Last updated on 2024-11-22 09:49:41 CET.
| Package | NOTE | OK |
|---|---|---|
| poolfstat | 10 | 3 |
Current CRAN status: NOTE: 10, OK: 3
Version: 2.2.0
Check: Rd files
Result: NOTE
checkRd: (-1) add.leaf.Rd:46: Lost braces; missing escapes or markup?
46 | By default the function tests all the possible positions of a newly added edge connecting the candidate leaf to the graph with both non-admixed (including a new rooting with the candidate leaf as an outgroup) and admixed edges. If n_e is the the number of non-admixed edges of the original graph, the number of tested graphs for non-admixed edges equals n_e+1. The newly added node is named "N-"{name of the leaf to add} (or with more N if the name already exists). For admixed edges, the number of tested graphs equals n_e*(n_e-1)/2 and for a given tested graph, three nodes named "S-"{name of the leaf to add}, "S1-"{name of the leaf to add} and "S2-"{name of the leaf to add} (or with more S if the name already exists) are added and the admixture proportions are named with a letter (A to Z depending on the number of admixed nodes already present in the graph).
| ^
checkRd: (-1) add.leaf.Rd:46: Lost braces; missing escapes or markup?
46 | By default the function tests all the possible positions of a newly added edge connecting the candidate leaf to the graph with both non-admixed (including a new rooting with the candidate leaf as an outgroup) and admixed edges. If n_e is the the number of non-admixed edges of the original graph, the number of tested graphs for non-admixed edges equals n_e+1. The newly added node is named "N-"{name of the leaf to add} (or with more N if the name already exists). For admixed edges, the number of tested graphs equals n_e*(n_e-1)/2 and for a given tested graph, three nodes named "S-"{name of the leaf to add}, "S1-"{name of the leaf to add} and "S2-"{name of the leaf to add} (or with more S if the name already exists) are added and the admixture proportions are named with a letter (A to Z depending on the number of admixed nodes already present in the graph).
| ^
checkRd: (-1) add.leaf.Rd:46: Lost braces; missing escapes or markup?
46 | By default the function tests all the possible positions of a newly added edge connecting the candidate leaf to the graph with both non-admixed (including a new rooting with the candidate leaf as an outgroup) and admixed edges. If n_e is the the number of non-admixed edges of the original graph, the number of tested graphs for non-admixed edges equals n_e+1. The newly added node is named "N-"{name of the leaf to add} (or with more N if the name already exists). For admixed edges, the number of tested graphs equals n_e*(n_e-1)/2 and for a given tested graph, three nodes named "S-"{name of the leaf to add}, "S1-"{name of the leaf to add} and "S2-"{name of the leaf to add} (or with more S if the name already exists) are added and the admixture proportions are named with a letter (A to Z depending on the number of admixed nodes already present in the graph).
| ^
checkRd: (-1) add.leaf.Rd:46: Lost braces; missing escapes or markup?
46 | By default the function tests all the possible positions of a newly added edge connecting the candidate leaf to the graph with both non-admixed (including a new rooting with the candidate leaf as an outgroup) and admixed edges. If n_e is the the number of non-admixed edges of the original graph, the number of tested graphs for non-admixed edges equals n_e+1. The newly added node is named "N-"{name of the leaf to add} (or with more N if the name already exists). For admixed edges, the number of tested graphs equals n_e*(n_e-1)/2 and for a given tested graph, three nodes named "S-"{name of the leaf to add}, "S1-"{name of the leaf to add} and "S2-"{name of the leaf to add} (or with more S if the name already exists) are added and the admixture proportions are named with a letter (A to Z depending on the number of admixed nodes already present in the graph).
| ^
checkRd: (-1) generate.graph.params.Rd:33: Lost braces; missing escapes or markup?
