# Loading the data
library(dplyr)
library(assertr)
library(readr)
library(tidyr)
library(daff)
## read_csv2 uses ; as a field separator
#CPtrait <- read_csv2("data-raw/05_CPtrait.csv") %>%
#select(-`#`)
Alltraits <- read_csv("data-intermediate/11MD_trait.csv")
## read corrected
genus_updated <- read_csv2("data-intermediate/CPgenus_updated.csv", col_types = "_cnnn")
family_updated <- read_csv2("data-intermediate/CPfamily_updated.csv", col_types = "_cnnn")
# add traits by genus
by_genus <- left_join(Alltraits, genus_updated) %>%
verify(nrow(.) == nrow(Alltraits))
# count number of NAs by
by_genus$CPI1 %>%
is.na() %>% sum()
# add trait by family
by_family <- left_join(by_genus, family_updated, by = "family") %>%
verify(nrow(.) == nrow(Alltraits))
by_family_merged <- by_family %>%
mutate(CPF1 = ifelse(is.na(CPI1.x), CPI1.y, CPI1.x)) %>%
mutate(CPF2 = ifelse(is.na(CPI2.x), CPI2.y, CPI2.x)) %>%
mutate(CPF3 = ifelse(is.na(CPI3.x), CPI3.y, CPI3.x)) %>%
select(-starts_with("CPI")) %>%
rename(CP1 = CPF1, CP2 = CPF2, CP3 = CPF3)
by_family_merged$CP1 %>%
is.na() %>% sum()
by_family_merged %>% glimpse()
stopifnot(nrow(by_family_merged) == nrow(Alltraits))
write.csv(by_family_merged, "data-intermediate/12CP_trait.csv", row.names = FALSE)
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