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(v1.7.0.9000) package size

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dr. M.S. (Matthijs) Berends
2021-05-30 22:14:38 +02:00
parent f1d9b489c5
commit f406319503
43 changed files with 305 additions and 283 deletions
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40
data-raw/reproduction_of_microorganisms.R
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@ -872,12 +872,12 @@ View(old_new)
# set new MO codes as names to existing data sets
rsi_translation$mo <- mo_name(rsi_translation$mo, language = NULL)
microorganisms.codes$mo <- mo_name(microorganisms.codes$mo, language = NULL)
microorganisms.translation <- AMR:::microorganisms.translation %>%
bind_rows(tibble(mo_old = AMR:::microorganisms.translation$mo_new, mo_new = mo_old)) %>%
filter(!mo_old %in% MOs$mo) %>%
mutate(mo_new = mo_name(mo_new, language = NULL)) %>%
bind_rows(old_new %>% select(mo_old, mo_new)) %>%
distinct(mo_old, .keep_all = TRUE)
# microorganisms.translation <- AMR:::microorganisms.translation %>%
# bind_rows(tibble(mo_old = AMR:::microorganisms.translation$mo_new, mo_new = mo_old)) %>%
# filter(!mo_old %in% MOs$mo) %>%
# mutate(mo_new = mo_name(mo_new, language = NULL)) %>%
# bind_rows(old_new %>% select(mo_old, mo_new)) %>%
# distinct(mo_old, .keep_all = TRUE)
# arrange the data sets to save
MOs <- MOs %>% arrange(fullname)
@ -911,23 +911,23 @@ devtools::load_all(".")
rsi_translation$mo <- as.mo(rsi_translation$mo)
microorganisms.codes$mo <- as.mo(microorganisms.codes$mo)
class(microorganisms.codes$mo) <- c("mo", "character")
microorganisms.translation <- microorganisms.translation %>%
# (to do: add last package version to column pkg_version)
left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
by = c("mo_new" = "fullname")) %>%
mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>%
left_join(microorganisms[, c("fullname", "mo")], # as is microorganisms
by = c("name" = "fullname")) %>%
select(mo_old, mo_new = mo) %>%
filter(!is.na(mo_old), !is.na(mo_new))
class(microorganisms.translation$mo_old) <- "character" # no class <mo> since those aren't valid MO codes
class(microorganisms.translation$mo_new) <- c("mo", "character")
# microorganisms.translation <- microorganisms.translation %>%
# # (to do: add last package version to column pkg_version)
# left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
# by = c("mo_new" = "fullname")) %>%
# mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>%
# left_join(microorganisms[, c("fullname", "mo")], # as is microorganisms
# by = c("name" = "fullname")) %>%
# select(mo_old, mo_new = mo) %>%
# filter(!is.na(mo_old), !is.na(mo_new))
# class(microorganisms.translation$mo_old) <- "character" # no class <mo> since those aren't valid MO codes
# class(microorganisms.translation$mo_new) <- c("mo", "character")
# save those to the package
usethis::use_data(rsi_translation, overwrite = TRUE, version = 2)
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
# saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
# to save microorganisms.translation internally to the package
source("data-raw/_internals.R")
# source("data-raw/_internals.R")
# load new data sets again
devtools::load_all(".")
@ -935,7 +935,7 @@ devtools::load_all(".")
# and check: these codes should not be missing (will otherwise throw a unit test error):
AMR::microorganisms.codes %>% filter(!mo %in% MOs$mo)
AMR::rsi_translation %>% filter(!mo %in% MOs$mo)
AMR:::microorganisms.translation %>% filter(!mo_new %in% MOs$mo)
# AMR:::microorganisms.translation %>% filter(!mo_new %in% MOs$mo)
# update the example_isolates data set
example_isolates$mo <- as.mo(example_isolates$mo)