Man pages for mstaniak/SharedPeptidesIso
| add_effect_counts | Add counts of levels of random effects to list of design... |
| add_independent_unit | Add vector with independent unit to list of design matrices |
| add_protein_design | Add design matrix for proteins |
| add_response | Add response to list of design matrices |
| apqgmodel-methods | Extract raw fit from IsoAPQModel object |
| apqmodeldesign-methods | Extract protein model design from IsoAPQModelDesign object |
| apqmodel-methods | Extract model design from IsoAPQModel object |
| fit_iso_fixed_model | Fit a model based on model design |
| fit_iso_full_model | Fit a model based on model design |
| fit_iso_random_model | Fit a model based on model design |
| get_candidate_formula | Get updated formula for use in lmer |
| get_design_matrices | Get design matrices |
| get_empty_design | Design matrices for model with just proteins |
| get_fixed_design | Get design matrices for model with no random effects |
| get_full_design | Design matrices for full model |
| get_full_model_information | Extract model information from optim() output and model... |
| get_gradient_fixed | Nonlinear mixed effects model based on isotopic distribution |
| get_gradient_full | Nonlinear mixed effects model based on isotopic distribution |
| get_gradient_full_unit | Analytical gradient within a single independent unit |
| get_gradient_random | Nonlinear mixed effects model based on isotopic distribution |
| get_gradient_random_unit | Analytical gradient within a single independent unit |
| get_hessian | Get hessian based on model design and parameters |
| get_iso_fixed_gradient | Analytical gradient for the full model |
| get_iso_fixed_loglikelihood | Negative log-likelihood for a full model based on... |
| get_iso_full_gradient | Analytical gradient for the full model |
| get_iso_full_loglikelihood | Negative log-likelihood for a full model based on... |
| get_iso_random_gradient | Analytical gradient for the full model |
| get_iso_random_loglikelihood | Negative log-likelihood for a full model based on... |
| get_neglog_fixed | Negative log-likelihood for a full model |
| get_neglog_full | Negative log-likelihood for a full model |
| get_neglog_full_unit | Negative log-likelihood within a single independent unit |
| get_neglog_random | Negative log-likelihood for a full model |
| get_neglog_random_unit | Negative log-likelihood within a single independent unit |
| get_protein_matrix | Create design matrix for proteins |
| get_random_design | Get design matrices for model with no fixed effects |
| get_random_model_information | Extract model information from optim() output and model... |
| isoapqmodel | S4 class to represent a nonlinear mixed effects model based... |
| isoapqmodeldesign | Create a description of model design for nonlinear mixed... |
| parse_formula | Get design matrices and response from formula and input data |
