.Rhistory (Chriss-MacBook-Pro.local's conflicted copy 2020-03-18)

preds_long <- preds_merged %>%
# Rename columns
rename(species_orig=X, species_closest=closestSp,
value=predVal, value_lo=lcl_predInt, value_hi=ucl_predInt) %>%
# Format columns
mutate(species_orig=gsub("_", " ", species_orig),
species_closest=gsub("_", " ", species_closest)) %>%
# Add nutrient
left_join(file_key, by="file") %>%
# Add units
left_join(select(key, type, nutrient, units), by="nutrient") %>%
mutate(nutrient_unit=paste0(nutrient, " (", units, ")")) %>%
# Rearrange columns
select(file, type, nutrient_unit, nutrient, units, everything())
# Reshape data
preds_wide <- preds_long %>%
select(nutrient, species_orig, value) %>%
spread(key="nutrient", value="value") %>%
# Rename columns
rename(protein_g="Protein",
fat_g="Total fat",
omega3_g="Omega-3 fatty acids",
omega6_g="Omega-6 fatty acids",
iron_mg="Iron",
zinc_mg="Zinc",
vitA_ug="Vitamin A",
vitB12_ug="Vitamin B12",
vitD_ug="Vitamin D")
# Check species names
spp_suggest_list <- freeR::suggest_names(preds_wide$species_orig)
spp_key <- tibble(species_orig=names(spp_suggest_list), species=NA)
for(i in 1:nrow(spp_key)){
spp_suggest <- spp_suggest_list[i][[1]]
spp_suggest1 <- ifelse(length(spp_suggest)==0, "", spp_suggest)
spp_key$species[i] <- spp_suggest1
}
# Add correct names to data and continue to correct
preds_wide1 <- preds_wide %>%
left_join(spp_key, by="species_orig") %>%
select(species, species_orig, everything()) %>%
mutate(species=ifelse(is.na(species), species_orig, species),
species=ifelse(species=="", species_orig, species)) %>%
mutate(species=recode(species,
# "Corydoras kristinae"="",
# "Cyprichromis jumbo"="",
# "Cyprichromis zebra"="",
"Hemibarbus longibarbis"="Hemibarbus maculatus",
# "Macrocephenchelys soela"="",
# "Puntius parvus"="",
"Sebastes marinus"="Sebastes norvegicus", # WORMS
"Takifugu fasciatus"="Takifugu fasciatus"))
# Check names
freeR::check_names(preds_wide1$species)
# Add commmon names
rfishbase::sci_to_common(preds_wide1$species)
?freeR::fishbase
# Check names
spp_key <- freeR::fishbase(dataset="species", species=preds_wide1$species, cleaned=T)
View(spp_key)
freeR::complete(spp_key)
# Try 1. FishBase species page
spp_key <- freeR::fishbase(dataset="species", species=species, cleaned=F)
species <- preds_wide1$species[1:20]
# Try 1. FishBase species page
spp_key <- freeR::fishbase(dataset="species", species=species, cleaned=F)
spp_key1 <- spp_key %>%
select(species, comm_name)
View(spp_key)
spp_key1 <- spp_key %>%
select(species, comm_name)
View(spp_key)
# Try 1. FishBase species page
spp_key <- freeR::fishbase(dataset="species", species=species, cleaned=T)
spp_key1 <- spp_key %>%
select(species, comm_name)
View(spp_key1)
spp_key1 <- spp_key %>%
select(species, comm_name) %>%
arrange(comm_name)
spp_key1 <- spp_key %>%
select(species, comm_name) %>%
arrange(comm_name)
# Try 2. FishBase common name page
spp_missing <- spp_key1$species[is.na(spp_key1$comm_name)]
spp_missing
?sci_to_common
spp_key2 <- rfishbase::sci_to_common(species_list=spp_missing, server = "fishbase")
View(spp_key2)
spp_key2_english <- spp_key2 %>%
filter(Language=="English") %>%
select(Species, CommName) %>%
rename(species=Species, comm_name=CommName)
spp_key2_english <- spp_key2 %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
View(spp_key2_english)
species <- preds_wide1$species[1:100]
