diff --git a/lphy/doc/distributions/Cauchy.md b/lphy/doc/distributions/Cauchy.md new file mode 100644 index 000000000..3e3acfd99 --- /dev/null +++ b/lphy/doc/distributions/Cauchy.md @@ -0,0 +1,18 @@ +Cauchy distribution +=================== +Cauchy(Number **median**, Number **scale**) +------------------------------------------- + +The Cauchy distribution. + +### Parameters + +- Number **median** - the median of the Cauchy distribution. +- Number **scale** - the scale of the Cauchy distribution. + +### Return type + +- Double + + + diff --git a/lphy/doc/distributions/Geometric.md b/lphy/doc/distributions/Geometric.md new file mode 100644 index 000000000..614c8caaf --- /dev/null +++ b/lphy/doc/distributions/Geometric.md @@ -0,0 +1,17 @@ +Geometric distribution +====================== +Geometric(Double **p**) +----------------------- + +The probability distribution of the number of failures before the first success given a fixed probability of success p, supported on the set { 0, 1, 2, 3, ... }. + +### Parameters + +- Double **p** - the probability of success. + +### Return type + +- Integer + + + diff --git a/lphy/doc/distributions/Weibull.md b/lphy/doc/distributions/Weibull.md new file mode 100644 index 000000000..bef0809a6 --- /dev/null +++ b/lphy/doc/distributions/Weibull.md @@ -0,0 +1,18 @@ +Weibull distribution +==================== +Weibull(Number **alpha**, Number **beta**) +------------------------------------------ + +The Weibull distribution. + +### Parameters + +- Number **alpha** - the first shape parameter of the Weibull distribution. +- Number **beta** - the second shape parameter of the Weibull distribution. + +### Return type + +- Double + + + diff --git a/lphy/doc/functions/aminoAcids.md b/lphy/doc/functions/aminoAcids.md new file mode 100644 index 000000000..8598aadd3 --- /dev/null +++ b/lphy/doc/functions/aminoAcids.md @@ -0,0 +1,15 @@ +aminoAcids function +=================== +aminoAcids() +------------ + +The amino acid data type. + + + +### Return type + +- SequenceType + + + diff --git a/lphy/doc/functions/rangeInt.md b/lphy/doc/functions/rangeInt.md new file mode 100644 index 000000000..e63ebb6cf --- /dev/null +++ b/lphy/doc/functions/rangeInt.md @@ -0,0 +1,18 @@ +rangeInt function +================= +rangeInt(Integer **start**, Integer **end**) +-------------------------------------------- + +The range of integers from start to end. Boundaries are included. + +### Parameters + +- Integer **start** - start of the range (inclusive) +- Integer **end** - end of the range (inclusive) + +### Return type + +- Integer[] + + + diff --git a/lphy/doc/types/MetaDataAlignment.md b/lphy/doc/types/MetaDataAlignment.md new file mode 100644 index 000000000..49433bd01 --- /dev/null +++ b/lphy/doc/types/MetaDataAlignment.md @@ -0,0 +1,25 @@ +MetaDataAlignment +================= +Methods +------- + +- **ages** + - gets the ages of these taxa as an array of doubles. +- **charset** + - return a partition alignment. If the string doesn't match charset's syntax, then check if the string matches a defined name in the nexus file. Otherwise it is an error. The string is referred to one partition at a call, but can be multiple blocks, such as d.charset("2-457\3 660-896\3"). +- **dataType** + - get the data type of this alignment. +- **getTaxaNames** + - The names of the taxa. +- **length** + - gets the number of taxa. +- **nchar** + - The number of characters/sites. +- **nodeCount** + - the total number of nodes (left + internal) in a binary tree with these taxa. +- **stateCount** + - the number of possible states in the alignment. +- **taxa** + - the taxa of the alignment. +- **taxaNames** + - The names of the taxa. \ No newline at end of file