add L7.qmd

BB/Ref.bib

@@ -45809,3 +45809,43 @@ barcante2020cyanobacteria
     year = {2008}
 }
 
+@Article{tatters2025benthic,
+    title       = {Benthic cyanobacterial accumulations and associated cyanotoxins in coastal urban stormwater pond networks},
+    author      = {Tatters, Avery O. and Clevenger, Courtney and Strangman, Wendy K. and Oehrle, Stuart and Kudela, Raphael M. and Aukamp, Jessica and Wan, Yongshan},
+    year        = 2025,
+    journal     = {Harmful Algae},
+    publisher   = {Elsevier BV},
+    volume      = 144,
+    pages       = 102833,
+    url         = {http://dx.doi.org/10.1016/j.hal.2025.102833},
+    issn        = {1568-9883},
+    doi         = {10.1016/j.hal.2025.102833}
+}
+
+@Article{maurer2024temporal,
+    title       = {Temporal Dynamics of Cyanobacterial Bloom Community Composition and Toxin Production from Urban Lakes},
+    author      = {Maurer, Julie A. and Xia, Runjie and Kim, Andrew M. and Oblie, Nana and Hefferan, Sierra and Xie, Hannuo and Slitt, Angela and Jenkins, Bethany D. and Bertin, Matthew J.},
+    year        = 2024,
+    journal     = {ACS ES&T Water},
+    publisher   = {American Chemical Society (ACS)},
+    volume      = 4,
+    pages       = {3423–3432},
+    url         = {http://dx.doi.org/10.1021/acsestwater.4c00266},
+    issn        = {2690-0637},
+    doi         = {10.1021/acsestwater.4c00266},
+    number      = 8}
+
+@article{paerl2016duelling,
+   author = {Paerl, Hans W. and Otten, Timothy G.},
+   title = {Duelling ‘CyanoHABs’: unravelling the environmental drivers controlling dominance and succession among diazotrophic and non-N2-fixing harmful cyanobacteria},
+   journal = {Environmental Microbiology},
+   volume = {18},
+   number = {2},
+   pages = {316-324},
+   doi = {10.1111/1462-2920.13035},
+   url = {https://enviromicro-journals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.13035},
+   eprint = {https://enviromicro-journals.onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13035},
+   year = {2016}
+}
+
+

_metadata-protected.yml

@@ -34,4 +34,4 @@ website:
           - text: Codes
             url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/src/branch/{{< var branch >}}
           - text: Issue
-            url: https://git.drwater.net/manuscript/{{< var reponame >}}/issues
+            url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/issues

_metadata-public.yml

@@ -33,4 +33,4 @@ website:
           - text: Codes
             url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/src/branch/{{< var branch >}}
           - text: Issue
-            url: https://git.drwater.net/manuscript/{{< var reponame >}}/issues
+            url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/issues

