Man pages for natureanalytics-ca/BycatchEstimator
Generic Model-Based Bycatch Estimation Procedure
| areaDivide | Function to divide up areas. Input grid areas, returns East... |
| areafunc | Stratum designations from Scott-Denton paper, and shrimp... |
| areaGOM | Function to convert new areas to old areas from Kevin... |
| BycatchEstimator-package | Bycatch Estimator |
| bycatchFit | Bycatch model fitting routine |
| bycatchSetup | Bycatch estimation model setup |
| CheckForPositives | Function to look for positive and zero observations across... |
| CheckForPositivesPlot | Same for plotting |
| dataCheck | Make plots and tables of the data |
| deltaEstimatorMean | Function for Pennington(1983) method mean |
| deltaEstimatorSE2 | Function for Pennington(1983) method SE of the mean squAred |
| deltaEstimatorVar | Function for Pennington(1983) method variance |
| findBestModelFunc | Function to find best model by information criteria, by model... |
| fishTimeFunc | Function to calculate number of hours fished in each day... |
| FitModelFunc | Function to fit a specified model formula and print outputs |
| FitModelFuncCV | Function to fit a specified model formula and print outputs... |
| getdatefunc | Function to convert data in excel format with date and time... |
| getdatefunc2 | Function 2 to convert data in excel format with date and time... |
| getDesignEstimates | Function to make design based estimates of bycatch from the... |
| getME | Calculate mean error |
| getPooling | Function to setup pooling if requested for design estimators |
| getRange | Function to find range of a numerical variable |
| getRMSE | Calculate RMSE |
| getSimDeltaLN | Generate mean and standard error of predictions for delta... |
| getSimSE | Generate standard errors of predictions from simulation from... |
| gettimefunc2 | Convert time in excel format |
| Gm | Function for Pennington(1983) method |
| goodman.var | Exact variance of the product of two independent variables,... |
| ilogit | Inverse logit |
| length.unique | Function to count the number of unique levels in a vector |
| LLSIM_BUM_Example_logbook | LLSIM-based example logbook program data set |
| LLSIM_BUM_Example_observer | LLSIM-based example observer program data set |
| lnorm.mean | Calculate lognormal mean and standard error from normal mean... |
| lnorm.se | lnorm.se |
| logdatExample | Logbook simple example data set |
| lo.se | Variance of a product from Lo et al. (1992) |
| makeIndexVar | Function to get an abundance index with SE |
| makePredictions | Function to predict CPUE without variances to get predictions... |
| makePredictionsDeltaVar | Generate standard errors and confidence intervals of... |
| makePredictionsNoVar | Generate predictions without estimating variance |
| makePredictionsSimVarBig | Generate standard errors and confidence intervals of... |
| MakeSummary | Function to make data summarizes including ratio estimate at |
| mostfreqfunc | Function to find mode of a categorical variable |
| norm.mean | Calculate normal mean from lognormal mean and se |
| norm.se | Calculate standard error from lognormal mean and se |
| obsdatExample | Observer simple example data set |
| outlierCountFunc | Function to count outliers, defined as more than numSD... |
| plotCrossVal | Function to plot boxplots of RMSE and ME across folds |
| plotIndex | Function to plot abundance index plus minus standard error |
| plotSums | Function to plot either total positive trips (binomial) or... |
| plotSumsValidate | Function to plot total catch by all models plus a validation... |
| ratio.func | Basic ratio estimator with variance (Cochran) |
| ratioVar | Calculate variance of ratio estimator, from data already... |
| ResidualsFunc | Function plots residuals with both R and Dharma library and... |
| seasonfunc | Function to convert months into 2, 3 4 or 6 numbered seasons |
| simulateGammaDraw | simulateGammaDraw |
| simulateNegBin1Draw | simulateNegBin1Draw |
| simulateNegBinGam | Function to simulate DHARMa residuals from a negative... |
| simulateTMBTweedieDraw | simulateTMBTweedieDraw |
| simulateTweedie | Generate simulations to use as input to DHARMa residual... |
| standard.error | Standard error of a mean |
| yearfunc | Function to group the specified number of years together,... |
