R/writeLGRNodeNetwork.R
In BiomarkABS/PITcleanr: Cleans up PIT tag capture histories
Defines functions
writeLGRNodeNetwork
Documented in
writeLGRNodeNetwork
#' @title LGR Node Network
#'
#' @description Create data.frame describing all the observation nodes in the Lower Granite dam version of DABOM, including how they are related to one another
#'
#' @author Kevin See
#'
#'
#' @import dplyr stringr
#' @return NULL
#' @examples writeLGRNodeNetwork()
writeLGRNodeNetwork = function() {
bin_names = c('Clearwater',
'SW_Washington',
'NE_Oregon',
'Imnaha',
'Salmon')
bin_list = vector('list', length(bin_names))
names(bin_list) = bin_names
bin_list[['Clearwater']] = list('Lapwai' = list('LAP' =
list('LAP',
'MIS',
'SWT' =
list('SWT',
'WEB'))),
'Potlatch' = list('JUL' =
list('JUL',
'KHS' =
list('KHS',
'LBEARC',
'BIGBEC'),
'HLM' =
list('HLM',
'POTRWF',
'POTREF'),
'PCM')),
'Lolo' = list('LC1' =
list('LC1', 'LC2')),
'Lochsa' = list('LRL' =
list('LRL',
'LRU' =
list('LRU',
'FISTRP'))),
'SFClearwater' = list('SC1' =
list('SC1',
'SC2' =
list('SC2',
'CROTRP',
'CRT',
'REDTRP',
'REDR',
'RRT'))),
'ClearCreek' = list('CLC' =
list('CLC',
'KOOS')),
'Selway' = list('SW1' =
list('SW1',
'SW2'))
)
bin_list[['SW_Washington']] = list('Tucannon' =
list('LTR' =
list('LTR',
'MTR' =
list('MTR',
'UTR' =
list('UTR',
'TUCH',
'TFH')))),
'Almota' = list('ALMOTC'),
'Alpowa' = list('ALPOWC'),
'Penawawa' = list('PENAWC'),
'TenMileCreek' = list('TENMC2'),
'Asotin' = list('ACM' =
list('ACM',
'GEORGC',
'ASOTIC' =
list('ASOTIC',
'ACB' =
list('ACB',
'AFC',
'CCA')))))
bin_list[['NE_Oregon']] = list('JosephCreek' =
list('JOC' =
list('JOC',
'JOSEPC')),
'GrandeRonde' =
list('UpperGrandeRonde' =
list('UGR' =
list('UGR',
'CCW' =
list('CCW',
'CATHEW'),
'UGS' =
list('UGS',
'GRANDW')))),
'Wallowa' =
list('WR1' =
list('WR1',
'BCANF',
'WR2' =
list('WR2',
'LOSTIW',
'WALH'))),
'LookingGlass' =
list('LOOKGC',
'LOOH'),
'Wenaha' = list('WEN')
)
bin_list[['Imnaha']] = list('CowCreek' =
list('COC'),
'ImnahaRiver' =
list('IR1' =
list('IR1',
'IR2' =
list('IR2',
'CMP',
'BSC',
'LSHEEF',
'HORS3C',
'IR3' =
list('IR3',
'CZY',
'FREEZC',
'MAHOGC',
'IR4' =
list('IR4',
'IML' =
list('IML',
'IMNAHW' =
list('IMNAHW',
'IR5' =
list('IR5',
'GUMBTC',
'DRY2C')))))))))
bin_list[['Salmon']] = list('RapidRiver' =
list('RAPH',
'RPDTRP'),
'SFSalmon' =
list('SFG' =
list('SFG',
'ZEN' =
list('ZEN',
'LAKEC'),
'KRS' =
list('KRS',
'STR'),
'ESS' =
list('ESS',
'JOHNSC',
'YPP'))),
'BigCreek' =
list('TAY' =
list('TAY',
'BIG2C')),
'Panther' = list('PCA'),
'NFSalmon' =
list('NFS'),
'CarmenCreek' =
list('CRC'),
'Lemhi' =
list('LLR' =
list('LLR',
'AGC',
'KEN',
'HYC',
'WPC' =
list('WPC',
'WIMPYC'),
'BHC',
'LRW' =
list('LRW',
'LLS',
'BTL' =
list('BTL',
'BTM' =
list('BTM',
'BTU')),
'LCL',
'LB8',
'LBS',
'CAC',
'18M',
'HEC'))),
