R/writeDABOM.R
In KevinSee/DABOM: Dam Adult Branch Occupancy Model
Defines functions
writeDABOM
Documented in
writeDABOM
#' @title Write DABOM JAGS model
#'
#' @description This writes the overall JAGS model for a generic DABOM as a text file. It can then be modified depending on the observations for a particular valid tag list.
#'
#' @author Kevin See
#'
#' @param file_name name (with file path) to save the model as
#' @param time_varying Should the initial movement probabilities be time-varying? Default value is `FALSE`
#'
#' @inheritParams createDABOMcapHist
#'
#' @import dplyr stringr PITcleanr
#' @export
#' @return NULL
#' @examples writeDABOM()
writeDABOM = function(file_name = NULL,
parent_child = NULL,
configuration = NULL,
time_varying = FALSE) {
if(is.null(file_name)) file_name = 'DABOM.txt'
node_order = PITcleanr::buildNodeOrder(parent_child,
direction = "u")
# determine starting point (root_site)
root_site = node_order %>%
filter(node_order == 1) %>%
pull(node)
# how many nodes does each site have, what are their names and what column are they contained in?
# node_info = DABOM::getNodeInfo(parent_child,
# configuration)
node_info = PITcleanr::getNodeInfo(parent_child,
configuration) |>
filter(site_code != root_site)
# how many child sites does each parent site have?
parent_info = parent_child %>%
group_by(parent) %>%
mutate(n_child = n_distinct(child)) %>%
ungroup()
#--------------------------------------------
# write JAGS model
#--------------------------------------------
# open a connection to new model file
mod_conn = file(file_name, open = 'w')
write("model {\n",
mod_conn)
# detection priors
write("# Priors for detection probabilities \n",
mod_conn,
append = T)
node_info %>%
filter(site_code != root_site) %>%
mutate(prior = paste0("\t ", node, "_p ~ dbeta(1, 1);")) %>%
pull(prior) %>%
paste(collapse = "\n") %>%
write(file = mod_conn,
append = T)
# setting priors and matrices for transition probabilities
write("\n# Priors for transition probabilities \n",
mod_conn,
append = T)
for(site in unique(parent_info$parent)) {
n_branch = parent_info %>%
filter(parent == site) %>%
pull(n_child) %>%
unique()
if(n_branch == 1) {
move_prior_text = paste0("\t phi_", site, "[1] ~ dbeta(1, 1); \n",
"\t phi_", site, "[2] ~ dbeta(1, 1); \n")
} else {
move_prior_text = paste0("\t psi_", site, "[1, 1:n_branch_", site, "] ~ ddirch(", site, "_dirch_vec[1,]); \n",
"\t psi_", site, "[2, 1:n_branch_", site, "] ~ ddirch(", site, "_dirch_vec[2,]); \n",
"\n",
"\t omega_", site, "[1, 1:n_branch_", site, "] <- zero_vec[1:(n_branch_", site, ")]; \n",
"\t omega_", site, "[1, (n_branch_", site, " + 1)] <- 1; \n",
"\n",
"\t omega_", site, "[2, 1:n_branch_", site, "] <- psi_", site, "[1,]; \n",
"\t omega_", site, "[2, (n_branch_", site, " + 1)] <- 0; \n",
"\n",
"\t omega_", site, "[3, 1:n_branch_", site, "] <- psi_", site, "[2,]; \n",
"\t omega_", site, "[3, (n_branch_", site, " + 1)] <- 0; \n")
}
write(move_prior_text,
file = mod_conn,
append = T)
suppressWarnings(rm(n_branch))
}
# Where is each fish?
write(paste0("# Where is each fish? \n\n",
"\t for(i in 1:n_fish) { \n",
"\n"),
mod_conn,
append = T)
for(site in unique(parent_info$parent)) {
# how many branches past this site?
n_branch = parent_info %>%
filter(parent == site) %>%
pull(n_child) %>%
unique()
# what is the parent site?
parent_site = node_info %>%
filter(site_code == site) %>%
pull(parent_site) %>%
unique()
# what is the branch number of this site from its parent?
child_num = node_info %>%
filter(site_code == site) %>%
pull(child_num) %>%
unique()