33 | The graph needs to be specified by a three column (character) matrix corresponding for each edge (wether admixed or not) to i) the child node; ii) the parent node; iii) the admixture proportion. For non-admixed edge, the third column must be blank. An admixed node should be referred two times as a child node with two different parent node and two different admixture proportions coded as alpha and (1-alpha) (Note that the parentheses are mandatory) if alpha is the name of the admixture proportion. The root is automatically identified as a node only present in the parent node column. Several checks are made within the function but it is recommended to check the graph by plotting the resulting dot file named {outfileprefix.}dot using for instance the grViz() from the DiagrammeR package that may be called directly with plot or with the dot program (e.g., dot -Tpng inputgraph.dot in terminal). Note that the dot file may be easily customized (e.g., to change leave color, parameter names...). The fstats object should be of class fstats (see help(fstats) for details) containing estimates of F2 and F3 statistics and block jackknife as generated with the \code{\link{compute.fstats}} function with computeF3 set to TRUE. If no fstats object is provided, only graph parameters will be generated.
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checkRd: (-1) graph.params2qpGraphFiles.Rd:30: Lost braces; missing escapes or markup?
30 | This function generates the three files required by qpGraph: i) a file named {outfileprefix}.graph containing the graph in appropriate format; ii) a file named {outfileprefix}.fstats file containing the fstats estimates of fstats (and their covariance); iii) a file named {outfileprefix}.parqpGraph containing essential parameter information to run qpGraph (this may be edited by hand if other options are needed). The qpGraph software may then be run using the following options -p {outfileprefix}.parqpGraph -g {outfileprefix}.graph -o out.ggg -d out.dot.
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checkRd: (-1) graph.params2qpGraphFiles.Rd:30: Lost braces; missing escapes or markup?
30 | This function generates the three files required by qpGraph: i) a file named {outfileprefix}.graph containing the graph in appropriate format; ii) a file named {outfileprefix}.fstats file containing the fstats estimates of fstats (and their covariance); iii) a file named {outfileprefix}.parqpGraph containing essential parameter information to run qpGraph (this may be edited by hand if other options are needed). The qpGraph software may then be run using the following options -p {outfileprefix}.parqpGraph -g {outfileprefix}.graph -o out.ggg -d out.dot.
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checkRd: (-1) graph.params2qpGraphFiles.Rd:30: Lost braces; missing escapes or markup?
30 | This function generates the three files required by qpGraph: i) a file named {outfileprefix}.graph containing the graph in appropriate format; ii) a file named {outfileprefix}.fstats file containing the fstats estimates of fstats (and their covariance); iii) a file named {outfileprefix}.parqpGraph containing essential parameter information to run qpGraph (this may be edited by hand if other options are needed). The qpGraph software may then be run using the following options -p {outfileprefix}.parqpGraph -g {outfileprefix}.graph -o out.ggg -d out.dot.
| ^
checkRd: (-1) graph.params2qpGraphFiles.Rd:30: Lost braces; missing escapes or markup?
30 | This function generates the three files required by qpGraph: i) a file named {outfileprefix}.graph containing the graph in appropriate format; ii) a file named {outfileprefix}.fstats file containing the fstats estimates of fstats (and their covariance); iii) a file named {outfileprefix}.parqpGraph containing essential parameter information to run qpGraph (this may be edited by hand if other options are needed). The qpGraph software may then be run using the following options -p {outfileprefix}.parqpGraph -g {outfileprefix}.graph -o out.ggg -d out.dot.
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checkRd: (-1) graph.params2qpGraphFiles.Rd:30: Lost braces; missing escapes or markup?
30 | This function generates the three files required by qpGraph: i) a file named {outfileprefix}.graph containing the graph in appropriate format; ii) a file named {outfileprefix}.fstats file containing the fstats estimates of fstats (and their covariance); iii) a file named {outfileprefix}.parqpGraph containing essential parameter information to run qpGraph (this may be edited by hand if other options are needed). The qpGraph software may then be run using the following options -p {outfileprefix}.parqpGraph -g {outfileprefix}.graph -o out.ggg -d out.dot.
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