updating lifestage codes to newest set

inst/extdata/lifestage-codes.csv

@@ -1,65 +1,69 @@
-code,description_lifestage,simple_lifestage
---,Unspecified,adult
-AD,Adult,adult
-AL,Alevin,els
-BL,Blastula,els
-CS,Cleavage stage,els
-EG,Egg,els
-EL,Elver,juvenile
-EM,Embryo,els
-EX,Exponential growth phase (log),adult
-EY,"Eyed egg or stage, eyed embryo",els
-F0,F0 generation,adult
-F1,F1 generation,adult
-FI,Fingerling,juvenile
-FY,Fry,juvenile
-GA,Gastrula,els
-GE,Gestation,els
-GM,Gamete,els
-IM,Immature,juvenile
-JV,Juvenile,juvenile
-LC,Lactational,adult
-LR,Prolarva,els
-LV,Larva,els
-MA,Mature,adult
-ML,Morula,els
-MX,Multiple,adult
-NB,Newborn,els
-NC,Not coded,adult
-NE,Neonate,els
-NH,"New, newly or recent hatch",els
-NL,Neurala,els
-NOINT,Not intact,adult
-NR,Not reported,adult
-OO,"Oocyte, ova",els
-PA,Parr,juvenile
-PC,Pre-hatch,els
-PG,Post-spawning,adult
-PHT,Post-hatch,els
-PI,Post-molt,adult
-PJ,"Pre-, sub-, semi-, near adult, or peripubertal",juvenile
-PK,Post-smolt,juvenile
-PQ,Pre-larva,els
-PS,Pre-smolt,juvenile
-PT,Protolarvae,els
-PV,Post-larva,juvenile
-PW,Pre-spawning,adult
-RP,Mature reproductive,adult
-SA,Subadult,juvenile
-SC,"Yolk sac larvae, sac larvae",els
-SF,"Sac fry, yolk sac fry",els
-SI,Sexually immature,juvenile
-SM,Sexually mature,adult
-SMT,Smolt,juvenile
-SO,Sporeling,adult
-SP,Sperm,els
-SU,Swim-up,els
-SW,Spawning,adult
-TA,Tadpole,els
-UY,Underyearling,juvenile
-VI,Virgin,adult
-YA,Young adult,adult
-YE,Yearling,juvenile
-YO,Young,juvenile
-YY,Young of year,juvenile
-ZY,Zygote,els
+code,description_lifestage,simple_lifestage
+--,Unspecified,adult
+AD,Adult,adult
+AL,Alevin,els
+BL,Blastula,els
+CS,Cleavage stage,els
+EG,Egg,els
+EL,Elver,juvenile
+EM,Embryo,els
+EX,Exponential growth phase (log),adult
+EY,"Eyed egg or stage, eyed embryo",els
+F0,F0 generation,adult
+F1,F1 generation,adult
+F2,F2 generation,adult
+FI,Fingerling,juvenile
+FY,Fry,juvenile
+GA,Gastrula,els
+GE,Gestation,els
+GM,Gamete,els
+IM,Immature,juvenile
+JV,Juvenile,juvenile
+LC,Lactational,adult
+LR,Prolarva,els
+LV,Larva,els
+MA,Mature,adult
+ML,Morula,els
+MN,Mid-neurula,els
+MX,Multiple,adult
+NB,Newborn,els
+NC,Not coded,adult
+NE,Neonate,els
+NH,"New, newly or recent hatch",els
+NL,Neurala,els
+NOINT,Not intact,adult
+NR,Not reported,adult
+NU,Nauplii,els
+NY,Nymph,els
+OO,"Oocyte, ova",els
+PA,Parr,juvenile
+PC,Pre-hatch,els
+PG,Post-spawning,adult
+PHT,Post-hatch,els
+PI,Post-molt,adult
+PJ,"Pre-, sub-, semi-, near adult, or peripubertal",juvenile
+PK,Post-smolt,juvenile
+PQ,Pre-larva,els
+PS,Pre-smolt,juvenile
+PT,Protolarvae,els
+PV,Post-larva,juvenile
+PW,Pre-spawning,adult
+RP,Mature reproductive,adult
+SA,Subadult,juvenile
+SC,"Yolk sac larvae, sac larvae",els
+SF,"Sac fry, yolk sac fry",els
+SI,Sexually immature,juvenile
+SM,Sexually mature,adult
+SMT,Smolt,juvenile
+SO,Sporeling,adult
+SP,Sperm,els
+SU,Swim-up,els
+SW,Spawning,adult
+TA,Tadpole,els
+UY,Underyearling,juvenile
+VI,Virgin,adult
+YA,Young adult,adult
+YE,Yearling,juvenile
+YO,Young,juvenile
+YY,Young of year,juvenile
+ZY,Zygote,els

scripts/update-reference-datasets-02.R

@@ -47,7 +47,8 @@ reviewed_lifestage_code <-
   mutate(
     simple_lifestage = str_to_lower(simple_lifestage)
   ) |>
-  rename(description_lifestage = description)
+  rename(description_lifestage = description) |>
+  filter(fish_amphibian_flag)
 
 if (!vld_equal(sum(is.na(reviewed_lifestage_code$simple_lifestage[reviewed_lifestage_code$fish_amphibian_flag & !is.na(reviewed_lifestage_code$fish_amphibian_flag)])), 0)) {
   abort_chk("There should be no missing simple lifestage value, correct before proceeding")