====== Conversions to Pajek format ======
* [[.:conv:pitts|Medieval Russia trade network]]
===== Malaria =====
Two mode network genes X substrings (297 x 806).
The var genes of the human malaria parasite Plasmodium falciparum from
Rask, T. S., Hansen, D. A., Theander, T. G., Gorm Pedersen, A., & Lavstsen, T. (2010). Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer. PLoS Computational Biology, 6(9), e1000933. doi:10.1371/journal.pcbi.1000933
and available as MATLAB 5.0 MAT-file, Platform: MACI64, Created on: Fri Jun 27 09:17:09 2014 at http://danlarremore.com/bipartiteSBM . See also
* https://github.com/dblarremore/data_malaria_PLOSCompBiology_2013
* http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003268
Converted into Pajek format by Vladimir Batagelj, March 15, 2018. See [[notes:net:mlab]].
> library(R.matlab)
> setwd("C:/Users/batagelj/Downloads/data/FB100/larremore/malariaData")
> A <- readMat("malaria.mat")
> N1 <- unlist(A$geneSequenceHeaders,use.names=FALSE)
> N2 <- unlist(A$geneSequences,use.names=FALSE)
> N3 <- unlist(A$substrings,use.names=FALSE)
> nam <- file("names.txt","w")
> n1 <- length(N1); n3 <- length(N3)
> cat("*vertices",n1,"\n ",file=nam)
> cat(paste(1:n1,' "',N1,'"\n',sep=''),file=nam)
> cat("*vertices",n1,"\n ",file=nam)
> cat(paste(1:n1,' "',N2,'"\n',sep=''),file=nam)
> cat("*vertices",n3,"\n ",file=nam)
> cat(paste(n1+(1:n3),' "',N3,'"\n',sep=''),file=nam)
> close(nam)
> tit <- attr(A,"header")$description
{{pajek:data:zip:malaria.zip}}
===== Barents =====
A Barents Sea food web described in http://www.oikosjournal.org/appendix/oik-04138. Converted into Pajek format by Vladimir Batagelj, March 17, 2018 from the original (2014) and revised (2015) version of the data set (Ecological Archives E095-124-D1) http://www.esapubs.org/archive/ecol/E095/124/ .
A food web is an ecological network and its topological description consists of the list of nodes, i.e., trophospecies, the list of links, i.e., trophic interactions, and the direction of interactions (who is the prey and who is the predator). Food web topologies are widely used in ecology to describe structural properties of communities or ecosystems. The selection of trophospecies and trophic interactions can be realized in different manners so that many different food webs may be constructed for the same community. In the Barents Sea, many simple food webs have been constructed. We present a comprehensive food web topology for the Barents Sea ecosystem, from plankton to marine mammals. The protocol used to compile the data set includes rules for the selection of taxa and for the selection and documentation of the trophic links. The resulting topology, which includes 244 taxa and 1589 trophic links, can serve as a basis for topological analyses, comparison with other marine ecosystems, or as a basis to build simulation models of the Barents Sea ecosystem. The data set consists of three related tables: (1) the list of taxa, (2) the list of pairwise interactions, and (3) the list of bibliographical references.
The weights/codes on arcs:
- Link documented by quantitative data and published in peer-reviewed literature
- Link documented by quantitative data available in databases or published in gray literature
- Link reported from other sources of information (personal observations, fishermen's report, etc.)
- Plausible link. It has not been observed but it can be inferred from other observations on related species or other geographic areas
See also: http://www.oikosjournal.org/sites/oikosjournal.org/files/appendix/oik-04138.pdf
Related data set: http://dx.doi.org/10.5061/dryad.73r6j
==== Conversion ====
In the original TXT data files I replaced "\t" with ";" and saved the obtained files as CSV.
