Apoderoides Tutorial

3.2.1. Score at genus level

Let’s calculate the score of taxa in the loaded tree at genus level. Taxa with higher scores are more harmful to monophyly of genera, and such taxa are considered erroneous. The score is calculated by the next command:

#for the test tree
calc.Score(testTree)
#for the user imported tree
calc.Score(tree)

calc.Score() function returns a list of size two, containing two sets of scores based on the centroid and most recent common ancestor (MRCA) of checking ranks. In the above codes, we are checking the genus rank. Here, let’s have a look at the top 10 scores of the test tree based on the centroid.

calc.Score(testTree,show_progress=FALSE)[[1]][1:10,]
#>       OTU                         perCladeOTUScore sum   intruder outlier
#>  [1,] "Araucaria_cunninghamii"    "248"            "248" "0"      "248"  
#>  [2,] "Thuja_orientalis"          "22"             "22"  "2"      "20"   
#>  [3,] "Callitropsis_vietnamensis" "10"             "10"  "3"      "7"    
#>  [4,] "Callitropsis_funebris"     "8"              "8"   "2"      "6"    
#>  [5,] "Goniophlebium_niponicum"   "6"              "6"   "1"      "5"    
#>  [6,] "Dryopteris_crassirhizoma"  "5"              "5"   "1"      "4"    
#>  [7,] "Cyclosorus_dentatus"       "5"              "5"   "2"      "3"    
#>  [8,] "Juniperus_chinensis"       "5"              "5"   "3"      "2"    
#>  [9,] "Cupressus_duclouxiana"     "4"              "4"   "4"      "0"    
#> [10,] "Pteris_vittata"            "3"              "3"   "1"      "2"    
#>       #clade
#>  [1,] "136" 
#>  [2,] "121" 
#>  [3,] "124" 
#>  [4,] "123" 
#>  [5,] "65"  
#>  [6,] "49"  
#>  [7,] "87"  
#>  [8,] "125" 
#>  [9,] "126" 
#> [10,] "41"

The columns of the calculation results show the following information:

• “OTU”: The names of the tree tips.

• “perCladeOTUscore”: The final score of the tree tip calculated by “sum” divided by the number of taxa with the same “#clade”.

• “sum”: The sum of “intruder” and “outlier”.

• “intruder”: The intruder score of the tree tip.

• “outlier”: The outlier score of the tree tip.

• “#clade”: Identifier of clades of the same rank (Here, genus). Different clades have different #clade.

In short, the intruder score shows how many clades of the other ranks the tree tip is intruding, and the outlier score shows how far the tree tip is from the main clade of the belonging rank.

The result shows that “Araucaria_cunninghamii” is by far the top candidate to delete from the tree due to its high score.

Please note that this function assumes that all the names of tree tips are scientific names connected by underbars like “Homo_sapiens”. If the tree tips are named otherwise, please see the next chapter.

3.2.2. Score at the other rank

When you want to calculate score for the rank other than genus, or when the tree tips are not scientific names, you need a list of belonging ranks of the tree tips. Let’s see the rank list of the test tree called by the following command:

data("testRankList")

The contains of the rank list is like this:

data("testRankList")
testRankList[[1]][1:10]
#>  [1] "Wollemia_nobilis"                    
#>  [2] "Araucaria_bidwillii"                 
#>  [3] "Araucaria_araucana"                  
#>  [4] "Araucaria_angustifolia"              
#>  [5] "Ephedra_sinica"                      
#>  [6] "Ephedra_przewalskii"                 
#>  [7] "Ephedra_monosperma"                  
#>  [8] "Cathaya_argyrophylla"                
#>  [9] "Pseudotsuga_sinensis_var._wilsoniana"
#> [10] "Larix_gmelinii"

testRankList[[2]][1:10]
#>  [1] "Araucariaceae" "Araucariaceae" "Araucariaceae" "Araucariaceae"
#>  [5] "Ephedraceae"   "Ephedraceae"   "Ephedraceae"   "Pinaceae"     
#>  [9] "Pinaceae"      "Pinaceae"

The rank list is a list of size 2. The first element is equivalent to a character vector of the tree tips (obtained by, e.g., testTree$tip). The second element is a character vector of the rank names corresponding to the first element of the rank list. In this test data, the rank list indicates the family of the test tree tips. When the tree tips are not scientific names and you want to calculate the score for genus, you can calculate it by setting the genus names in the second element of the rank list.

Using this rank list, the score of test tree for family can be calculated by the following command:

calc.Score(testTree,testRankList)

The output can be interpreted just like the score for genus. The only difference is the score is based on monophyly of genus or family.