for loop - Creating empty matrix and filling in date matched values in R -
i'm quite new r , apologise in advance post not being in usual format (i tried using dput() got weird output , have no idea how upload datasets i'm sorry).
i have dataset 6 colums (site, startdate, enddate, photodate, species, indiv). example:
site year startdate enddate photodate species indiv m1_7 2012 19/07/2012 10/08/2012 20/07/2012 sylvicapra grimmia 1 m1_7 2012 19/07/2012 10/08/2012 23/07/2012 crocuta crocuta 1 m1_7 2012 19/07/2012 10/08/2012 23/07/2012 potamochoerus larvatus 1 m1_7 2012 19/07/2012 10/08/2012 25/07/2012 hystrix cristata 1 m1_7 2012 19/07/2012 10/08/2012 27/07/2012 potamochoerus larvatus 1 m1_7 2012 19/07/2012 10/08/2012 27/07/2012 sylvicapra grimmia 1 m1_7 2012 19/07/2012 10/08/2012 28/07/2012 hippotragus equinus 1 m1_7 2012 19/07/2012 10/08/2012 30/07/2012 crocuta crocuta 1 m1_7 2012 19/07/2012 10/08/2012 01/08/2012 equus q. boehmi 1 m1_7 2012 19/07/2012 10/08/2012 01/08/2012 crocuta crocuta 1 m1_7 2012 19/07/2012 10/08/2012 05/08/2012 potamochoerus larvatus 1 m1_7 2012 19/07/2012 10/08/2012 07/08/2012 hippotragus equinus 1 m1_9 2012 21/07/2012 11/08/2012 24/07/2012 pedetes capensis 1 m1_9 2012 21/07/2012 11/08/2012 24/07/2012 crocuta crocuta 2 m1_9 2012 21/07/2012 11/08/2012 24/07/2012 pedetes capensis 1 m1_9 2012 21/07/2012 11/08/2012 27/07/2012 pedetes capensis 1 m1_9 2012 21/07/2012 11/08/2012 01/08/2012 alcelaphus b. lichtensteinii 1 m1_9 2012 21/07/2012 11/08/2012 03/08/2012 pedetes capensis 1 m1_9 2012 21/07/2012 11/08/2012 04/08/2012 crocuta crocuta 1 m1_9 2012 21/07/2012 11/08/2012 06/08/2012 pedetes capensis 1 m1_9 2012 21/07/2012 11/08/2012 07/08/2012 pedetes capensis 1 m1_9 2012 21/07/2012 11/08/2012 08/08/2012 pedetes capensis 1 m1_11 2012 21/07/2012 11/08/2012 26/07/2012 mellivora capensis 1 m1_11 2012 21/07/2012 11/08/2012 03/08/2012 sylvicapra grimmia 1 m1_11 2012 21/07/2012 11/08/2012 07/08/2012 hystrix cristata 1 m1_11 2012 21/07/2012 11/08/2012 08/08/2012 potamochoerus larvatus 1 i've been trying write loop creates 49 column matrix column 1 corresponds site, column 2 sequence of dates between "startdate" , "enddate" within site, column 3:49 species names. within cells under columns 3:49, fill them data derived summing count data (indiv), particular species, @ particular date.
so far have been able create empty matrix corresponding want, have been unable fill in data. code have used:
mlele2012<- read.delim("c:\\multiple regression\\mlele 2012 empty matrix creation.txt") africa <- read.delim("c:\\species accumulation curves\\complete species list.txt") specieslistx<-unique(africa) specieslistx<-t(specieslistx) oldtemp<-null temp <- rep(0, length(specieslistx )) strptime(mlele2012$photodate, "%y-%m-%d") strptime(mlele2012$startdate, "%d/%m/%y") strptime(mlele2012$enddate, "%d/%m/%y") #create empty dataframe dimensions: no. of sites x no. of dates in each for(i in levels(mlele2012$site)) { ##for each site sitetemp <- subset(mlele2012, site == i) ###subset of dataset , particular site i## sitetemp$startdate<- as.date(sitetemp$startdate, "%d/%m/%y") sitetemp$enddate<- as.date(sitetemp$enddate, "%d/%m/%y") sitedatelist<-seq(as.date(sitetemp$startdate[1]), as.date(sitetemp$enddate[1]), "days") empty<-matrix(0,length(sitedatelist),length(specieslistx)) sitedatelist1<-as.character(sitedatelist) row.names(empty)<-(sitedatelist1) colnames(empty)<-specieslistx addsitecol<-matrix(0,length(sitedatelist),1) extendempty<-cbind(addsitecol,empty) extendempty[,1]<-i oldtemp<-rbind(oldtemp, extendempty) } write.csv(oldtemp, "mlele 2012 dry empty.csv") in addition, have been trying extract create matrix in same format/dimensions, without excess dates (i.e. dates in "photodate" column , not sequence between "startdate" , "enddate"). hoping somehow merge 2 matrices need. unfortunately code not work, although there doesn't seem error. here's second part of code:
for(i in mlele2012$site) { sitetemp <- subset(mlele2012, site == i) ###subset of dataset "allsites", particular site i## for(j in sitetemp$photodate){ datetemp <- subset(sitetemp, photodate == j) ###subset of dataset "africaa", particular date i# uniquespperdate <- unique(datetemp$species)###unique species within each date (row) i# temp <- rep(0, length(specieslistx)) #create temporary vector of 0s same length species list### for(a in uniquespperdate){ sptemp <- subset(datetemp , species == a) ###subset of dataset "sitetemp", particular sp j## countdata<-sum(sptemp$indiv) index <- pmatch(a, names(temp)) ###match unique species per date location on species list### #there problem here, works when run single line not within loop temp[index] <- countdata ###for locations listed in "index", assign count data temporary vector### names(temp)<- specieslistx } } oldtemp <- rbind(oldtemp, temp) ### bind new temp file old temp file, i.e. update list loop runs### } any appreciated. kindly let me know if there details can provide make question clearer.
i can of way there on sample with:
> ftable(xtabs(indiv~site+year+species, data=dat) ) species boehmi capensis cristata crocuta equinus grimmia larvatus lichtensteinii site year m1_11 2012 0 1 1 0 0 1 1 0 m1_7 2012 1 0 1 3 2 2 3 0 m1_9 2012 0 7 0 3 0 0 0 1 i did input data using genus/species 2 columns because did not offer requested dput version.
Comments
Post a Comment