Updated to exclude plots

code/04_buildHeader.Rmd

@@ -152,7 +152,8 @@ Pfe-o-05- 1707854
 ```{r, eval=T}
 header0 <- header0 %>% 
   filter(!PlotObservationID %in% c(1707776, 1707779:1707782, 1707849, 1707854)) %>% 
-  filter(Dataset != "$Coastal_Borja")
+  filter(Dataset != "$Coastal_Borja") %>% 
+  filter(Dataset != "$Coastal_Poland") 
 ```
 
 

code/06_buildDT.Rmd

@@ -63,19 +63,25 @@ DT0 <- readr::read_delim("../sPlot_data_export/sPlot_3_0_2_species_test.csv",
                                 x_ = col_double()
                               )
                          ) 
-nplots <- length(unique(DT0$PlotObservationID))
-nspecies <- length(unique(DT0$`Matched concept`))
+
 ```
 Match plots with those in `header`
 ```{r}
 load("../_output/header_sPlot3.0.RData")
 DT0 <- DT0 %>% 
   filter(PlotObservationID %in% unique(header$PlotObservationID))
+
+nplots <- length(unique(DT0$PlotObservationID))
+nspecies <- length(unique(DT0$`Matched concept`))
+# Plots in header but not in DT
+empty.plots <- header %>% 
+  filter(!PlotObservationID %in% unique(DT2$PlotObservationID)) %>% 
+  pull(PlotObservationID)
 ```
 
 
-The DT table includes `r nrow(DT0)` species * plot records, across `r nplots` plots. Before taxonomic resolution, there are `r nspecies` species .  
-\newline
+The DT table includes `r nrow(DT0)` species * plot records, across `r nplots` plots. Before taxonomic resolution, there are `r nspecies` species. There are `r length(empty.plots)`. These are plots where the only species reported in Turboveg 3 are not identified (and not in the taxonomic list). Should these be deleted from `header`?
+<br>
 
 
 ```{r, echo=F}

code/07_buildCWMs.Rmd

@@ -412,6 +412,14 @@ CWM <- CWM1 %>%
   arrange(PlotObservationID)
 
 ```
+
+```{r, echo=F}
+# align to header (to avoid recalculating cached CWMs)
+CWM <- CWM %>% 
+  filter(PlotObservationID %in% header$PlotObservationID)
+```
+
+
 ### 2.1 Explore CWM output
 ```{r, echo=F}
 knitr::kable(CWM %>% 

code/08_Documentation.Rmd

@@ -265,7 +265,7 @@ knitr::kable(CWM %>%
                   latex_options = "basic", 
                   full_width = F, position = "center")
 ```
-The CWM table contains `r nrow(CWM)` entries, i.e., the combination between `r CWM %>% distinct(PlotObservationID) %>% nrow()` unique plots, and `r CWM %>% distinct(variable) %>% nrow()`. 
+The CWM table contains `r nrow(CWM)` entries, i.e., the combination between `r CWM %>% distinct(PlotObservationID) %>% nrow()` unique plots, and `r CWM %>% distinct(variable) %>% nrow()` traits.