# how many children does parent site have?
if(length(parent_site) > 0) {
# if(!is.na(parent_site)) {
parent_n_child = parent_info %>%
filter(parent == parent_site) %>%
pull(n_child) %>%
unique()
} else {
parent_n_child = 0
}
if(n_branch == 1) {
if(parent_n_child > 1) {
fish_pos_text = paste0("\t\t eta_", site, "[i] ~ dbern(eta_", parent_site, "[i, ", child_num, "] * phi_", site, "[fish_type[i]]) \n")
} else if(parent_n_child == 1) {
fish_pos_text = paste0("\t\t eta_", site, "[i] ~ dbern(eta_", parent_site, "[i] * phi_", site, "[fish_type[i]]) \n")
} else if(parent_n_child == 0) {
fish_pos_text = paste0("\t\t eta_", site, "[i] ~ dbern(phi_", site, "[fish_type[i]]) \n")
}
}
if(n_branch > 1) {
if(length(child_num) > 0) {
# if(!is.na(child_num)) {
if(parent_n_child == 1) {
a_line = paste0("\t\t a_", site, "[i] ~ dcat( omega_", site, "[(eta_", parent_site, "[i] * fish_type[i] + 1), 1:(n_branch_", site, "+1)] ) \n")
} else {
a_line = paste0("\t\t a_", site, "[i] ~ dcat( omega_", site, "[(eta_", parent_site, "[i,", child_num, "] * fish_type[i] + 1), 1:(n_branch_", site, "+1)] ) \n")
}
fish_pos_text = paste0(a_line,
"\t\t\t for (j in 1:n_branch_", site, ") { \n",
"\t\t\t\t eta_", site, "[i,j] <- equals(a_", site, "[i],j) # equals(x,y) is a test for equality, returns [1,0] \n",
"\t\t\t }\n")
} else {
fish_pos_text = paste0("\t\t a_", site, "[i] ~ dcat( omega_", site, "[fish_type[i] + 1, 1:(n_branch_", site, "+1)] ) \n",
"\t\t\t for (j in 1:n_branch_", site, ") { \n",
"\t\t\t\t eta_", site, "[i,j] <- equals(a_", site, "[i],j) # equals(x,y) is a test for equality, returns [1,0] \n",
"\t\t\t }\n")
}
}
write(fish_pos_text,
file = mod_conn,
append = T)
suppressWarnings(rm(n_branch,
parent_site,
child_num,
parent_n_child,
a_line,
fish_pos_text))
}
write("\t} # end the n_fish loop \n",
file = mod_conn,
append = T)
# detection
write(paste0("\n# Were tags observed? \n\n",
"\t for (i in 1:n_fish) {\n"),
file = mod_conn,
append = T)
for(site in unique(node_info$site_code)) {
node_df = node_info %>%
filter(site_code == site)
# find parent site
parent_site = node_df %>%
select(child = site_code) %>%
distinct() %>%
left_join(parent_child,
by = "child") %>%
pull(parent)
dwn_site_pc = parent_child %>%
left_join(node_order,
by = join_by(child == node)) |>
arrange(path, node_order) %>%
filter(parent == parent_site)
if(nrow(dwn_site_pc) == 1) {
for(j in 1:nrow(node_df)) {
paste0("\t\t cap_hist[i,", node_df$matrix_col[j], "] ~ dbern( ", node_df$node[j], "_p * eta_", parent_site, "[i] );\n") %>%
write(file = mod_conn,
append = T)
}
} else {
child_num = dwn_site_pc %>%
mutate(id = 1:n()) %>%
filter(child == node_df$site_code[1]) %>%
pull(id)
for(j in 1:nrow(node_df)) {
paste0("\t\t cap_hist[i,", node_df$matrix_col[j], "] ~ dbern( ", node_df$node[j], "_p * eta_", parent_site, "[i,", child_num, "] );\n") %>%
write(file = mod_conn,
append = T)
}
}
suppressWarnings(rm(node_df,
parent_site,
dwn_site_pc,
child_num))
}
write(paste0("\t} # end the n_fish loop \n",
"}"),
file = mod_conn,
append = T)
close(mod_conn)
if(time_varying) {
mod_conn_init = file(file_name, open = 'r+')
# read in text file
mod_file_org = readLines(mod_conn_init)
# save a version of original
mod_file = mod_file_org
new_prior_text = paste0("\t # Set up time-varying movement probabilities for the initial branches\n",
