[R-sig-eco] Problem in Search and Association Loop

[Hanna Tuomisto]

Hi Alexandre,

R has converted your strings into factors. This may have happened already when you read the data from a file, and in that context it can be avoided:
read.csv(... , stringsAsFactors=FALSE)

You do not need a loop to combine the two data frames. First make sure you have the same column names in both:
colnames(new.data)[2] <- "epithet"

Then you can use rbind() and subsetting to combine the desired parts of the data frames:

output <- rbind(base[,-1], subset(new.data, !new.data[,"genus"] %in% base[,"genus"] | !new.data[,"epithet"] %in% base[,"epithet"]))

Good luck,
Hanna



On 5 Sep 2015, at 3:34 AM, Alexandre F. Souza wrote:

> Dear friends,
> 
> I am writing a loop to compare scientific plant names from one data frame
> in a second data frame containing a smaller set of potentially different
> plant names, and then to copy the associated abundances of the sp already
> present in the first database, and add the new species to the bottom.
> 
> I am receiving, however, an error message saying that factor levels are
> different. Can someone give me a hint on what can be happening?
> 
> Here you have the code
> 
> The base dataframe
> 
>> base
>        family           genus             epithet    abundance
> 1   Burseraceae   Coccoloba cf. cordifolia 224
> 2 Anacardiaceae    Tapirira     guianensis 112
> 3 Euphorbiaceae Pogonophora schomburgkiana 146
> 4 Anacardiaceae  Thyrsodium     spruceanum 115
> 5   Apocynaceae Himatanthus  phagedaenicus  47
> 6    Sapotaceae    Pouteria       coriacea  71
> 7 Malpighiaceae   Byrsonima        sericea  25
> 8  Polygonaceae   Coccoloba cf. cordifolia  29
> 9   Burseraceae     Protium   heptaphyllum  37
> 
> The new data data.frame
> 
>> new.data
>        genus            sp.new    abundance
> 1    Coccoloba cf. cordifolia   29
> 2      Protium   heptaphyllum   37
> 3    Bowdichia   virgilioides   15
> 4 Sclerolobium    densiflorum   15
> 5       Ocotea      glomerata   16
> 
> The Output table
> 
> 
> output= matrix(nrow = 10, ncol = 3)
> colnames(output) = c("genus", "epithet", "abundance")
> output
> 
> 
> for (i in 1:nrow(base)){
>  for (j in 1:nrow(new.data)){
>    if ((base[i,2] == new.data[j,1]) & (base[i,3] == new.data[j,2])){
>      output[i,1] = base[i,2]
>      output[i,2] = base[i,3]
>      output[i,3] = new.data[j,2]
>    }
>  }
> }
> 
> This is just the beginning of the code I plan. I stopped due to the error
> message.
> 
> Thank you very much in advance,
> 
> Alexandre
> 
> -- 
> Dr. Alexandre F. Souza
> Professor Adjunto III
> Universidade Federal do Rio Grande do Norte
> CB, Departamento de Ecologia
> Campus Universitário - Lagoa Nova
> 59072-970 - Natal, RN - Brasil
> lattes: lattes.cnpq.br/7844758818522706
> http://www.docente.ufrn.br/alexsouza
> 
> 	[[alternative HTML version deleted]]
> 
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---
Hanna Tuomisto
Department of Biology
FI-20014 University of Turku, FINLAND

e-mail: hanna.tuomisto at utu.fi
phone: +358-2-3335634
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