Additional Functions for Manipulating Data in treedata.table

Additional functions for manipulating data

treedata.table includes additional functions that allow the identification of discrete and continuous characters in a given dataset. We first load the dataset:

library(ape)
library(treedata.table)

# Load example data
data(anolis)
#Create treedata.table object with as.treedata.table
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)

## Tip labels detected in column: X

## Phylo object detected

## All tips from original tree/dataset were preserved

The detectCharacterType() function can be used to examine whether SVL is discrete or continuous:

detectCharacterType(anolis$dat$SVL)

## [1] "continuous"

We can further examine the type of characters we have in our dataset by using the detectAllCharacters() function:

detectAllCharacters(anolis$dat)

##  [1] "discrete"   "continuous" "continuous" "continuous" "continuous"
##  [6] "continuous" "continuous" "continuous" "continuous" "discrete"  
## [11] "discrete"

Summarizing this information in a table, we get:

cbind.data.frame(character=colnames(anolis$dat),type=detectAllCharacters(anolis$dat))

##                 character       type
## 1                       X   discrete
## 2                     SVL continuous
## 3               PCI_limbs continuous
## 4               PCII_head continuous
## 5  PCIII_padwidth_vs_tail continuous
## 6        PCIV_lamella_num continuous
## 7             awesomeness continuous
## 8               hostility continuous
## 9                attitude continuous
## 10               ecomorph   discrete
## 11                 island   discrete

Finally, we can use the filterMatrix() function to subset our dataset to only a certain type of characters. For instance, let’s extract all discrete characters in the Anolis dataset:

filterMatrix(anolis$dat, "discrete")

##                   X ecomorph      island
## 1              ahli       TG        Cuba
## 2           alayoni       TW        Cuba
## 3           alfaroi       GB        Cuba
## 4          aliniger       TC  Hispaniola
## 5          allisoni       TC        Cuba
## 6           allogus       TG        Cuba
## 7     altitudinalis       TC        Cuba
## 8           alumina       GB  Hispaniola
## 9         alutaceus       GB        Cuba
## 10      angusticeps       TW        Cuba
## 11      argenteolus        U        Cuba
## 12      argillaceus        U        Cuba
## 13          armouri       TG  Hispaniola
## 14    bahorucoensis       GB  Hispaniola
## 15         baleatus       CG  Hispaniola
## 16         baracoae       CG        Cuba
## 17        barahonae       CG  Hispaniola
## 18         barbatus        U        Cuba
## 19         barbouri        U  Hispaniola
## 20         bartschi        U        Cuba
## 21          bremeri       TG        Cuba
## 22         breslini       TG  Hispaniola
## 23     brevirostris        T  Hispaniola
## 24         caudalis        T  Hispaniola
## 25        centralis        U        Cuba
## 26   chamaeleonides        U        Cuba
## 27     chlorocyanus       TC  Hispaniola
## 28      christophei        U  Hispaniola
## 29        clivicola       GB        Cuba
## 30      coelestinus       TC  Hispaniola
## 31         confusus       TG        Cuba
## 32            cooki       TG Puerto Rico
## 33     cristatellus       TG Puerto Rico
## 34     cupeyalensis       GB        Cuba
## 35          cuvieri       CG Puerto Rico
## 36     cyanopleurus       GB        Cuba
## 37          cybotes       TG  Hispaniola
## 38      darlingtoni       TW  Hispaniola
## 39        distichus        T  Hispaniola
## 40  dolichocephalus       GB  Hispaniola
## 41        equestris       CG        Cuba
## 42       etheridgei        U  Hispaniola
## 43    eugenegrahami        U  Hispaniola
## 44        evermanni       TC Puerto Rico
## 45          fowleri        U  Hispaniola
## 46          garmani       CG Puerto Rico
## 47          grahami       TC Puerto Rico
## 48            guafe       TG        Cuba
## 49        guamuhaya        U        Cuba
## 50          guazuma       TW        Cuba
## 51        gundlachi       TG Puerto Rico
## 52        haetianus       TG  Hispaniola
## 53       hendersoni       GB  Hispaniola
## 54       homolechis       TG        Cuba
## 55            imias       TG        Cuba
## 56     inexpectatus       GB        Cuba
## 57        insolitus       TW  Hispaniola
## 58         isolepis       TC        Cuba
## 59            jubar       TG        Cuba
## 60            krugi       GB Puerto Rico
## 61       lineatopus       TG     Jamaica
## 62    longitibialis       TG  Hispaniola
## 63         loysiana        T        Cuba
## 64           lucius        U        Cuba
## 65     luteogularis       CG        Cuba
## 66       macilentus       GB        Cuba
## 67         marcanoi       TG  Hispaniola
## 68           marron        T  Hispaniola
## 69          mestrei       TG        Cuba
## 70        monticola        U  Hispaniola
## 71           noblei       CG        Cuba
## 72         occultus       TW Puerto Rico
## 73          olssoni       GB  Hispaniola
## 74         opalinus       TC     Jamaica
## 75       ophiolepis       GB        Cuba
## 76         oporinus       TC        Cuba
## 77         paternus       TW        Cuba
## 78         placidus       TW  Hispaniola
## 79        poncensis       GB Puerto Rico
## 80         porcatus       TC        Cuba
## 81           porcus        U        Cuba
## 82       pulchellus       GB Puerto Rico
## 83          pumilis        U        Cuba
## 84  quadriocellifer       TG        Cuba
## 85       reconditus        U     Jamaica
## 86         ricordii       CG  Hispaniola
## 87      rubribarbus       TG        Cuba
## 88           sagrei       TG        Cuba
## 89     semilineatus       GB  Hispaniola
## 90         sheplani       TW  Hispaniola
## 91          shrevei       TG  Hispaniola
## 92       singularis       TC  Hispaniola
## 93       smallwoodi       CG        Cuba
## 94          strahmi       TG  Hispaniola
## 95        stratulus       TC Puerto Rico
## 96      valencienni       TW     Jamaica
## 97        vanidicus       GB        Cuba
## 98     vermiculatus        U        Cuba
## 99         websteri        T  Hispaniola
## 100       whitemani       TG  Hispaniola