"\t # i indexes the origin of fish (wild/hatchery)\n",
"\t # j indexes the branch\n",
"\t # t indexes the time strata (e.g. week)\n\n",
"\t # prior on log odds ratio for initial week \n",
"\t for(i in 1:2) { \n",
"\t\t for(j in 1:(n_branch_", root_site, " - 1)) { \n",
"\t\t # somewhat informative, but fairly vague prior \n",
"\t\t\t lambda[i,j,1] ~ dnorm(-2, 1/16); \n",
"\t\t\t exp_lambda[i,j,1] <- exp(lambda[i,j,1]) * ", root_site, "_dirch_vec[i,j];\n",
"\t\t }\n",
"\t\t # set black box as baseline \n",
"\t\t for(t in 1:(n_strata)) { \n",
"\t\t\t lambda[i,n_branch_", root_site, ", t] <- 0; \n",
"\t\t\t exp_lambda[i,n_branch_", root_site, ", t] <- exp(lambda[i,n_branch_", root_site, ", t]) * ", root_site, "_dirch_vec[i,n_branch_", root_site, "]; \n",
"\t\t\t # get sum of all lambda's \n",
"\t\t\t sum_exp_lambda[i,t] <- sum(exp_lambda[i,,t]); \n",
"\t\t }\n",
"\t }\n",
"\n",
"\t # extract initial movement probabilities for week 1 \n",
"\t for(i in 1:2) { \n",
"\t\t for(j in 1:n_branch_", root_site, ") { \n",
"\t\t\t psi_", root_site, "[i,j,1] <- ifelse(", root_site, "_dirch_vec[i,j] == 0, 0, exp_lambda[i,j,1] / sum_exp_lambda[i,1]); \n",
"\t\t }\n",
"\t }\n",
"\t # variation in time-varying random walk movement probabilities \n",
"\t sigma_rw ~ dunif(0,10); \n",
"\t tau_rw <- pow(sigma_rw, -2); \n",
"\n",
"\t for(i in 1:2) { \n",
"\t\t for(t in 2:(n_strata)) { \n",
"\t\t\t for(j in 1:(n_branch_", root_site, " - 1)) { \n",
"\t\t\t\t epsilon[i,j,t] ~ dnorm(0, tau_rw); \n",
"\t\t\t\t # set lambda to any main bin that saw NO fish to 0 \n",
"\t\t\t\t lambda[i,j,t] <- ifelse(", root_site, "_dirch_vec[i,j] == 0, 0, lambda[i,j,t - 1] + epsilon[i,j,t]); \n",
"\t\t\t\t exp_lambda[i,j,t] <- exp(lambda[i,j,t]) * ", root_site, "_dirch_vec[i,j]; \n",
"\t\t\t }\n",
"\t\t\t for (j in 1:(n_branch_", root_site, ")) { \n",
"\t\t\t\t psi_", root_site, "[i,j,t] <- (exp_lambda[i,j,t] / sum_exp_lambda[i,t]); \n",
"\t\t\t }\n",
"\t\t }\n",
"\t }\n",
"\n",
"\t for(t in 1:n_strata) { \n",
"\t\t omega_", root_site, "[1, 1:n_branch_", root_site, ", t] <- zero_vec[1:(n_branch_", root_site, ")]; \n",
"\t\t omega_", root_site, "[1, (n_branch_", root_site, " + 1), t] <- 1; \n",
"\n",
"\t\t omega_", root_site, "[2, 1:n_branch_", root_site, ", t] <- psi_", root_site, "[1,,t]; \n",
"\t\t omega_", root_site, "[2, (n_branch_", root_site, " + 1), t] <- 0; \n",
"\n",
"\t\t omega_", root_site, "[3, 1:n_branch_", root_site, ", t] <- psi_", root_site, "[2,,t]; \n",
"\t\t omega_", root_site, "[3, (n_branch_", root_site, " + 1), t] <- 0; \n",
"\t }\n")
# where in the model file are the priors that need to be replace?
line_range = range(str_which(mod_file, paste0('psi_', root_site)))
# drop all those lines but the first (including one addtional line at the end)
mod_file = mod_file[-c((line_range[1]+1):(line_range[2]+1))]
# replace first line with new text
mod_file[line_range[1]] = new_prior_text
# in the "where are the fish" section, be sure to index the dam_strata
mod_file[str_which(mod_file, paste0("a_", root_site, "\\[i\\] ~ dcat"))] = paste0("\t\t a_", root_site, "[i] ~ dcat( omega_", root_site, "[fish_type[i] + 1, 1:(n_branch_", root_site, "+1), dam_strata[i]] )")
# overwrite text file
writeLines(mod_file, mod_conn_init)
close(mod_conn_init)
rm(mod_conn_init)
}
}
KevinSee/DABOM documentation built on April 4, 2024, 9:28 a.m.