# Try 1. FishBase species page
spp_key1_orig <- freeR::fishbase(dataset="species", species=species, cleaned=T)
spp_key1 <- spp_key1_orig %>%
select(species, comm_name) %>%
arrange(comm_name)
spp_key1
# Try 2. FishBase common name page
spp_missing_from_try1 <- spp_key1$species[is.na(spp_key1$comm_name)]
spp_missing_from_try1
spp_key2_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "fishbase")
spp_key2 <- spp_key2 %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
spp_missing_from_try1
# Try 2. FishBase common name page (English names)
spp_missing_from_try1 <- spp_key1$species[is.na(spp_key1$comm_name)]
spp_key2_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "fishbase")
spp_key2_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "fishbase")
spp_key2_orig
spp_key2_inv_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "sealifebase")
View(spp_key2_inv_orig)
spp_key2_orig <- rbind(spp_key2_fin_orig, spp_key2_inv_orig) %>%
filter(!is.na(ComName))
spp_key2_fin_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "fishbase")
spp_key2_orig <- rbind(spp_key2_fin_orig, spp_key2_inv_orig) %>%
filter(!is.na(ComName))
View(spp_key2_orig)
spp_key2_eng <- spp_key2_orig %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
View(spp_key2_english)
spp_key2_orig <- rbind(spp_key2_fin_orig, spp_key2_inv_orig) %>%
filter(!is.na(ComName))
spp_key2_eng <- spp_key2_orig %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
View(spp_key2_fin_orig)
rbind(spp_key2_fin_orig, spp_key2_inv_orig)
spp_key2_orig <- rbind(spp_key2_fin_orig, spp_key2_inv_orig) %>%
filter(!is.na(ComName))
View(spp_key2_orig)
spp_key2_eng <- spp_key2_orig %>%
filter(Language=="English")
table(spp_key2_orig$Language)
View(spp_key2_eng)
spp_key2_eng <- spp_key2_orig %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
spp_key1 <- spp_key1_orig %>%
select(species, comm_name) %>%
filter(!is.na(comm_name))
species[!species %in% spp_key1$species]
# Try 2. FishBase common name page (English names)
spp_missing_from_try1 <- species[!species %in% spp_key1$species]
# Try 3. FishBase common name page (not English)
spp_done <- c(spp_key1$species, spp_key2_eng$species)
spp_missing_from_try12 <- species[!species %in% spp_done]
spp_missing_from_try12
spp_key3_orig <- spp_key2_orig %>%
filter(Language!="English")
spp_key3_orig <- spp_key2_orig %>%
filter(species %in% spp_missing_from_try12)
spp_missing_from_try12 <- species[!species %in% spp_done]
spp_missing_from_try12
spp_key3_orig <- spp_key2_orig %>%
filter(species %in% spp_missing_from_try12)
spp_key3_orig <- spp_key2_orig %>%
filter(Species %in% spp_missing_from_try12)
View(spp_key3_orig)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(grepl("::punct::", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(grepl("[:punct:]", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(!grepl("[:punct:]", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(grepl("[:punct:]", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(grepl("[[:punct:]]", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(grepl("[:punct:]", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(!grepl("[:punct:]", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(!grepl("[[:punct:]]", Species))
View(spp_key3_orig)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with punctuation
filter(grepl("[[:punct:]]", Species))
!
