diff --git a/README.Rmd b/README.Rmd index dc972f5..f6cc826 100644 --- a/README.Rmd +++ b/README.Rmd @@ -91,9 +91,9 @@ x **Estimation of IBD coefficients** -The `IBDestimate()` function estimates the coefficients of _identity-by-descent_ (IBD) between pairs of individuals, from the available marker data. +The `ibdEstimate()` function estimates the coefficients of _identity-by-descent_ (IBD) between pairs of individuals, from the available marker data. ```{r} -k = IBDestimate(x, ids = bros) +k = ibdEstimate(x, ids = bros) k ``` diff --git a/README.md b/README.md index 2a653a0..092af46 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,6 @@ -forrel -================================================================= +# forrel @@ -11,8 +10,7 @@ status](https://www.r-pkg.org/badges/version/forrel)](https://CRAN.R-project.org [![](https://cranlogs.r-pkg.org/badges/last-month/forrel?color=yellow)](https://cran.r-project.org/package=forrel) -Introduction ------------- +## Introduction The goal of **forrel** is to provide forensic pedigree computations and relatedness inference from genetic marker data. The **forrel** package @@ -38,8 +36,7 @@ The most important analyses currently supported by **forrel** are: - Import of pedigree data and frequency databases from the `Familias` software. -Installation ------------- +## Installation To get the current official version of **forrel**, install from CRAN as follows: @@ -56,8 +53,7 @@ GitHub: devtools::install_github("magnusdv/forrel") ``` -An example ----------- +## An example In this short introduction, we first demonstrate simulation of marker data for a pair of siblings. Then - pretending the relationship is @@ -127,15 +123,20 @@ x **Estimation of IBD coefficients** -The `IBDestimate()` function estimates the coefficients of +The `ibdEstimate()` function estimates the coefficients of *identity-by-descent* (IBD) between pairs of individuals, from the available marker data. ``` r -k = IBDestimate(x, ids = bros) +k = ibdEstimate(x, ids = bros) +#> Estimating 'kappa' coefficients +#> Initial search value: (0.333, 0.333, 0.333) +#> Pairs of individuals: 1 +#> bro1 vs. bro2: estimate = (0.149, 0.551, 0.3), iterations = 16 +#> Total time: 0.005 secs k -#> id1 id2 N k0 k1 k2 -#> 1 bro1 bro2 100 0.1484924 0.5513491 0.3001585 +#> id1 id2 N k0 k1 k2 +#> 1 bro1 bro2 100 0.1486 0.55139 0.30002 ``` The theoretical expectation for non-inbred full siblings is