Two additional functions in treedata.table are designed to examine and modify column and row names in any dataset. For instance, we can ask if the Anolis dataset has column names:

hasNames(anolis$dat, "col")

##  col 
## TRUE

It does have column names. Let’s just remove the column names and check if hasNames() can detect this change. Here’s our new dataset:

data=anolis$dat
colnames(data)<-NULL
head(data,2)

##                                                                        
## 1    ahli 4.039125 -3.248286  0.3722519 -1.042219 -2.4147423 -0.2416517
## 2 alayoni 3.815705  3.408886 -1.7833585  2.208451  0.9496969 -0.2590322
##                               
## 1 -0.1734769 0.6443771 TG Cuba
## 2  0.1273443 0.2959732 TW Cuba

Let’s run hasNames() on our new dataset:

hasNames(data, "col")

##   col 
## FALSE

Now, we can create new column names using the forceNames() function:

data <- forceNames(data, "col")

The new dataset, with column names (n1…), looks like this:

head(data,2)

##        n1       n2        n3         n4        n5         n6         n7
## 1    ahli 4.039125 -3.248286  0.3722519 -1.042219 -2.4147423 -0.2416517
## 2 alayoni 3.815705  3.408886 -1.7833585  2.208451  0.9496969 -0.2590322
##           n8        n9 n10  n11
## 1 -0.1734769 0.6443771  TG Cuba
## 2  0.1273443 0.2959732  TW Cuba

And we can finally ask whether our new dataset actually have column names by running the hasNames() function again:

hasNames(data, "col")

##  col 
## TRUE

We can apply the same procedure for columns (col), rows (row) or both (rowcol).

- Additional functions for manipulating data