Insecta 0 0 0 0
## 10 Ephemeroptera 0 0 0 0
## 5 Baetidae 0 0 0 0
## 1 Acentrella 0 0 0 0
## 2 Acentrella parvula 34 0 26 11
## 3 Acentrella turbida 3 0 0 9
## 6 Baetis 0 0 0 0
## 7 Baetis flavistriga 54 0 0 6
## 8 Baetis intercalaris 78 21 0 0
## 9 Baetis pluto 23 23 0 12
## 12 Zygoptera 0 0 10 108
## 4 Argia 0 0 0 0
NOTES
This package is currently under development and the code has not been tested extensively!
Moreover, there is some work needed to make the package more user friendly!
It currently can reproduce the appendix of Cuffney et al. (2007), but may break with other data!
Please use only ITIS as taxonomic back-end, as others have not been tested yet.
dpac_g() and option='K' are currently not available.
Please report any issues or bugs.
TODOs
- ADD DPAC_g
- No classification information available?
References
Cuffney, T. F., Bilger, M. D. & Haigler, A. M. Ambiguous taxa: effects on the characterization and interpretation of invertebrate assemblages. Journal of the North American Benthological Society 26, 286–307 (2007).
EDiLD/restax documentation built on May 6, 2019, 3:04 p.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.
restax
restax is a R package with implements the methods of Cuffney et al. (2007) to
resolve ambiguous taxa.
Methods
Currently the following functions are available:
- Remove parent, keep children (RPKC) :
rpkc_*() - Merge children with parent (MCWP) :
mcwp_*() - Remove parent or merge children (RPMC) :
rpmc_*() - Distribute parent among children (DPAC) :
dpac_*()
Variants
All functions are available in two variants:
*_s: Resolve separately for each sample.*_g: Resolve for a group of samples.
Options
Moreover, some functions have additional options:
rpkc_g() and dpac_g()
option = 'C': if the ambiguous parent has no child in a sample, substitute the most frequently occurring child for the parent.option = 'L': if the ambiguous parent has no child in a sample, substitute all of the children associated with the parent in the grouped data.
mcwp_*()
level = 'Family': remove all ambiguous parents above the specified level (here family) before resolving ambiguous taxa.
Installation
restax is currently only available on github. To install restax use:
install.packages('devtools')
require(devtools)
install_github('restax', 'EDiLD')
require(restax)
Example
Let's say we have our data in the wide format (as commonly used in community ecology). Here we have data of 5 samples (S1-S4, A) with 12 taxa:
require(restax)
data(samp)
samp
## Insecta Ephemeroptera Baetidae Acentrella Acentrella parvula
## S1 0 0 4 10 34
## S2 6 0 0 30 0
## S3 0 100 0 5 26
## S4 0 0 8 0 11
## A 6 100 12 45 71
## Acentrella turbida Baetis Baetis flavistriga Baetis intercalaris
## S1 3 0 54 78
## S2 0 44 0 21
## S3 0 35 0 0
## S4 9 100 6 0
## A 12 179 60 99
## Baetis pluto Zygoptera Argia
## S1 23 0 0
## S2 23 0 0
## S3 0 10 0
## S4 12 100 8
## A 58 110 8
restax currently accepts only the transposed wide format. So we need to reformat it
df <- data.frame(t(samp), stringsAsFactors = FALSE)
df[ , 'taxon'] <- rownames(df)
df
## S1 S2 S3 S4 A taxon
## Insecta 0 6 0 0 6 Insecta
## Ephemeroptera 0 0 100 0 100 Ephemeroptera
## Baetidae 4 0 0 8 12 Baetidae
## Acentrella 10 30 5 0 45 Acentrella
## Acentrella parvula 34 0 26 11 71 Acentrella parvula
## Acentrella turbida 3 0 0 9 12 Acentrella turbida
## Baetis 0 44 35 100 179 Baetis
## Baetis flavistriga 54 0 0 6 60 Baetis flavistriga
## Baetis intercalaris 78 21 0 0 99 Baetis intercalaris
## Baetis pluto 23 23 0 12 58 Baetis pluto
## Zygoptera 0 0 10 100 110 Zygoptera
## Argia 0 0 0 8 8 Argia
The first step is to retrieve taxonomic information about our taxa:
This is done via the get_hier() function,
which uses taxize to query ITIS:
df_w <- get_hier(df, taxa.var = 'taxon', db = 'itis')
df_w