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Defines functions writeDABOM
Documented in writeDABOM
#' @title Write DABOM JAGS model
#'
#' @description This writes the overall JAGS model for a generic DABOM as a text file. It can then be modified depending on the observations for a particular valid tag list.
#'
#' @author Kevin See
#'
#' @param file_name name (with file path) to save the model as
#' @param time_varying Should the initial movement probabilities be time-varying? Default value is `FALSE`
#'
#' @inheritParams createDABOMcapHist
#'
#' @import dplyr stringr PITcleanr
#' @export
#' @return NULL
#' @examples writeDABOM()
writeDABOM = function(file_name = NULL,
parent_child = NULL,
configuration = NULL,
time_varying = FALSE) {
if(is.null(file_name)) file_name = 'DABOM.txt'
node_order = PITcleanr::buildNodeOrder(parent_child,
direction = "u")
# determine starting point (root_site)
root_site = node_order %>%
filter(node_order == 1) %>%
pull(node)
# how many nodes does each site have, what are their names and what column are they contained in?
# node_info = DABOM::getNodeInfo(parent_child,
# configuration)
node_info = PITcleanr::getNodeInfo(parent_child,
configuration) |>
filter(site_code != root_site)
# how many child sites does each parent site have?
parent_info = parent_child %>%
group_by(parent) %>%
mutate(n_child = n_distinct(child)) %>%
ungroup()
#--------------------------------------------
# write JAGS model
#--------------------------------------------
# open a connection to new model file
mod_conn = file(file_name, open = 'w')
write("model {\n",
mod_conn)
# detection priors
write("# Priors for detection probabilities \n",
mod_conn,
append = T)
node_info %>%
filter(site_code != root_site) %>%
mutate(prior = paste0("\t ", node, "_p ~ dbeta(1, 1);")) %>%
pull(prior) %>%
paste(collapse = "\n") %>%
write(file = mod_conn,
append = T)
# setting priors and matrices for transition probabilities
write("\n# Priors for transition probabilities \n",
mod_conn,
append = T)
for(site in unique(parent_info$parent)) {
n_branch = parent_info %>%
filter(parent == site) %>%
pull(n_child) %>%
unique()
if(n_branch == 1) {
move_prior_text = paste0("\t phi_", site, "[1] ~ dbeta(1, 1); \n",
"\t phi_", site, "[2] ~ dbeta(1, 1); \n")
} else {
move_prior_text = paste0("\t psi_", site, "[1, 1:n_branch_", site, "] ~ ddirch(", site, "_dirch_vec[1,]); \n",
"\t psi_", site, "[2, 1:n_branch_", site, "] ~ ddirch(", site, "_dirch_vec[2,]); \n",
"\n",
"\t omega_", site, "[1, 1:n_branch_", site, "] <- zero_vec[1:(n_branch_", site, ")]; \n",
"\t omega_", site, "[1, (n_branch_", site, " + 1)] <- 1; \n",
"\n",
"\t omega_", site, "[2, 1:n_branch_", site, "] <- psi_", site, "[1,]; \n",
"\t omega_", site, "[2, (n_branch_", site, " + 1)] <- 0; \n",
"\n",
"\t omega_", site, "[3, 1:n_branch_", site, "] <- psi_", site, "[2,]; \n",
"\t omega_", site, "[3, (n_branch_", site, " + 1)] <- 0; \n")
}
write(move_prior_text,
file = mod_conn,
append = T)
suppressWarnings(rm(n_branch))
}
# Where is each fish?
write(paste0("# Where is each fish? \n\n",
"\t for(i in 1:n_fish) { \n",
"\n"),
mod_conn,
append = T)
for(site in unique(parent_info$parent)) {
# how many branches past this site?
n_branch = parent_info %>%
filter(parent == site) %>%
pull(n_child) %>%
unique()
# what is the parent site?
parent_site = node_info %>%
filter(site_code == site) %>%
pull(parent_site) %>%
unique()
# what is the branch number of this site from its parent?
child_num = node_info %>%
filter(site_code == site) %>%
pull(child_num) %>%
unique()