'UpperSalmon' = list('USE' =
list('USE',
'USI' =
list('USI',
'VC2' =
list('VC2',
'VC1'),
'YFK' =
list('YFK',
'YANKFK',
'CEY'),
'STL' =
list('STL',
'SAWT'),
'SALEFT',
'PAHH',
'RFL'))),
'BearValley' = list('BRC')
)
bin_all = list('GRA' =
list('GRA',
'Clearwater' = bin_list[['Clearwater']],
'SW_Washington' = bin_list[['SW_Washington']],
'NE_Oregon' = bin_list[['NE_Oregon']],
'Imnaha' = bin_list[['Imnaha']],
'Salmon' = bin_list[['Salmon']]))
site_df_init = tibble(SiteID = unlist(bin_all),
path = names(unlist(bin_all))) %>%
mutate(path = stringr::str_replace(path,
'[[:digit:]]$',
''),
path = stringr::str_replace(path,
'SC$',
'SC1'),
path = stringr::str_replace(path,
'USI1',
'USI'),
path = stringr::str_replace(path,
'LRW1',
'LRW'),
path = ifelse(SiteID %in% c('IR1', 'IR4'),
stringr::str_replace(path,
'IR$',
SiteID),
path)) %>%
mutate(path = ifelse(stringr::str_sub(path, start = -nchar(SiteID)) != SiteID,
paste(path, SiteID, sep = '.'),
path))
network_descrip = stringr::str_split(site_df_init$path,
'\\.',
simplify = T)
colnames(network_descrip) = paste0('Step', 1:ncol(network_descrip))
site_df = site_df_init %>%
bind_cols(network_descrip %>%
as.data.frame()) %>%
mutate(across(starts_with('Step'),
as.character)) %>%
mutate(SiteID = factor(SiteID,
levels = unique(site_df_init$SiteID))) %>%
arrange(SiteID)
return(site_df)
}
BiomarkABS/PITcleanr documentation built on Feb. 22, 2025, 9:21 a.m.
R Package Documentation
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Defines functions writeLGRNodeNetwork
Documented in writeLGRNodeNetwork
#' @title LGR Node Network
#'
#' @description Create data.frame describing all the observation nodes in the Lower Granite dam version of DABOM, including how they are related to one another
#'
#' @author Kevin See
#'
#'
#' @import dplyr stringr
#' @return NULL
#' @examples writeLGRNodeNetwork()
writeLGRNodeNetwork = function() {
bin_names = c('Clearwater',
'SW_Washington',
'NE_Oregon',
'Imnaha',
'Salmon')
bin_list = vector('list', length(bin_names))
names(bin_list) = bin_names
bin_list[['Clearwater']] = list('Lapwai' = list('LAP' =
list('LAP',
'MIS',
'SWT' =
list('SWT',
'WEB'))),
'Potlatch' = list('JUL' =
list('JUL',
'KHS' =
list('KHS',
'LBEARC',
'BIGBEC'),
'HLM' =
list('HLM',
'POTRWF',
'POTREF'),
'PCM')),
'Lolo' = list('LC1' =
list('LC1', 'LC2')),
'Lochsa' = list('LRL' =
list('LRL',
'LRU' =
list('LRU',
'FISTRP'))),
'SFClearwater' = list('SC1' =
list('SC1',
'SC2' =
list('SC2',
'CROTRP',
'CRT',
'REDTRP',
'REDR',
'RRT'))),
'ClearCreek' = list('CLC' =
list('CLC',
'KOOS')),
'Selway' = list('SW1' =
list('SW1',
'SW2'))
)
bin_list[['SW_Washington']] = list('Tucannon' =
list('LTR' =
list('LTR',
'MTR' =
list('MTR',
'UTR' =
list('UTR',
'TUCH',
'TFH')))),
'Almota' = list('ALMOTC'),
'Alpowa' = list('ALPOWC'),
