workflowPsi.Rd
If the sequences are not aligned (paired.samples = FALSE
), the function executes these steps.
Computes the autosum of the sequences with autoSum
.
Computes the distance matrix with distanceMatrix
.
Uses the distance matrix to compute the least cost matrix with leastCostMatrix
.
Extracts the cost of the least cost path with leastCost
.
Computes the dissimilarity measure psi with the function psi
.
Delivers an output of type "list" (default), "data.frame" or "matrix", depending on the user input, through formatPsi
.
If the sequences are aligned (paired.samples = TRUE
), these steps are executed:
Computes the autosum of the sequences with autoSum
.
Sums the distances between paired samples with distancePairedSamples
.
Computes the dissimilarity measure psi with the function psi
.
Delivers an output of type "list" (default), "data.frame" or "matrix", depending on the user input, through formatPsi
.
workflowPsi( sequences = NULL, grouping.column = NULL, time.column = NULL, exclude.columns = NULL, method = "manhattan", diagonal = FALSE, format = "dataframe", paired.samples = FALSE, same.time = FALSE, ignore.blocks = FALSE, parallel.execution = TRUE )
sequences | dataframe with multiple sequences identified by a grouping column generated by |
---|---|
grouping.column | character string, name of the column in |
time.column | character string, name of the column with time/depth/rank data. |
exclude.columns | character string or character vector with column names in |
method | character string naming a distance metric. Valid entries are: "manhattan", "euclidean", "chi", and "hellinger". Invalid entries will throw an error. |
diagonal | boolean, if |
format | string, type of output. One of: "data.frame", "matrix". If |
paired.samples | boolean, if |
same.time | boolean. If |
ignore.blocks | boolean. If |
parallel.execution | boolean, if |
A list, matrix, or dataframe, with sequence names and psi values.
data("sequencesMIS") #prepare sequences MIS.sequences <- prepareSequences( sequences = sequencesMIS, grouping.column = "MIS", if.empty.cases = "zero", transformation = "hellinger" ) #execute workflow to compute psi MIS.psi <- workflowPsi( sequences = MIS.sequences, grouping.column = "MIS", time.column = NULL, exclude.columns = NULL, method = "manhattan", diagonal = FALSE, parallel.execution = FALSE ) MIS.psi#> A B psi #> 1 MIS-1 MIS-2 2.6492377 #> 2 MIS-1 MIS-3 2.3280158 #> 3 MIS-1 MIS-4 2.6104038 #> 4 MIS-1 MIS-5 2.0253240 #> 5 MIS-1 MIS-6 1.9691034 #> 6 MIS-1 MIS-7 1.6285033 #> 7 MIS-1 MIS-8 1.9617028 #> 8 MIS-1 MIS-9 1.8356375 #> 9 MIS-1 MIS-10 2.6031041 #> 10 MIS-1 MIS-11 1.7753995 #> 11 MIS-1 MIS-12 2.0907673 #> 12 MIS-2 MIS-3 0.5613996 #> 13 MIS-2 MIS-4 0.4893352 #> 14 MIS-2 MIS-5 2.1466342 #> 15 MIS-2 MIS-6 0.7398286 #> 16 MIS-2 MIS-7 1.8617663 #> 17 MIS-2 MIS-8 1.1775915 #> 18 MIS-2 MIS-9 1.4053206 #> 19 MIS-2 MIS-10 0.7293816 #> 20 MIS-2 MIS-11 1.4124383 #> 21 MIS-2 MIS-12 0.7288371 #> 22 MIS-3 MIS-4 0.6257469 #> 23 MIS-3 MIS-5 1.0617244 #> 24 MIS-3 MIS-6 0.4998365 #> 25 MIS-3 MIS-7 1.0310238 #> 26 MIS-3 MIS-8 0.6901092 #> 27 MIS-3 MIS-9 0.7556862 #> 28 MIS-3 MIS-10 0.6800549 #> 29 MIS-3 MIS-11 0.7622108 #> 30 MIS-3 MIS-12 0.5492251 #> 31 MIS-4 MIS-5 2.6972018 #> 32 MIS-4 MIS-6 0.6515961 #> 33 MIS-4 MIS-7 1.9334300 #> 34 MIS-4 MIS-8 1.0620704 #> 35 MIS-4 MIS-9 1.7816734 #> 36 MIS-4 MIS-10 1.4130480 #> 37 MIS-4 MIS-11 1.9332674 #> 38 MIS-4 MIS-12 0.9327703 #> 39 MIS-5 MIS-6 1.4256233 #> 40 MIS-5 MIS-7 0.7710992 #> 41 MIS-5 MIS-8 1.2352032 #> 42 MIS-5 MIS-9 0.8695324 #> 43 MIS-5 MIS-10 0.8504797 #> 44 MIS-5 MIS-11 0.9038762 #> 45 MIS-5 MIS-12 0.7249898 #> 46 MIS-6 MIS-7 1.1532327 #> 47 MIS-6 MIS-8 0.7069980 #> 48 MIS-6 MIS-9 0.9136826 #> 49 MIS-6 MIS-10 0.7631732 #> 50 MIS-6 MIS-11 1.1294040 #> 51 MIS-6 MIS-12 0.6062822 #> 52 MIS-7 MIS-8 0.9481572 #> 53 MIS-7 MIS-9 0.6515808 #> 54 MIS-7 MIS-10 0.7753695 #> 55 MIS-7 MIS-11 0.8991964 #> 56 MIS-7 MIS-12 0.7177108 #> 57 MIS-8 MIS-9 0.7375359 #> 58 MIS-8 MIS-10 0.7666966 #> 59 MIS-8 MIS-11 0.5502679 #> 60 MIS-8 MIS-12 0.5361810 #> 61 MIS-9 MIS-10 0.5283006 #> 62 MIS-9 MIS-11 0.5366605 #> 63 MIS-9 MIS-12 0.5879649 #> 64 MIS-10 MIS-11 0.6595176 #> 65 MIS-10 MIS-12 0.4226933 #> 66 MIS-11 MIS-12 0.5406600