Namespace clash

[cl-roberts]

Issue

The function compute.catch.biomass() is created twice; both instances produce the same outputs but take different inputs. In plotting/compute_plot_products.R the function takes a file path as input...

pws-herring-basa/plotting/compute_plot_products.R

Lines 61 to 92 in caef7da

	compute.catch.biomass <- function(model.dir, nyr, years){
	data <- read.data.files(model.dir)
	weight.at.age <- data$waa[1:nyr,]
	fb.nya <- data$foodbait_catch[1:nyr,]
	pound.nya <- data$pound_catch[1:nyr,]
	gillnet.nya <- data$gillnet_catch[1:nyr,]
	seine.yield <- data$seine_yield[1:nyr]
	fb.nya.biomass <- weight.at.age * fb.nya
	pound.nya.biomass <- weight.at.age * pound.nya
	gillnet.nya.biomass <- weight.at.age * gillnet.nya
	fb.biomass.annual <- rowSums(fb.nya.biomass) # Now sum the biomass over all age classes for each year
	pound.biomass.annual <- rowSums(pound.nya.biomass)
	gillnet.biomass.annual <- rowSums(gillnet.nya.biomass)
	fb.biomass.annual <- replace(fb.biomass.annual, fb.biomass.annual == 0, NA)
	pound.biomass.annual <- replace(pound.biomass.annual, pound.biomass.annual == 0, NA)
	gillnet.biomass.annual <- replace(gillnet.biomass.annual, gillnet.biomass.annual == 0, NA)
	seine.yield <- replace(seine.yield, seine.yield == 0, NA)
	# Matrix of catches by gear type in mt
	total.catch <- cbind(fb.biomass.annual, pound.biomass.annual, gillnet.biomass.annual, seine.yield)
	total.catch[is.na(total.catch)] <- 0
	total.catch.biomass <- rowSums(total.catch) # total catches by year in mt
	return(total.catch.biomass)
	}

...whereas the compute.catch.biomass() created in functions/fun_read_dat.R takes a data object.

pws-herring-basa/functions/fun_read_dat.R

Lines 133 to 162 in caef7da

	compute.catch.biomass <- function(data, nyr){
	weight.at.age <- data$waa[1:nyr,]
	fb.nya <- data$foodbait_catch[1:nyr,]
	pound.nya <- data$pound_catch[1:nyr,]
	gillnet.nya <- data$gillnet_catch[1:nyr,]
	seine.yield <- data$seine_yield[1:nyr]
	fb.nya.biomass <- weight.at.age * fb.nya
	pound.nya.biomass <- weight.at.age * pound.nya
	gillnet.nya.biomass <- weight.at.age * gillnet.nya
	fb.biomass.annual <- rowSums(fb.nya.biomass) # Now sum the biomass over all age classes for each year
	pound.biomass.annual <- rowSums(pound.nya.biomass)
	gillnet.biomass.annual <- rowSums(gillnet.nya.biomass)
	fb.biomass.annual <- replace(fb.biomass.annual, fb.biomass.annual == 0, NA)
	pound.biomass.annual <- replace(pound.biomass.annual, pound.biomass.annual == 0, NA)
	gillnet.biomass.annual <- replace(gillnet.biomass.annual, gillnet.biomass.annual == 0, NA)
	seine.yield <- replace(seine.yield, seine.yield == 0, NA)
	# Matrix of catches by gear type in mt
	total.catch <- cbind(fb.biomass.annual, pound.biomass.annual, gillnet.biomass.annual, seine.yield)
	total.catch[is.na(total.catch)] <- 0
	total.catch.biomass <- rowSums(total.catch) # total catches by year in mt
	return(total.catch.biomass)
	}

This throws in error when executing plotting/plot_management_outputs.R because the former script is sourced in line 4 but then supplies a data object to the function in line 52.

pws-herring-basa/plotting/plot_management_outputs.R

Line 4 in caef7da

source(file=paste0(here::here("plotting/", "compute_plot_products.R")))

pws-herring-basa/plotting/plot_management_outputs.R

Lines 51 to 52 in caef7da

	raw.data <- read.data.files(model.dir)
	total.catch.biomass <- compute.catch.biomass(raw.data$PWS_ASA.dat, nyr) %>% round(., 2)

Also note that plotting/compute_plot_products.R sources functions/fun_read_dat.R in line 3.

Solution

Resolve namespace clash. I commented out lines 61-92 in plotting/compute_plot_products.R to accommodate the use case in plotting/plot_management_outputs.R.