render compile

coding/_common.R

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+set.seed(1014)
+
+# knitr::opts_chunk$set(
+# comment = "#>",
+# collapse = TRUE,
+# cache = TRUE,
+# fig.retina = 2,
+# fig.width = 6,
+# fig.asp = 2 / 3,
+# fig.show = "hold"
+# )
+
+# options(
+#   dplyr.print_min = 6,
+#   dplyr.print_max = 6,
+#   pillar.max_footer_lines = 2,
+#   pillar.min_chars = 15,
+#   stringr.view_n = 6,
+#   # Temporarily deactivate cli output for quarto
+#   cli.num_colors = 0,
+#   cli.hyperlink = FALSE,
+#   pillar.bold = TRUE,
+#   width = 77 # 80 - 3 for #> comment
+# )
+
+ggplot2::theme_set(ggplot2::theme_gray(12))
+
+# use results: "asis" when setting a status for a chapter
+status <- function(type) {
+  status <- switch(type,
+    polishing = "should be readable but is currently undergoing final polishing",
+    restructuring = "is undergoing heavy restructuring and may be confusing or incomplete",
+    drafting = "is currently a dumping ground for ideas, and we don't recommend reading it",
+    complete = "is largely complete and just needs final proof reading",
+    stop("Invalid `type`", call. = FALSE)
+  )
+
+  class <- switch(type,
+    polishing = "note",
+    restructuring = "important",
+    drafting = "important",
+    complete = "note"
+  )
+
+  cat(paste0(
+    "\n",
+    ":::: status\n",
+    "::: callout-", class, " \n",
+    "You are reading the work-in-progress second edition of R for Data Science. ",
+    "This chapter ", status, ". ",
+    "You can find the complete first edition at <https://r4ds.had.co.nz>.\n",
+    ":::\n",
+    "::::\n"
+  ))
+}

coding/lesson9.qmd

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+---
+title: 第9次课练习
+---
+
+```{r}
+require(tidyverse)
+# require(ggplot2)
+require(palmerpenguins)
+
+penguins |>
+  select(species, flipper_length_mm, body_mass_g,
+    bill_length_mm, sex) |>
+  filter(!is.na(sex)) |>
+  ggplot(aes(
+    x = species,
+    y = body_mass_g
+    )) +
+geom_jitter(colour = "white",
+  fill = "gray80", size = 1, shape = 21, width = 0.4) +
+geom_violin(fill = "orange", alpha = 0.4) +
+stat_summary(fun = mean) +
+scale_size_continuous(range = c(.5, 2)) +
+# ggsci::scale_fill_d3() +
+ylab("Body mass (g)") +
+ggtitle("Body mass and flipper length") +
+theme(axis.text.x = element_text(angle = 90),
+  panel.background = element_rect(fill = NA)
+)
+
+ggplot2::last_plot()
+
+
+ggsave("../img/penguins.pdf", width = 4, heigh = 3)
+
++
+dwfun::theme_sci(5, 5)
+
+
+p1 <- ggplot(penguins, aes(x = island, fill = species)) +
+  geom_bar(position = "fill")
+p2 <- ggplot(penguins, aes(x = species, fill = island)) +
+  geom_bar(position = "fill")
+
+require(patchwork)
+((p1 / p2) | p1)
+
+
+
+
+```
+
+
+
+# 消光系数
+
+```{r}
+licordata <- readRDS("../data/licordata.RDS")
+require(tidyverse)
+
+licordata |>
+  group_by(date, site) |>
+  nest(.key = "lightdf") |>
+  mutate(m = purrr::map(
+    lightdf,
+    ~ (lm(log(UP + 1) ~ depth, data = .x))
+  )) |>
+  mutate(k = purrr::map_dbl(m, ~
+  -coef(.x)[2])) |>
+  ggplot(aes(date, k)) +
+geom_point(aes(fill = site))
+
+Iz = I0 * exp(-zk)
+
+
+
+
+
+
+```
+

coding/main.qmd

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+---
+title: 实时代码
+date: last-modified
+---
+
+```{r}
+```
+
+