Package: halk 0.0.5

Paul Frater

halk: Methods to Create Hierarchical Age Length Keys for Age Assignment

Provides methods for implementing hierarchical age length keys to estimate fish ages from lengths using data borrowing. Users can create hierarchical age length keys and use them to assign ages given length.

Authors:Paul Frater [aut, cre]

halk_0.0.5.tar.gz
halk_0.0.5.tar.gz(r-4.5-noble)halk_0.0.5.tar.gz(r-4.4-noble)
halk_0.0.5.tgz(r-4.4-emscripten)halk_0.0.5.tgz(r-4.3-emscripten)
halk.pdf |halk.html✨
halk/json (API)

# Install 'halk' in R:

install.packages('halk', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

laa_data - Example length-at-age data
laa_data_few_ages - Example length-at-age data
laa_data_low_age_n - Example length-at-age data
laa_data_low_n - Example length-at-age data
length_data - Example length data
spp_data - Example length-at-age data
spp_data_few_ages - Example length-at-age data
spp_data_low_age_n - Example length-at-age data
spp_data_low_n - Example length-at-age data
spp_length_data - Example length data
wb_spp_data - Separate species, county, waterbody example length-at-age and length data
wb_spp_laa_data - Separate species, county, waterbody example length-at-age and length data
wb_spp_length_data - Separate species, county, waterbody example length-at-age and length data

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

10 exports 0.09 score 21 dependencies 3 scripts 268 downloads

Last updated 10 months agofrom:029c2facb1. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 30 2024
R-4.5-linux	OK	Aug 30 2024

Exports:%>%assign_ages bin_lengths calc_chi_score calc_ks_score calc_mse calc_rmse integral_quotient make_alk make_halk

Dependencies:cli cpp11 dplyr fansi generics glue lifecycle magrittr pillar pkgconfig purrr R6 rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr

Introduction to the halk

Rendered fromhalk.Rmdusingknitr::rmarkdownon Aug 30 2024.

Last update: 2023-09-23
Started: 2023-02-13

Citation

Readme and manuals

Help Manual

Help page	Topics
Adjusts data to account for plus group or minimum age	adjust_ages adjust_plus_min_ages adjust_plus_min_ages_df
Convert ages from/to ordered factor	ages_as_integer ages_as_ordered ages_as_ordered_factor
Assign ages to non-aged data based on a fitted age model	assign_ages
Assign associated age-length key attributes to a data.frame	assign_alk_attributes
Simple function that returns NA values	assign_na_age
Convert a vector of lengths into binned values	bin_lengths
Calculate mean-squared-error (MSE) and root mean-squared-error (RMSE) of estimated ages	calc_mse calc_rmse
Backend helper function to compute MSE or RMSE	calc_mse_
Compute test statistics for comparing actual and estimated ages	calc_chi_score calc_ks_score calc_stat_scores
Check for age/length data in the data being estimated or predicted	check_agelen_data check_age_data check_length_data
Check the model type and return standardized version	check_model_type
Compute the quotient of integrals as a measure of percent error between two curves	integral_quotient
Example length-at-age data	laa_data laa_data_few_ages laa_data_low_age_n laa_data_low_n spp_data spp_data_few_ages spp_data_low_age_n spp_data_low_n
Example length data	length_data spp_length_data
Make an age-length key out of length-at-age data	make_alk
Create a hierarchical age-length key (HALK)	make_halk
Count number of length-at-age samples or age groups at each level and return those with greater than equal to the minimum desired number	min_age_groups min_count_laa_data min_samples
Simple helper function to rename size and age column names to age and length	rename_laa_cols
Check for species in columns and/or levels and add to levels if present	add_spp_level is_spp_in_data is_spp_in_levels rm_spp_level spp_level spp_levels
Separate species, county, waterbody example length-at-age and length data	wb_spp_data wb_spp_laa_data wb_spp_length_data