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12)
View(spp_key3_orig)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(grepl("?", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(grepl("/?", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(grepl("\\?", Species))
View(spp_key3_orig)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(grepl("\?", Species))
?grepls
?grepl
grepl("\?", spp_key2_orig$Species)
grepl("\\?", spp_key2_orig$Species)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(grepl("\\?", Species))
str(spp_key2_orig)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(grepl("\\?", Species %>%  as.character()))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(grep("\\?", Species))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(grepl("\\?", ComName))
View(spp_key3_orig)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove species with ?s
filter(!grepl("\\?", ComName))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
filter(!grepl("[:punct:]", ComName))
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
# filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, ComName=comm_name)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
# filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
View(spp_key3_orig)
spp_key3_orig <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
View(spp_key3_orig)
spp_key3 <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
spp_key2 <- spp_key2_orig %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
spp_key2_orig <- rbind(spp_key2_fin_orig, spp_key2_inv_orig) %>%
filter(!is.na(ComName))
spp_key2 <- spp_key2_orig %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
# Try 3. FishBase common name page (not English)
spp_done <- c(spp_key1$species, spp_key2_eng$species)
spp_missing_from_try12 <- species[!species %in% spp_done]
spp_key3 <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
# Merge names
spp_key <- rbind(spp_key1, spp_key2, spp_key3)
anyDuplicated(spp_key$species)
View(spp_key)
spp_key3 <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
View(spp_key3)
spp_key3 <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName) %>%
ungroup()
# Merge names
spp_key <- rbind(spp_key1, spp_key2, spp_key3)
View(spp_key)
spp_key3 <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
# filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName) %>%
ungroup()
# Merge names
spp_key <- rbind(spp_key1, spp_key2, spp_key3)
# Try 1. FishBase species page
spp_key1_orig <- freeR::fishbase(dataset="species", species=species, cleaned=T)
spp_key1 <- spp_key1_orig %>%
select(species, comm_name) %>%
filter(!is.na(comm_name))
# Try 2. FishBase common name page (English names)
spp_missing_from_try1 <- species[!species %in% spp_key1$species]
spp_key2_fin_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "fishbase")
spp_key2_inv_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "sealifebase")
spp_key2_orig <- rbind(spp_key2_fin_orig, spp_key2_inv_orig) %>%
filter(!is.na(ComName))
spp_key2 <- spp_key2_orig %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
spp_missing_from_try1
species <- preds_wide1$species
# Try 1. FishBase species page
spp_key1_orig <- freeR::fishbase(dataset="species", species=species, cleaned=T)
spp_key1 <- spp_key1_orig %>%
select(species, comm_name) %>%
filter(!is.na(comm_name))
# Try 2. FishBase common name page (English names)
spp_missing_from_try1 <- species[!species %in% spp_key1$species]
spp_key2_fin_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "fishbase")
spp_key2_inv_orig <- rfishbase::sci_to_common(species_list= spp_missing_from_try1, server = "sealifebase")
spp_key2_orig <- rbind(spp_key2_fin_orig, spp_key2_inv_orig) %>%
filter(!is.na(ComName))
spp_key2 <- spp_key2_orig %>%
filter(Language=="English") %>%
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName)
# Try 3. FishBase common name page (not English)
spp_done <- c(spp_key1$species, spp_key2$species)
spp_missing_from_try12 <- species[!species %in% spp_done]
spp_key3 <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
# filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName) %>%
ungroup()
# Merge names
spp_key <- rbind(spp_key1, spp_key2, spp_key3)
spp_key3 <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName) %>%
ungroup()
# Merge names
spp_key <- rbind(spp_key1, spp_key2, spp_key3)
spp_key3 <- spp_key2_orig %>%
# Remove species already completed
filter(Species %in% spp_missing_from_try12) %>%
# Remove common name with ?s
filter(!grepl("\\?", ComName)) %>%
# Remove common names with punctuation
# filter(!grepl("[:punct:]", ComName)) %>%
# Take first option
group_by(Species) %>%
slice(1) %>%
# Format columns
select(Species, ComName) %>%
rename(species=Species, comm_name=ComName) %>%
ungroup()
# Merge names
spp_key <- rbind(spp_key1, spp_key2, spp_key3)
View(spp_key)
# Merge names
spp_key <- rbind(spp_key1, spp_key2, spp_key3) %>%
arrange(species)