Adapted 00_check_data to sPlot3.0.2 and rerun

code/00_CheckData.Rmd

@@ -18,11 +18,13 @@ always_allow_html: yes
 **Timestamp:** `r date()`  
 **Drafted:** Francesco Maria Sabatini  
 **Revised:** Stephan Hennekens  
-**Version:** 1.2
+**Version:** 1.3
   
 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.  
 *Changes to v1.2* - based on dataset sPlot_3.0.1, received on 29/06/2019 from SH
+*Changes to v1.3* - based on dataset sPlot_3.0.2, received on 24/07/2019 from SH  
+
 
 ***
 Key Problems:  
@@ -46,7 +48,7 @@ library(xlsx)
 # Check Header file
 Import with parse
 ```{r}
-header <- readr::read_delim("../sPlot_data_export/sPlot 3.0.1_header.csv", locale = locale(encoding = 'UTF-8'),
+header <- readr::read_delim("../sPlot_data_export/sPlot_3_0_2_header.csv", locale = locale(encoding = 'UTF-8'),
                             delim="\t", col_types=cols(
   PlotObservationID = col_double(),
   PlotID = col_double(),
@@ -129,7 +131,8 @@ knitr::kable(header %>%
                   full_width = F, position = "center")
 ```
 
-Plots without location uncertainty (by dataset)
+Plots without location uncertainty (by dataset).  
+We could probably assign at least a broad location, with wide uncertainty to the 2020 plots in the Egypt Nile delta dataset.
 
 
 ```{r}
@@ -142,6 +145,15 @@ knitr::kable(header %>%
                   full_width = F, position = "center")
 ```
 
+Big datasets without coordinate uncertainty are:  
+Czechia_nvd  
+Germany_vegetweb2  
+Poland  
+Slovenia  
+
+--> Talk to contributors and ask for 'average' uncertainty (e.g. 100 m)
+
+
 ```{r, echo=F}
 nNAs <- nrow(header %>% filter(is.na(`Location uncertainty (m)`)))
 ```
@@ -156,7 +168,7 @@ knitr::kable(table(header$`Plants recorded`, exclude=NULL),
     kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), 
                   full_width = F, position = "center")
 ```
-OK - Values not available for EVA's datasets. Ask Milan if we can simply assume 'All vascular plants'
+--> Values not available for EVA's datasets. Ask Milan if we can simply assume 'All vascular plants'
 
 
 2) Import field 'Herbs identified (y/n)' into header (SH)  
@@ -166,7 +178,7 @@ knitr::kable(table(header$`Herbs identified (y/n)`, exclude=NULL),
     kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), 
                   full_width = F, position = "center")
 ```
-OK - Values not available for EVA's datasets. According to SH, we can simply assume Y.
+--> Values not available for EVA's datasets. According to SH, we can simply assume Y.
 
 
 
@@ -176,7 +188,7 @@ OK - Values not available for EVA's datasets. According to SH, we can simply ass
 
 # Check DT table
 ```{r }
-DT0 <- readr::read_delim("../sPlot_data_export/sPlot 3.0.1_species.csv", 
+DT0 <- readr::read_delim("../sPlot_data_export/sPlot_3_0_2_species.csv", 
                             delim="\t", 
                          col_type = cols(
                                 PlotObservationID = col_double(),
@@ -227,6 +239,9 @@ knitr::kable(DT0 %>%
     kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), 
                   full_width = F, position = "center")
 
+```
+
+```{r}
 # in db British_Columbia_meadows this seems to depend on lichen\moss species
 knitr::kable(head(DT0 %>% 
   filter(`Cover %` ==0  & is.na(`Cover code`) & Taxonomy=="British_Columbia_meadows") %>% 
@@ -234,7 +249,9 @@ knitr::kable(head(DT0 %>%
   caption="Example from British Columbia meadows db (only first 10 rows)") %>%
     kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), 
                   full_width = F, position = "center")
+```
 
+```{r}
 
 # in db USA_VegBank there seem to be species with only p\a values, next to species with also cover (FMS will have to solve this)
 knitr::kable(head(DT0 %>%