# how many children does parent site have?
if(length(parent_site) > 0) {
# if(!is.na(parent_site)) {
parent_n_child = parent_info %>%
filter(parent == parent_site) %>%
pull(n_child) %>%
unique()
} else {
parent_n_child = 0
}
if(n_branch == 1) {
if(parent_n_child > 1) {
fish_pos_text = paste0("\t\t eta_", site, "[i] ~ dbern(eta_", parent_site, "[i, ", child_num, "] * phi_", site, "[fish_type[i]]) \n")
} else if(parent_n_child == 1) {
fish_pos_text = paste0("\t\t eta_", site, "[i] ~ dbern(eta_", parent_site, "[i] * phi_", site, "[fish_type[i]]) \n")
} else if(parent_n_child == 0) {
fish_pos_text = paste0("\t\t eta_", site, "[i] ~ dbern(phi_", site, "[fish_type[i]]) \n")
}
}
if(n_branch > 1) {
if(length(child_num) > 0) {
# if(!is.na(child_num)) {
if(parent_n_child == 1) {
a_line = paste0("\t\t a_", site, "[i] ~ dcat( omega_", site, "[(eta_", parent_site, "[i] * fish_type[i] + 1), 1:(n_branch_", site, "+1)] ) \n")
} else {
a_line = paste0("\t\t a_", site, "[i] ~ dcat( omega_", site, "[(eta_", parent_site, "[i,", child_num, "] * fish_type[i] + 1), 1:(n_branch_", site, "+1)] ) \n")
}
fish_pos_text = paste0(a_line,
"\t\t\t for (j in 1:n_branch_", site, ") { \n",
"\t\t\t\t eta_", site, "[i,j] <- equals(a_", site, "[i],j) # equals(x,y) is a test for equality, returns [1,0] \n",
"\t\t\t }\n")
} else {
fish_pos_text = paste0("\t\t a_", site, "[i] ~ dcat( omega_", site, "[fish_type[i] + 1, 1:(n_branch_", site, "+1)] ) \n",
"\t\t\t for (j in 1:n_branch_", site, ") { \n",
"\t\t\t\t eta_", site, "[i,j] <- equals(a_", site, "[i],j) # equals(x,y) is a test for equality, returns [1,0] \n",
"\t\t\t }\n")
}
}
write(fish_pos_text,
file = mod_conn,
append = T)
suppressWarnings(rm(n_branch,
parent_site,
child_num,
parent_n_child,
a_line,
fish_pos_text))
}
write("\t} # end the n_fish loop \n",
file = mod_conn,
append = T)
# detection
write(paste0("\n# Were tags observed? \n\n",
"\t for (i in 1:n_fish) {\n"),
file = mod_conn,
append = T)
for(site in unique(node_info$site_code)) {
node_df = node_info %>%
filter(site_code == site)
# find parent site
parent_site = node_df %>%
select(child = site_code) %>%
distinct() %>%
left_join(parent_child,
by = "child") %>%
pull(parent)
dwn_site_pc = parent_child %>%
left_join(node_order,
by = join_by(child == node)) |>
arrange(path, node_order) %>%
filter(parent == parent_site)
if(nrow(dwn_site_pc) == 1) {
for(j in 1:nrow(node_df)) {
paste0("\t\t cap_hist[i,", node_df$matrix_col[j], "] ~ dbern( ", node_df$node[j], "_p * eta_", parent_site, "[i] );\n") %>%
write(file = mod_conn,
append = T)
}
} else {
child_num = dwn_site_pc %>%
mutate(id = 1:n()) %>%
filter(child == node_df$site_code[1]) %>%
pull(id)
for(j in 1:nrow(node_df)) {
paste0("\t\t cap_hist[i,", node_df$matrix_col[j], "] ~ dbern( ", node_df$node[j], "_p * eta_", parent_site, "[i,", child_num, "] );\n") %>%
write(file = mod_conn,
append = T)
}
}
suppressWarnings(rm(node_df,
parent_site,
dwn_site_pc,
child_num))
}
write(paste0("\t} # end the n_fish loop \n",
"}"),
file = mod_conn,
append = T)
close(mod_conn)
if(time_varying) {
mod_conn_init = file(file_name, open = 'r+')
# read in text file
mod_file_org = readLines(mod_conn_init)
# save a version of original
mod_file = mod_file_org
new_prior_text = paste0("\t # Set up time-varying movement probabilities for the initial branches\n",
