biotechs_conosur_explore.Rmd

---
title: "Biotechs Conosur"
editor_options: 
  chunk_output_type: console
---

## Session setup

```{r setup}
pacman::p_load(tidyverse)
# pacman::p_load(tidyverse) # only explore after querying 
# conflicted::conflict_prefer("filter", "dplyr")
```

```{r}
biotech_conosur <- readr::read_csv("data/biotech_conosur_2024-06-26.csv")
dat <- readr::read_csv("data/plagas_conosur_23.csv")
```

```{r eval=FALSE}
dat %>% glimpse
```

```{r eval=FALSE}
biotech_conosur %>% 
  count(FIELD_plantingSeason) 
```

## Spodoptera

```{r}
spod <- dat %>% 
  # count(FIELD_plantingDate, OBS_observationRefCd) %>% 
  filter(str_detect(OBS_observationRefCd, "DSSF|SF9_SUB")) # %>% mutate(RDR_damage_class=NA, EAR_damage_class=NA)

spod |> distinct(OBS_observationRefCd, OBS_descriptorAbbreviation)
```

```{r eval=FALSE}
hibs <- c("DK7272TRE", "DK7210PRO4", "DK7210RR2", "DK7272VT3P", "NEXT226PWUE", "NK842VIPTERA3")

spod %>% 
  filter(commercialName %in% hibs) %>% 
  ggplot()+
  facet_wrap("FIELD_pipeline") + 
  aes(y=commercialName, x=OBS_numValue) +
  geom_boxplot(alpha=.5) +
  # geom_(alpha=.5, height =.1) + 
  facet_grid(.~OBS_observationRefCd)
```

## Diatraea

Nro de orificios por tallo

```{r}
dia <- dat %>% 
  # count(FIELD_plantingDate, OBS_observationRefCd) %>% 
  filter(str_detect(OBS_observationRefCd, "NOHAS")) # %>% mutate(RDR_damage_class=NA, EAR_damage_class=NA)
```

```{r eval=FALSE}
hibs <- c("DK7272TRE", "DK7210PRO4", "DK7210RR2", "DK7272VT3P", "NEXT226PWUE", "NK842VIPTERA3")

dia %>% 
  filter(commercialName %in% "DK7210RR2") %>% 
# count(OBS_numValue)
  # filter(commercialName %in% hibs) %>% 
  ggplot()+
  aes(y=commercialName, x=OBS_numValue) +
  geom_boxplot(alpha=.5) +
  geom_point(alpha=.5, height =.1) + 
  facet_grid(.~OBS_observationRefCd)
```
 > hacer mapa


















```{r}
spod_veg %>% 
  pivot_wider(names_from = OBS_code, 
              values_from = OBS_numValue)-> spod_wide
```


```{r}
field = "ATUCK1_QUIMILI_RYK_F"	
season = "2020"	
hyb =	"DK7210VT3P"

biotech %>% 
  filter(FIELD_name==field, FIELD_plantingSeason==season, commercialName==hyb) %>% 
  select(FIELD_name, FIELD_plantingSeason, commercialName, OBS_code, OBS_numValue) %>% 
  arrange(OBS_code)
```

```{r}
pull(DSSFN)
  ggplot()+
  aes(x=DSSFN, y=DSSFP) +
  geom_point(alpha=.5) + 
  facet_grid(FIELD_Country~ FIELD_plantingSeason, scales="free")
```

```{r eval=FALSE}
spod_veg %>% 
  filter(OBS_numValue>100) %>% 
  select(FIELD_Country, FIELD_plantingSeason, FIELD_name, OBS_code, OBS_numValue)

field1 = "ATUCK1_RIOMUERTO_VICENTIN_F"	
season1 = "2020"	
# hyb =	"DK7210VT3P"

spod_veg %>% 
  filter(FIELD_name==field1, FIELD_plantingSeason==season1) %>% 
  select(FIELD_Country, FIELD_plantingSeason, FIELD_name, OBS_code, OBS_numValue) %>% 
  arrange(OBS_code) %>% 
  data.frame
```

```{r}
spod_veg %>% 
  filter(OBS_code=="DSSFN", FIELD_year==2023) %>% 
  select(FIELD_Country, FIELD_year, FIELD_name, OBS_code, OBS_numValue) %>% 
  data.frame

```

### Ear Damage

```{r}
ear_damage <- biotech_conosur %>% 
  filter(str_detect(OBS_code, "DAEAR|HZ9|SF9")) %>%
  filter(str_detect(OBS_code, "SUB")) # %>%
  # mutate(EAR_damage_class =
  #          cut(OBS_numValue, 
  #              breaks=c(-Inf, 0.01, 2, 4, Inf), 
  #              labels=c("No Damage","Low Damage","Medium Damage","High Damage"))
         # ) # %>% filter(!is.na(EAR_damage_class))
```

```{r eval=FALSE}
ear_damage %>% 
  ggplot()+
  aes(x=OBS_numValue, OBS_code, col=OBS_code) +
  geom_violin(alpha=.5) + 
  geom_jitter(alpha=.5, height =.1) + 
  facet_grid(FIELD_Country~ FIELD_year, scales="free")
```

```{r eval=FALSE}
ear_damage %>% 
  filter(OBS_numValue>100) %>% 
  select(FIELD_Country, FIELD_year, FIELD_name, OBS_code, OBS_numValue)
```