## $comm
## S1 S2 S3 S4 A taxon
## 11 0 6 0 0 6 Insecta
## 10 0 0 100 0 100 Ephemeroptera
## 5 4 0 0 8 12 Baetidae
## 1 10 30 5 0 45 Acentrella
## 2 34 0 26 11 71 Acentrella parvula
## 3 3 0 0 9 12 Acentrella turbida
## 6 0 44 35 100 179 Baetis
## 7 54 0 0 6 60 Baetis flavistriga
## 8 78 21 0 0 99 Baetis intercalaris
## 9 23 23 0 12 58 Baetis pluto
## 12 0 0 10 100 110 Zygoptera
## 4 0 0 0 8 8 Argia
##
## $hier
## Kingdom Subkingdom Infrakingdom Superphylum Phylum Subphylum
## 11 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 10 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 5 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 1 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 2 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 3 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 6 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 7 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 8 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 9 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 12 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## 4 Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda
## Class Subclass Infraclass Order Suborder Family
## 11 Insecta <NA> <NA> <NA> <NA> <NA>
## 10 Insecta Pterygota Palaeoptera Ephemeroptera <NA> <NA>
## 5 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 1 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 2 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 3 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 6 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 7 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 8 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 9 Insecta Pterygota Palaeoptera Ephemeroptera Pisciforma Baetidae
## 12 Insecta Pterygota Palaeoptera Odonata Zygoptera <NA>
## 4 Insecta Pterygota Palaeoptera Odonata Zygoptera Coenagrionidae
## Genus Species taxon
## 11 <NA> <NA> Insecta
## 10 <NA> <NA> Ephemeroptera
## 5 <NA> <NA> Baetidae
## 1 Acentrella <NA> Acentrella
## 2 Acentrella Acentrella parvula Acentrella parvula
## 3 Acentrella Acentrella turbida Acentrella turbida
## 6 Baetis <NA> Baetis
## 7 Baetis Baetis flavistriga Baetis flavistriga
## 8 Baetis Baetis intercalaris Baetis intercalaris
## 9 Baetis Baetis pluto Baetis pluto
## 12 <NA> <NA> Zygoptera
## 4 Argia <NA> Argia
##
## $taxa.var
## [1] "taxon"
##
## attr(,"class")
## [1] "wide_class"
We need to specify the column containing the taxon names. This function returns the original data and accompanying taxonomic information.
To resolve ambiguous taxa using the RPKC-S method (remove parents, keep childs - per sample) for sample A we use:
df_res <- rpkc_s(df_w, value.var = 'A')
df_res$comm
## taxon A
## 11 Insecta 0
## 10 Ephemeroptera 0
## 5 Baetidae 0
## 1 Acentrella 0
## 2 Acentrella parvula 71
## 3 Acentrella turbida 12
## 6 Baetis 0
## 7 Baetis flavistriga 60
## 8 Baetis intercalaris 99
## 9 Baetis pluto 58
## 12 Zygoptera 0
## 4 Argia 8
We see that only the 5 Baetidae species and Argia sp. are kept, all others (as they are parents) are set to zero.
Similarly, all samples can be resolved with on call by omitting value.var. However, this currently works only with group variants
*_g() . If group is ommited all samples are used as grouping variables.
Here we resolve all samples simultaneously using all samples as group using the RPMC-G variant:
# remove sample A
df <- data.frame(t(samp[1:4, ]), stringsAsFactors = FALSE)
df[ , 'taxon'] <- rownames(df)
# get hierachy
df_w <- get_hier(df, taxa.var = 'taxon', db = 'itis')
# resolve
df_rpmc <- rpmc_g(df_w)
# same as
# rpmc_g(df_w, group = group = c('S1', 'S2', 'S3', 'S4'))
df_rpmc$comm
## taxon S1 S2 S3 S4
## 11 Insecta 0 0 0 0
## 10 Ephemeroptera 0 0 0 0
## 5 Baetidae 0 0 0 0
## 1 Acentrella 0 0 0 0
## 2 Acentrella parvula 34 0 26 11
## 3 Acentrella turbida 3 0 0 9
## 6 Baetis 0 0 0 0
## 7 Baetis flavistriga 54 0 0 6
## 8 Baetis intercalaris 78 21 0 0
## 9 Baetis pluto 23 23 0 12
## 12 Zygoptera 0 0 10 108
## 4 Argia 0 0 0 0
NOTES
This package is currently under development and the code has not been tested extensively! Moreover, there is some work needed to make the package more user friendly!
It currently can reproduce the appendix of Cuffney et al. (2007), but may break with other data!
Please use only ITIS as taxonomic back-end, as others have not been tested yet.
dpac_g() and option='K' are currently not available.
Please report any issues or bugs.
TODOs
- ADD DPAC_g
- No classification information available?
References
Cuffney, T. F., Bilger, M. D. & Haigler, A. M. Ambiguous taxa: effects on the characterization and interpretation of invertebrate assemblages. Journal of the North American Benthological Society 26, 286–307 (2007).
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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