Examine fully crossed structures.Rmd

---
title: "Reclassify 10% structures"
author: "Xiao Yang"
date: "4/13/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

require(sf)
require(tidyverse)
```

## export the fully crossed structures (dll) reclassify in GEE

```{r}
grod = st_read("outputs/GROD_reclassified_uncertain_20200211.shp")

grod = grod %>%
  mutate(grod_id = 1:nrow(grod))

st_write(grod, dsn = "outputs/GROD_v1_6classes_withID_20200530.shp")
  
subGrod = grod %>% 
  filter(class %in% c("Dam", "Low_Permeable_Dams", "Locks"))



print("how many structures in total?")
subGrod %>% nrow()
subGrod %>% st_drop_geometry() %>% group_by(class) %>% count() %>% ungroup

## add index just for this step
subGrod = subGrod %>% 
  mutate(index = 1:nrow(.))

subGrod %>% 
  ggplot() + 
  geom_bar(aes(x = class)) +
  theme(axis.text.x.bottom = element_text(hjust = 1, angle = 45)) +
  labs(x = "", y = "Count")

st_write(subGrod, dsn = "outputs/subGrod_fully_crossed_classes_20200530.shp")
```

## latest results

```{r}
range_index = tibble(name = c("Galit", "Riley", "Mike"), initIndex = c(1, 16874, 8437), maxIndex = c(8436, 25307, 16873))

require(foreach)
fileInfo = tibble(
  filePath = dir(path = "data/fully_crossed_structures", full.names = T),
  filename = dir(path = "data/fully_crossed_structures")
) %>% 
  separate(filename, into = c("name", NA), sep = "_")

dat = foreach(i = 1:nrow(fileInfo), .combine = "rbind") %do% {
  read_csv(fileInfo$filePath[i]) %>% 
    mutate(name = fileInfo$name[i])
} %>% 
  select(-`system:index`, -`.geo`) %>% 
  mutate(class = as.factor(class), name = as.factor(name)) %>% 
  rename(class_new = class) %>% 
  st_as_sf(coords = c("lon", "lat"), crs = 4326)

dat = dat %>% mutate(row.id = 1:nrow(dat))

ref = st_read("outputs/subGrod_fully_crossed_classes_20200530.shp")
ref = ref %>% mutate(col.id = 1:nrow(ref))

test = st_is_within_distance(dat, ref, dist = 500)
test = test %>% as_tibble()

merged = dat %>% left_join(test, by = "row.id") %>% left_join(ref %>% as_tibble(), by = "col.id") %>% 
  group_by(row.id, col.id) %>% 
  mutate(dist = st_distance(geometry.x, geometry.y)[1, 1]) %>% 
  ungroup()

## for structures with multiple matches, choose the one with minimal distance 
merged_final = merged %>% 
  group_by(row.id) %>% 
  slice_min(order_by = dist) %>% 
  ungroup()

## no. of structures finished mapping and some stats
progress = merged_final %>% 
  left_join(range_index, by = "name") %>% 
  filter(index >= initIndex, index <= maxIndex) %>% 
  st_drop_geometry() %>% 
  group_by(name) %>% 
  summarise(currentIndex = max(index),
            NoMapped = currentIndex - first(initIndex),
            initIndex = first(initIndex),
            nUncertain = sum(class_new == "Uncertain"),
            nChanged = n()) %>% 
  ungroup()

progress %>% 
  mutate(rateOfChange = nChanged / NoMapped,
         rateOfUncertain = nUncertain / NoMapped) %>% 
  select(-currentIndex)

# now need to filled in the structures are left unchanged
merged_unchanged = ref %>% 
  filter(
    (index >= progress[1, ]$initIndex & index <= progress[1, ]$currentIndex) | 
      (index >= progress[2, ]$initIndex & index <= progress[2, ]$currentIndex) | 
      (index >= progress[3, ]$initIndex & index <= progress[3, ]$currentIndex)) %>% 
  filter(!(index %in% merged_final$index)) %>% 
  mutate(class_new = class,
         geometry.x = geometry) %>% 
  select(index, grod_id, class_new, geometry.x, class)


currentDll = merged_final %>% 
  select(index, grod_id, class_new, geometry.x, class) %>% 
  as_tibble() %>% 
  rbind(merged_unchanged %>% st_drop_geometry())

save(currentDll, file = "outputs/currentDll_7_16_2020.RData")
```

## flow diagram

```{r}
library(flipPlots)

stats = currentDll %>% 
  group_by(class, class_new) %>% 
  count() %>% 
  ungroup()

SankeyDiagram(stats[, 1:2],
              link.color = "Source",
              variables.share.values = T,
              label.show.varname = F,
              label.show.percentages = T,
              weights = stats$n,
              font.size = 18)
```