Man pages for famuvie/breedR
Statistical Methods for Forest Genetic Resources Analysts
| additive_genetic | Build an additive_genetic model |
| additive_genetic_animal | Build an additive-genetic animal model |
| additive_genetic_competition | Build an additive-genetic competition model |
| as.triplet | Represent a symmetric matrix in triplet format |
| bispline_incidence | Incidence Matrix of Bidimensional Splines |
| breedr_ar | Build an autoregressive model |
| breedr_blocks | Build a blocks model |
| breedr_effect | Constructor for a generic breedR effect |
| breedR.get.HOME | Determine the user's home directory |
| breedR.get.USER | Determine the user name |
| breedR.option | Set and get global options for breedR |
| breedR.os | Check host OS |
| breedR.os.32or64bit | test 32/64 bits architecture |
| breedR.os.type | Return platform string |
| breedR-package | Frequentist and Bayesian methods for breeders, quantitative... |
| breedr_progsf90_repo | Default repository for PROGSF90 binaries |
| breedR.remote | Perform a job remotely |
| breedr_splines | Build a splines model |
| build_grid | Build an encompassing grid |
| build_pedigree | Build pedigree |
| b.values | Breeding values |
| check_pedigree | Check the rules for a well-formed pedigree |
| check_progsf90 | Checks installation of PROGSF90 binaries |
| check_var.ini | Check initial variances specification |
| compare.plots | Compare two or more ggplots of the same kind |
| competition | Build a virtual competition model |
| coordinates_breedR | breedR coordinates methods |
| default_initial_variance | Default initial value for variance components |
| determine.n.knots | Determine a sensible number of knots |
| diagonal | Constructor for a diagonal random effect |
| distribute_knots_uniformgrid | Distribute knots uniformly in a grid |
| douglas | Multi-site Douglas-fir dataset |
| effect_group | Constructor for a group of effects |
| effect_type | Type of a (group of) effect(s) |
| extract_block | Extract a block of lines from a section of the REML log |
| Extract.metagene | Extract or replace data in a metagene object |
| fill_holes | Find and fill all the holes in a vector |
| fixed | Constructor for a fixed effect |
| fixef | Extract fixed-effects estimates |
| generic | Build a generic model |
| genetic | Build an genetic model |
| get_efnames | Get names of effects |
| get_ntraits | Extract the number of traits |
| get_param | Parameters of a breedR component |
| get_pedigree | Get the Pedigree from an object |
| get_structure | Covariance structure of a breedR component |
| globulus | Eucalyptus Globulus dataset |
| install_progsf90 | Install PROGSF90 binary dependencies |
| is_numericlog | Test whether a string from a REML log is numeric |
| larix | Longitudinal Larix dataset |
| loc_grid | Lattice of spatial locations |
| m1 | A small Metagene synthesized dataset |
| m4 | Metagene synthesized dataset with four generations |
| neighbours.at | 'move' an arrangement in a given direction |
| ngenerations | Number of generations |
| nindividuals | Number of individuals |
| node2lattice_mapping | Define mapping between a lattice and nodes |
| normalise_coordinates | Normalise coordinates specification |
| parse.txtmat | Parse a matrix from a text output robustly |
| permanent_environmental_competition | Build an permanent-environmental competition model |
| pf90_code_missing | Determine a numeric code for missing observations |
| pf90_default_heritability | Default formula for heritability |
| plot.remlf90 | Spatial plot of a model's fit components |
| progsf90 | progsf90 class |
| random | Constructor for a random effect |
| ranef | Extract the modes of the random effects |
| read.metagene | Metagene Data Input |
| remlf90 | Inference with REMLF90 |
| remote | Control and view a remote breedR-queue of submitted jobs |
| renderpf90 | Render a progsf90 effect |
| renderpf90.matrix | Render a sparse matrix into non-zero values and column... |
| retrieve_remote | Retrieve results stored in some remote directory |
| sim.spatial | Simulate a spatial structure |
| simulation | Simulation of phenotypes and model components |
| spatial | Build a spatial model |
| spatial.plot | Plot an spatially arranged continuous variable |
| splat | 'Splat' arguments to a function |
| validate_variance | Check properties for a covariance matrix |
| variogram | Empirical variograms of residuals |
| vcov.remlf90 | Covariance matrix of a fitted remlf90 object |
| vgram.matrix | Variogram of a matrix |
