Update CI_1_Generate_reports.R

R/CI_1_Generate_reports.R

@@ -6,6 +6,7 @@
 library(dplyr)
 library(forcats)
 library(ggplot2)
+library(gt)
 library(here)
 library(kableExtra)
 library(knitr)
@@ -19,7 +20,6 @@ webshot::install_phantomjs()
 
 ### Start ###
 rm(list = ls())
-renv::status()
 
 
 
@@ -54,18 +54,22 @@ sites <- read_csv(
     values_transform = list (n = as.character)
   ) %>%
   pivot_wider(names_from = "x", values_from = "n") %>%
-  mutate(plot = str_replace(plot, "-", "_"),
-         plot = str_replace(plot, "L_", "L"),
-         plot = str_replace(plot, "W_", "W"),
-         id = str_c(plot, survey_year, sep = "_"),
-         plot = factor(plot),
-         id = factor(id),
-         vegetation_cover = as.numeric(vegetation_cover)) %>%
-  filter(!(site == "C" & (survey_year == "seeded" |
-                            survey_year == "2018" |
-                            survey_year == "2019" |
-                            survey_year == "2020" |
-                            survey_year == "2021")))
+  mutate(
+    plot = str_replace(plot, "-", "_"),
+    plot = str_replace(plot, "L_", "L"),
+    plot = str_replace(plot, "W_", "W"),
+    id = str_c(plot, survey_year, sep = "_"),
+    plot = factor(plot),
+    id = factor(id),
+    vegetation_cover = as.numeric(vegetation_cover)
+  ) %>%
+  filter(
+    !(site == "C" & (survey_year == "seeded" |
+                       survey_year == "2018" |
+                       survey_year == "2019" |
+                       survey_year == "2020" |
+                       survey_year == "2021"))
+  )
 
 
 
@@ -151,9 +155,8 @@ values <- seq(from = 0, to = 100, by = 5)
 
 ### Check typos of sites cover ###
 data <- sites %>%
-  filter(!str_detect(id, "_seeded$")) %>%
-  filter(!(vegetation_cover %in% values) &
-           !is.na(vegetation_cover))
+  #filter(!str_detect(id, "_seeded$")) %>%
+  filter(!(vegetation_cover %in% values) & !is.na(vegetation_cover))
 
 file <- here("tests", "testthat", "warnings_sites_typos.png")
 
@@ -167,10 +170,10 @@ if(count(data) == 0) {
 
 } else {
 
-  data #%>%
-    #gt() %>%
-    #tab_options(table.font.size = px(10)) %>%
-    #gtsave(file)
+  data %>%
+    gt() %>%
+    tab_options(table.font.size = px(10)) %>%
+    gtsave(file)
 
 }
 
@@ -230,7 +233,8 @@ data <- species %>%
   select(id, survey_year, vegetation_cover, value, diff) %>%
   filter(!str_detect(id, "_seeded$")) %>%
   filter(diff > 20 | diff < -5) %>%
-  arrange(survey_year, id, diff)
+  arrange(survey_year, id, diff) #%>%
+  #mutate(warning_name == "warnings_different_total_cover")
 
 file <- here("tests", "testthat", "warnings_different_total_cover.png")