Genodive sample datamatric Patch#
Genodive sample datamatric simulator#

Use the ‘Shift’ key to select all columns with loci A - H.Delimiters: check ‘comma.’ Click ‘Next.’.Text Import Wizard: select ‘Delimited,’ click ‘Next.’.Excel menu: ‘File > Import > CSV File > Import.’ Navigate to file.Note that in Excel, the columns with the loci must be explicitly defined as ‘text,’ otherwise Excel is likely to interpret them as times. From your file system, you can open it with Excel. If( ! dir.exists( paste0( here(), '/downloads'))) dir.create( paste0( here(), '/downloads')) py( system.file( 'extdata', '', package = 'LandGenCourse'), paste0( here(), '/downloads/'), overwrite= FALSE) # FALSEĬheck that the file is now in the folder downloads within your project folder. Linking paternity to ecological variables Nested model (NMLPE) for hierarchical sampling designs A quick note on controlling for population structure in RDA Redundancy Analysis (RDA): a multivariate GEA Latent Factor Mixed Models (LFMM): a univariate GEA How does changing resolution affect these metrics? Convert conductance into effective distance Setting cost values and calculating conductance

Simulated data: 2-island model with admixture Benchmarking file import and export options

Genodive sample datamatric simulator#

Run simulator using a previously defined parameter set

Genodive sample datamatric Patch#

Calculate Hanski’s index Si with source patch parameters Fit spatially varying coefficients model with package ‘spmoran’ Spatial filtering with MEM using package ‘spmoran’ Fit spatial simultaneous autoregressive error models (SAR) Fit models with spatially correlated error (GLS) with package ‘nlme’ Test regression residuals for spatial autocorrelation Assess correlation between trait and environment Estimate genetic and non-genetic variance components from a common garden experiment Specify spatial weights and calculate Moran’s I Create Mantel correlogram for genetic data Are genetic differentiation and diversity related? What determines genetic differentiation among sites? Spatial distribution of genetic structure Aggregate genetic data at population level (allele frequencies) Basic checking of markers and populations Use ‘terra’ and ‘tmap’ to display categorical map with color scheme

Convert ‘SpatialPointsDataFrame’ to ‘sf’ object Sample landscape metrics within buffer around sampling locations Display raster data and overlay sampling locations, extract data View information stored in ‘genind’ object