"\t # i indexes the origin of fish (wild/hatchery)\n",
"\t # j indexes the branch\n",
"\t # t indexes the time strata (e.g. week)\n\n",
"\t # prior on log odds ratio for initial week \n",
"\t for(i in 1:2) { \n",
"\t\t for(j in 1:(n_branch_", root_site, " - 1)) { \n",
"\t\t # somewhat informative, but fairly vague prior \n",
"\t\t\t lambda[i,j,1] ~ dnorm(-2, 1/16); \n",
"\t\t\t exp_lambda[i,j,1] <- exp(lambda[i,j,1]) * ", root_site, "_dirch_vec[i,j];\n",
"\t\t }\n",
"\t\t # set black box as baseline \n",
"\t\t for(t in 1:(n_strata)) { \n",
"\t\t\t lambda[i,n_branch_", root_site, ", t] <- 0; \n",
"\t\t\t exp_lambda[i,n_branch_", root_site, ", t] <- exp(lambda[i,n_branch_", root_site, ", t]) * ", root_site, "_dirch_vec[i,n_branch_", root_site, "]; \n",
"\t\t\t # get sum of all lambda's \n",
"\t\t\t sum_exp_lambda[i,t] <- sum(exp_lambda[i,,t]); \n",
"\t\t }\n",
"\t }\n",
"\n",
"\t # extract initial movement probabilities for week 1 \n",
"\t for(i in 1:2) { \n",
"\t\t for(j in 1:n_branch_", root_site, ") { \n",
"\t\t\t psi_", root_site, "[i,j,1] <- ifelse(", root_site, "_dirch_vec[i,j] == 0, 0, exp_lambda[i,j,1] / sum_exp_lambda[i,1]); \n",
"\t\t }\n",
"\t }\n",
"\t # variation in time-varying random walk movement probabilities \n",
"\t sigma_rw ~ dunif(0,10); \n",
"\t tau_rw <- pow(sigma_rw, -2); \n",
"\n",
"\t for(i in 1:2) { \n",
"\t\t for(t in 2:(n_strata)) { \n",
"\t\t\t for(j in 1:(n_branch_", root_site, " - 1)) { \n",
"\t\t\t\t epsilon[i,j,t] ~ dnorm(0, tau_rw); \n",
"\t\t\t\t # set lambda to any main bin that saw NO fish to 0 \n",
"\t\t\t\t lambda[i,j,t] <- ifelse(", root_site, "_dirch_vec[i,j] == 0, 0, lambda[i,j,t - 1] + epsilon[i,j,t]); \n",
"\t\t\t\t exp_lambda[i,j,t] <- exp(lambda[i,j,t]) * ", root_site, "_dirch_vec[i,j]; \n",
"\t\t\t }\n",
"\t\t\t for (j in 1:(n_branch_", root_site, ")) { \n",
"\t\t\t\t psi_", root_site, "[i,j,t] <- (exp_lambda[i,j,t] / sum_exp_lambda[i,t]); \n",
"\t\t\t }\n",
"\t\t }\n",
"\t }\n",
"\n",
"\t for(t in 1:n_strata) { \n",
"\t\t omega_", root_site, "[1, 1:n_branch_", root_site, ", t] <- zero_vec[1:(n_branch_", root_site, ")]; \n",
"\t\t omega_", root_site, "[1, (n_branch_", root_site, " + 1), t] <- 1; \n",
"\n",
"\t\t omega_", root_site, "[2, 1:n_branch_", root_site, ", t] <- psi_", root_site, "[1,,t]; \n",
"\t\t omega_", root_site, "[2, (n_branch_", root_site, " + 1), t] <- 0; \n",
"\n",
"\t\t omega_", root_site, "[3, 1:n_branch_", root_site, ", t] <- psi_", root_site, "[2,,t]; \n",
"\t\t omega_", root_site, "[3, (n_branch_", root_site, " + 1), t] <- 0; \n",
"\t }\n")
# where in the model file are the priors that need to be replace?
line_range = range(str_which(mod_file, paste0('psi_', root_site)))
# drop all those lines but the first (including one addtional line at the end)
mod_file = mod_file[-c((line_range[1]+1):(line_range[2]+1))]
# replace first line with new text
mod_file[line_range[1]] = new_prior_text
# in the "where are the fish" section, be sure to index the dam_strata
mod_file[str_which(mod_file, paste0("a_", root_site, "\\[i\\] ~ dcat"))] = paste0("\t\t a_", root_site, "[i] ~ dcat( omega_", root_site, "[fish_type[i] + 1, 1:(n_branch_", root_site, "+1), dam_strata[i]] )")
# overwrite text file
writeLines(mod_file, mod_conn_init)
close(mod_conn_init)
rm(mod_conn_init)
}
}
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