'Penawawa' = list('PENAWC'),
'TenMileCreek' = list('TENMC2'),
'Asotin' = list('ACM' =
list('ACM',
'GEORGC',
'ASOTIC' =
list('ASOTIC',
'ACB' =
list('ACB',
'AFC',
'CCA')))))
bin_list[['NE_Oregon']] = list('JosephCreek' =
list('JOC' =
list('JOC',
'JOSEPC')),
'GrandeRonde' =
list('UpperGrandeRonde' =
list('UGR' =
list('UGR',
'CCW' =
list('CCW',
'CATHEW'),
'UGS' =
list('UGS',
'GRANDW')))),
'Wallowa' =
list('WR1' =
list('WR1',
'BCANF',
'WR2' =
list('WR2',
'LOSTIW',
'WALH'))),
'LookingGlass' =
list('LOOKGC',
'LOOH'),
'Wenaha' = list('WEN')
)
bin_list[['Imnaha']] = list('CowCreek' =
list('COC'),
'ImnahaRiver' =
list('IR1' =
list('IR1',
'IR2' =
list('IR2',
'CMP',
'BSC',
'LSHEEF',
'HORS3C',
'IR3' =
list('IR3',
'CZY',
'FREEZC',
'MAHOGC',
'IR4' =
list('IR4',
'IML' =
list('IML',
'IMNAHW' =
list('IMNAHW',
'IR5' =
list('IR5',
'GUMBTC',
'DRY2C')))))))))
bin_list[['Salmon']] = list('RapidRiver' =
list('RAPH',
'RPDTRP'),
'SFSalmon' =
list('SFG' =
list('SFG',
'ZEN' =
list('ZEN',
'LAKEC'),
'KRS' =
list('KRS',
'STR'),
'ESS' =
list('ESS',
'JOHNSC',
'YPP'))),
'BigCreek' =
list('TAY' =
list('TAY',
'BIG2C')),
'Panther' = list('PCA'),
'NFSalmon' =
list('NFS'),
'CarmenCreek' =
list('CRC'),
'Lemhi' =
list('LLR' =
list('LLR',
'AGC',
'KEN',
'HYC',
'WPC' =
list('WPC',
'WIMPYC'),
'BHC',
'LRW' =
list('LRW',
'LLS',
'BTL' =
list('BTL',
'BTM' =
list('BTM',
'BTU')),
'LCL',
'LB8',
'LBS',
'CAC',
'18M',
'HEC'))),
'UpperSalmon' = list('USE' =
list('USE',
'USI' =
list('USI',
'VC2' =
list('VC2',
'VC1'),
'YFK' =
list('YFK',
'YANKFK',
'CEY'),
'STL' =
list('STL',
'SAWT'),
'SALEFT',
'PAHH',
'RFL'))),
'BearValley' = list('BRC')
)
bin_all = list('GRA' =
list('GRA',
'Clearwater' = bin_list[['Clearwater']],
'SW_Washington' = bin_list[['SW_Washington']],
'NE_Oregon' = bin_list[['NE_Oregon']],
'Imnaha' = bin_list[['Imnaha']],
'Salmon' = bin_list[['Salmon']]))
site_df_init = tibble(SiteID = unlist(bin_all),
path = names(unlist(bin_all))) %>%
mutate(path = stringr::str_replace(path,
'[[:digit:]]$',
''),
path = stringr::str_replace(path,
'SC$',
'SC1'),
path = stringr::str_replace(path,
'USI1',
'USI'),
path = stringr::str_replace(path,
'LRW1',
'LRW'),
path = ifelse(SiteID %in% c('IR1', 'IR4'),
stringr::str_replace(path,
'IR$',
SiteID),
path)) %>%
mutate(path = ifelse(stringr::str_sub(path, start = -nchar(SiteID)) != SiteID,
paste(path, SiteID, sep = '.'),
path))
network_descrip = stringr::str_split(site_df_init$path,
'\\.',
simplify = T)
colnames(network_descrip) = paste0('Step', 1:ncol(network_descrip))
site_df = site_df_init %>%
bind_cols(network_descrip %>%
as.data.frame()) %>%
mutate(across(starts_with('Step'),
as.character)) %>%
mutate(SiteID = factor(SiteID,
levels = unique(site_df_init$SiteID))) %>%
arrange(SiteID)
return(site_df)
}
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