> VV <- read.table("SpeciesList2015.csv",sep=";",header=TRUE)
> head(VV)
TROPHOSPECIES ABBREVIATION PHYLUM_SUBPYLUM CLASS
1 DETRITUS DET_IND Detritus Detritus
2 AUTOTHROPH_FLAGELLAT AUT_FLA Autotroph flagellates Autotroph flagellates
3 BACTERIA_INDET BAC_IND Picoplankton Picoplankton
4 DIATOM DIATOM Microplankton Microplankton
5 HETEROTROPH_FLAGELLAT HET_FLA Heterotroph flagellates Heterotroph flagellates
6 ICE_ALGAE ICE_ALG Ice algae Ice algae
ORDER FAMILY GROUP
1 Detritus Detritus 1_Plankton
2 Autotroph flagellates Autotroph flagellates 1_Plankton
3 Picoplankton Picoplankton 1_Plankton
4 Microplankton Microplankton 1_Plankton
5 Heterotroph flagellates Heterotroph flagellates 1_Plankton
6 Ice algae Ice algae 1_Plankton
> typeof(VV)
[1] "list"
> nam <- file("namesLong.nam","w")
> n <- nrow(VV)
> n
[1] 233
> cat("*vertices",n,"\n ",file=nam)
> cat(paste(1:n,' "',VV[,1],'"\n',sep=''),file=nam)
> close(nam)
>
> net <- file("Barents.net","w")
> cat("*vertices",n,"\n ",file=net)
> cat(paste(1:n,' "',VV[,2],'"\n',sep=''),file=net)
> Names <- as.character(VV[,1])
> head(Names)
[1] "DETRITUS" "AUTOTHROPH_FLAGELLAT" "BACTERIA_INDET"
[4] "DIATOM" "HETEROTROPH_FLAGELLAT" "ICE_ALGAE"
> V <- factor(Names,levels=Names,ordered=TRUE)
> head(V)
[1] DETRITUS AUTOTHROPH_FLAGELLAT BACTERIA_INDET DIATOM
[5] HETEROTROPH_FLAGELLAT ICE_ALGAE
233 Levels: DETRITUS < AUTOTHROPH_FLAGELLAT < BACTERIA_INDET < ... < URSUS_MARITIMUS
> AA <- read.table("PairWiseList2015.csv",sep=";",header=TRUE)
> head(AA)
PWKEY PREDATOR PREY CODE
1 ACA_SPP-ACA_SPP ACARTIA_SPP ACARTIA_SPP 2
2 ACA_SPP-AUT_FLA ACARTIA_SPP AUTOTHROPH_FLAGELLAT 1
3 ACA_SPP-DIATOM ACARTIA_SPP DIATOM 1
4 ACA_SPP-HET_FLA ACARTIA_SPP HETEROTROPH_FLAGELLAT 1
5 ACA_SPP-MIX_FLA ACARTIA_SPP MIXOTROPH_FLAGELLATES 4
6 ACA_SPP-PROZOO ACARTIA_SPP PROTOZOOPLANKTON 1
> pred <- factor(as.character(AA$PREDATOR),levels=Names,ordered=TRUE)
> prey <- factor(as.character(AA$PREY),levels=Names,ordered=TRUE)
> cat("*arcs\n ",file=net)
> cat(paste(as.integer(pred),as.integer(prey),AA$CODE,"\n"),file=net)
> close(net)
>
> clu <- file("phylum.clu","w")
> lev <- levels(VV[,3])
> head(lev)
[1] "Annelida" "Arthropoda" "Autotroph flagellates"
[4] "Bryozoa" "Chaetognatha" "Chordata"
> cat("%",paste(1:length(lev),' "',lev,'" ',sep=''),'\n',file=clu)
> cat("*vertices",n,"\n ",file=clu)
> cat(paste(as.integer(VV[,3]),'\n',sep=''),file=clu)
> close(clu)
> clu <- file("class.clu","w")
> lev <- levels(VV[,4])
> head(lev)
[1] "Actinopterygii" "Anthozoa" "Appendicularia"
[4] "Ascidiacea" "Asteroidea" "Autotroph flagellates"
> cat("%",paste(1:length(lev),' "',lev,'" ',sep=''),'\n',file=clu)
> cat("*vertices",n,"\n ",file=clu)
> cat(paste(as.integer(VV[,4]),'\n',sep=''),file=clu)
> close(clu)
> clu <- file("order.clu","w")
> lev <- levels(VV[,5])
> head(lev)
[1] "Actiniaria" "Actinopterygii" "Alcyonacea" "Amphinomida"
[5] "Amphipoda" "Amphipoda/Gammarida"
> cat("%",paste(1:length(lev),' "',lev,'" ',sep=''),'\n',file=clu)
> cat("*vertices",n,"\n ",file=clu)
> cat(paste(as.integer(VV[,5]),'\n',sep=''),file=clu)
> close(clu)
> clu <- file("family.clu","w")
> lev <- levels(VV[,6])
> head(lev)
[1] "Acartiidae" "Actinopterygii" "Agonidae" "Alcidae" "Ammodytidae"
[6] "Amphinomidae"
> cat("%",paste(1:length(lev),' "',lev,'" ',sep=''),'\n',file=clu)
> cat("*vertices",n,"\n ",file=clu)
> cat(paste(as.integer(VV[,6]),'\n',sep=''),file=clu)
> close(clu)
> clu <- file("group.clu","w")
> lev <- levels(VV[,7])
> head(lev)
[1] "1_Plankton" "2_Benthos" "3_Fish" "4_Birds" "5_Mammals"
> cat("%",paste(1:length(lev),' "',lev,'" ',sep=''),'\n',file=clu)
> cat("*vertices",n,"\n ",file=clu)
> cat(paste(as.integer(VV[,7]),'\n',sep=''),file=clu)
> close(clu)
Some editing of the obtained Pajek files:
* formating and additional comments
* NA replaced with 0
The same procedure was applied also to original (2014) data with 244 species.
{{pajek:data:zip:barents.zip|Original 2014}}, {{pajek:data:zip:barents2015.zip|Revised 2015}}