Created table to summarize plots without coordinates

code/00_CheckData.Rmd

@@ -19,7 +19,7 @@ always_allow_html: yes
 **Revised:** Stephan Hennekens  
 **Version:** 1.1
   
-This report checks for consistency of the dataset used for constructing sPlot 3.0. 
+This report checks for consistency of the dataset used for constructing sPlot 3.0.  
 *Changes to v1.1* - Added check to species data. Created To Do list.
   
 ```{r results="hide", message=F, warning=F}
@@ -37,6 +37,7 @@ library(ggforce)
 library(xlsx)
 ```
 
+# Check Header file
 ```{r}
 #Import sPlot data
 header <- readr::read_delim("../sPlot_data_export/sPlot_data_header.csv", 
@@ -70,15 +71,6 @@ header.fix <- header %>%
 
 write_csv(header.fix, path = "../sPlot_data_export/sPlot_data_header_fix1.csv")
 ```
-Other known problems still to be fixed:  
-1) Import field 'Plants Recorded' into header (SH) - create dictionary of possible factors (FMS)  
-2) Import field 'Herbs identified' into header (SH)  
-3) Formations - Assign zeros to columns (Forest, Grassland, Shrubland, Wetland, Sparse), when at least one 1 is present (FMS)  
-4) Link to EUNIS cross-link table, and assign Faber-Langedon Formation (FMS)  
-5) Assign plot elevation using external sources (FMS)  
-
-  
-  
 
 Reimport with parse
 ```{r}
@@ -143,8 +135,32 @@ knitr::kable(problems(header) %>%
                   full_width = F, position = "center")
 ```
 
+Plots without coordinates (by dataset)
+```{r}
+knitr::kable(header %>%
+  dplyr::select(PlotObservationID, `TV2 relevé number`, Dataset, Longitude, Latitude) %>%
+  filter(is.na(Longitude) | is.na(Latitude)) %>% 
+  group_by(Dataset) %>%
+  summarize(n()), 
+  caption="Number of plots without coordinates per dataset") %>%
+    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), 
+                  full_width = F, position = "center")
+```
+
+
+
+Other known problems still to be fixed:  
+1) Import field 'Plants Recorded' into header (SH) - create dictionary of possible factors (FMS)  
+2) Import field 'Herbs identified' into header (SH)  
+3) Formations - Assign zeros to columns (Forest, Grassland, Shrubland, Wetland, Sparse), when at least one 1 is present (FMS)  
+4) Link to EUNIS cross-link table, and assign Faber-Langedon Formation (FMS)  
+5) Assign plot elevation using external sources (FMS)  
+
+  
+
+
 
-Check DT table
+# Check DT table
 ```{r}
 DT0 <- readr::read_delim("../sPlot_data_export/sPlot_data_species.csv", 
                             delim="\t", 
@@ -231,7 +247,7 @@ knitr::kable(table(header$Dataset), caption="Plots per dataset") %>%
     kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F, position = "center")
 ```
 
-Check geographic coordinates and print summary for each dataset
+# Check geographic coordinates
 ```{r, message=F, eval=T, cache=T}
 countries <- map_data("world")
 ggworld <- ggplot(countries, aes(x=long, y=lat, group = group)) +
@@ -261,7 +277,6 @@ for(d in levels(header$Dataset)){
 ```
 
 ```{r, cache=T, warning=F}
-not_all_na <- function(x) {!all(is.na(x))}
 for(dd in 1:nlevels(header$Dataset)){
   d <- levels(header$Dataset)[dd]
   datasel <- header %>%
@@ -274,7 +289,7 @@ for(dd in 1:nlevels(header$Dataset)){
 ```
 
 
-Other observed problems:  
+# Other observed problems:  
 Some plots in the Hungary dataset have a altitude >5000 m (!)  
 
 ```{r, eval=F, echo=F}