coding/L7.qmd

@@ -0,0 +1,170 @@
+---
+title: "RWEP L7- Data Transform"
+---
+
+# Data Source
+
+
+```{r}
+dailylanddf <- readr::read_csv("../data/chinawq/daily_land.csv")
+metadatadf <- readxl::read_xls("../data/chinawq/metadata_and_statistics.xls")
+monthlylanddf <- readr::read_csv("../data/chinawq/monthly_ocean.csv")
+weeklylanddf <- readr::read_csv("../data/chinawq/weekly_land.csv")
+```
+
+
+```{r}
+require(tidyverse)
+dailylanddf
+
+
+dailylanddf |>
+  select(.data$MonitoringLocationIdentifier, .data$LongitudeMeasure_WGS84)
+
+dailylanddf |>
+  select("MonitoringLocationIdentifier", "LongitudeMeasure_WGS84")
+
+
+dailylanddf |>
+  select(1:3)
+
+
+dailylanddf |>
+  rename(x = 1) |>
+  rename(y = 2)
+```
+
+
+
+# 内置function
+
+
+```{r}
+
+dailylanddf |>
+  select(1:3) |>
+  rename_all(\(x) c("a", "b", "c")) |>
+  rename_all(\(x) paste0(x, "_new"))
+
+dailylanddf |>
+  select(1:3) |>
+  rename_all(~ c("a", "b", "c")) |>
+  rename_all(~ paste0(., "_new"))
+
+
+dailylanddf |>
+  select(1:3) |>
+  rename_all(~ c("x", "y", "z"))
+```
+
+```{r}
+fulldatadf <- readr::read_csv("../data/chinawq/full_dataset.csv")
+
+datadf <- fulldatadf |>
+  select(lon = 2, lat = 3, date = 4, varname = 5, value = 6) |>
+  mutate(value = as.numeric(value)) |>
+  tidyr::pivot_wider(names_from = varname, values_from = value)
+
+saveRDS(datadf, "../data/chinawq/datadf.rds")
+```
+
+
+# 统计
+
+## 统计每月的DO的平均值
+
+```{r}
+datadf <- readRDS("../data/chinawq/datadf.rds")
+
+datadf |>
+  select(1:7) |>
+  mutate(month = month(date)) |>
+  select(lon, lat, month, date, everything()) |>
+  group_by(month) |>
+  summarize(DO_mean = mean(DO, na.rm = TRUE), DO_sd = sd(DO, na.rm = TRUE)) |>
+  ggplot(aes(x = month, y = DO_mean)) +
+  geom_point() +
+  geom_smooth(method = "loess") +
+  geom_errorbar(aes(ymin = DO_mean - DO_sd, ymax = DO_mean + DO_sd))
+```
+
+
+```{r}
+datadf |>
+  select(1:7) |>
+  mutate(month = month(date)) |>
+  mutate(year = year(date)) |>
+  select(lon, lat, year, month, date, everything()) |>
+  summarize(
+    DO_mean = mean(DO, na.rm = TRUE),
+    DO_sd = sd(DO, na.rm = TRUE),
+    .by = c(year, month)
+  ) |>
+  ggplot(aes(x = month, y = DO_mean)) +
+  geom_point() +
+  geom_smooth(method = "loess") +
+  geom_errorbar(aes(ymin = DO_mean - DO_sd, ymax = DO_mean + DO_sd)) +
+  facet_wrap(~year)
+```
+
+
+```{r}
+datadf |>
+  select(1:7) |>
+  mutate(month = month(date)) |>
+  mutate(year = year(date)) |>
+  select(-lon, -lat, -date) |>
+  group_by(year, month) |>
+  summarize_all(\(x) mean(x, na.rm = TRUE))
+```
+
+## nest
+
+```{r}
+
+for (isite in 1:10) {
+  m <- datadf |>
+    select(1:7) |>
+    tidyr::nest(wqdf = -c(lon, lat)) |>
+    pull(wqdf) |>
+    nth(isite) |>
+    lm(formula = DO ~ pH, data = _)
+  slope <- coef(m)[2]
+  print(slope)
+}
+```
+
+## purrr::map
+
+```{r}
+
+ datadf |>
+   select(1:7) |>
+   tidyr::nest(wqdf = -c(lon, lat)) |>
+   slice(1:10) |>
+   mutate(
+     m = purrr::map(
+       wqdf,
+       \(x) {
+         lm(formula = DO ~ pH, data = x)
+       }
+     )
+   ) |>
+   mutate(slope = purrr::map_dbl(m, \(x) coef(x)[2])) |>
+   mutate(
+     p = purrr::map(wqdf, \(x) {
+       x |>
+         ggplot(aes(x = pH, y = DO)) +
+         geom_smooth(method = "lm") +
+         geom_point()
+     })
+   ) |>
+   pull(p) |>
+   patchwork::wrap_plots() +
+   patchwork::plot_layout(ncol = 2)
+```
+
+
+
+
+

data/chinawq/Monitoring_sites/Monitoring_sites.cpg

@@ -0,0 +1 @@
+UTF-8

data/chinawq/Monitoring_sites/Monitoring_sites.prj

@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]