OpenIMBCR

AIC | calculate AIC from a likelihood function optimization... |

AICc | calculate AICc from a likelihood function optimization... |

akaike_predict | testing : us Akaike weights to predict across a series of... |

akaike_weight_predictions | testing : accepts a list of akaike predictions (as returned... |

akaike_weights | calculate Akaike weights from a vector of AIC values |

balance_zero_transects | testing : drop some zero transects so that zero transects are... |

bartuszevige_intercept_test | Frequentist slope intercept test first described by... |

BIC | calculated BIC from a likelihood function optimization... |

binary_reclassify | preform a binary reclassification on an input raster, with... |

birdcode_fieldname | hidden function that greps for four-letter-codes |

buffer_grid_unit | generate a square buffer around a single input feature |

buildUnmarkedDistanceDf | accepts a named raster stack of covariates, an IMBCR... |

build_unmarked_gds | accepts a formatted IMBCR SpatialPointsDataFrame and builds... |

calc_dist_bins | accepts a Spatial*DataFrame object with a distance... |

calc_interpatch_distance | hidden function that will calculate interpatch distance using... |

calc_k | estimates a K parameter (upper-bound of integration) as a... |

calc_mean_patch_area | hidden function that will use SDMTools to calculate the mean... |

calc_patch_count | hidden function that will use SDMTools to calculate the... |

calc_total_area | shorthand total area calculation function |

check_correlation_matrix | testing : |

check_peasons_product_moment | accepts a variable name an an input data.frame and conducts a... |

commonname_fieldname | hidden function that greps for four-letter-codes |

distance_fieldname | hidden function that greps for the distance field name |

downsample_by_normal_dist | testing : downsample records in a continuous 'distances'... |

downsample_by_quantile | downsample records in a continuous 'distances' distribution... |

expit | expit link function |

extract_by | extract an input raster dataset using polygon feature(s).... |

extract_by_large_df | testing: chunk out the task of extracting buffers from a... |

extractByTransect | extract (and optionally, summarize using the fun= argument)... |

fetchImbcrToLandfireMetadata | fetch IMBCR Metadata to Landfire code conversions |

gdistsamp_find_optimal_k | testing: there is some ambiguity in selecting a good... |

gdistsamp_find_optimal_key_func | testing: attempt to fit a series of different detection... |

gdistsamp_find_optimal_k_with_transect_downsampling | testing : given a user-specified mixture distribution, try... |

gdistsamp_refit_model | re-fit a model specified by a formula object |

imbcr_single_season_pooled_1km_distance | fit the single-season distance model of Royle (2004) to... |

imbcrTableToShapefile | parse a source CSV (published by BCR) for IMBCR data and... |

l_buffer_grid_units | testing: generalization of the buffer_grid_units function... |

l_calc_stat | testing: std lapply implementation to benchmark against... |

logit | logit link function |

mCombinations | testing : hidden function to derive a data.frame of all... |

par_buffer_grid_units | testing: generalization of buffer_grid_unit with parallel... |

par_calc_stat | shorthand function that applies an arbitrary, user-supplied... |

parseDetectionsBySpecies | accepts a SpatialPointsDataFrame of IMBCR data and parses... |

parseLayerDsn | built-in (hidden) function that will accept the full path of... |

parseStationCountsAsOccupancy | accepts a list of data.frames (as returned by... |

parseStationLevelMetadata | parse relavent metadata for estimating p-detection and leave... |

partialPredict | build a response plot for a given variable using a fitted... |

par_unmarked_predict | testing: use the parallel package to predict across a large... |

permutations | recursively calculate all possible permutations of an input... |

pool_by_transect_year | hidden function that summarizes imbcr transect covariate data... |

randomWalk_dAIC | testing: perform a random walk on an unmarked dataframe with... |

readOGRfromPath | built-in (hidden) function that will accept the full path of... |

recursiveFindFile | recursively find all files in folder (root) that match the... |

scrub_imbcr_df | kludging to back-fill any transect stations in an imbcr... |

scrub_unmarked_dataframe | hidden function used to clean-up an unmarked data.frame... |

SE | calculate SE from a likelihood function optimization... |

singleSeasonOccupancy | testing: fit a single-season occupancy model assumes a... |

singleSeasonRN | testing : fit the single-season, two-state occupancy model of... |

spatial_join | shorthand vector extraction function that performs a spatial... |

stripCommonName | strip non-essential characters and spaces from a species... |

timeperiod_fieldname | hidden function that greps for the timeperiod field name |

transect_fieldname | hidden function that greps for the transect field name |

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