Second draft for NO_GJEN_001 #67
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
anders-kolstad
requested changes
Dec 13, 2024
There was a problem hiding this comment.
I did a rapid reviw of this updated version of NO_GJEN_001 and would requests some minor edits before merging. Theu are mainly formatting issues tha I can fix myself. Will pick this up again next year.
See PR review checklist #84
| @@ -59,29 +59,29 @@ source(here::here("_common.R")) | |||
| ```{r} | |||
| #| echo: false | |||
| meta <- readxl::read_xlsx("../metadata.xlsx") | |||
| st <- meta |> | |||
| filter(Variable == "status") |> | |||
| st <- meta %>% | |||
There was a problem hiding this comment.
Why did you change the pipe operator? Best to use the native R pipe, no?
|
|
||
| - **Quantification of uncertainty around indicator scores.** Here we used the standard deviation in the vegetation heights for reference (NiN) polygons within each region to quantify the uncertainty around scaled indicator scores. We did this because the method used in `eaTools::ea_spread()` function is a bootstrapping approach which resulted in extremely small uncertainty estimates due to the large number of polygons included in our analysis. [In the future, a better method for quantifying uncertainty is needed.](https://github.com/NINAnor/eaTools/issues/17) Perhaps by running sensitivity analyses that test several variations of the points mentioned above can form the basis for quantifying an error margin around indicator values. | ||
| - **Selection of scaling function and define threshold value for good ecological condition.** In the investigation part of how to calculate the encroachment index (not presented here), we tested three different scaling functions (Sigmoid (as presented in an earlier version), Exponential and Linear) where we ended up using the Linear scaling function. However, further testing of scaling functions should be done in the future, especially in regards to defining a threshold value for good ecological condition. Here we only define the upper and lower limits of ecological condition. However the results presented in section 10.4 suggests that it would be beneficial for the encroachment index to also have a threshold value for good ecological condition (X~60~). One way could be to calculate the 90th percentile for vegetation height in the reference polygons and set this as X~60~, but a proper threshold value should be investigated. |
| ifelse(region_id == 2, 'Midt-Norge', | ||
| ifelse(region_id == 3, 'Østlandet', | ||
| ifelse(region_id == 4, 'Vestlandet', 'Sørlandet'))))) %>% | ||
| mutate(region = case_when( |
| for(i in 1:length(ecosysttypes)){ | ||
|
|
||
| ecosysttype <- ecosysttypes[i] | ||
|
|
||
| # Import median LiDAR heights for NiN polygons (references) | ||
| # Import median LiDAR heights for NiN MI polygons (references) |
There was a problem hiding this comment.
Good to specify that it is from MI
| @@ -730,41 +786,50 @@ Import the reference vegetation heights generated in GEE and define the upper li | |||
|
|
|||
| ecosysttypes <- c("vaatmark", "aapne", "semi") | |||
|
|
|||
| # Need to filter out the ones where data is also on semi-natural types that are not in a good condition | |||
| nin_good_condition <- st_read("/data/P-Prosjekter2/412421_okologisk_tilstand_2024/Data/NiN/nin_cleaned_condition.shp") %>% | |||
There was a problem hiding this comment.
adding quiet = T wil supress messages from st_read()
|
|
||
| The gjengroing condition indicator scores are on average above 0.8 and therefore indicate a good overall condition in Norway (@fig-regional-level-enc-forest). Østlandet comes out best for våtmark and semi-naturlig åpne ecosystems. Nord-Norge has poorest condition for semi-naturlig åpne ecosystems, while vestlandet has the poorest scores for våtmark." | ||
| The encroachment condition indicator scores are on average above 0.8 and therefore indicate a good overall condition in Norway (@fig-regional-level-enc-forest). Østlandet comes out best for wetland and semi-natural ecosystems. Nord-Norge has poorest condition for semi-natural ecosystems, while Vestlandet has the poorest scores for wetland. | ||
|
|
||
| ### 10.1 Scaled indicator values at the level of homogeneous ecosystem areas {#sec-HEA} | ||
|
|
There was a problem hiding this comment.
set warning: false
There was a problem hiding this comment.
use use legend.position.inside instead of legend.position
| plot.title = element_text(size=10)) + | ||
| ggtitle('C) Semi-naturlig condition') | ||
| theme(legend.position = c(0.8, 0.4)) + | ||
| ggtitle('C) Semi-naturlig') | ||
|
|
||
|
|
||
|
|
There was a problem hiding this comment.
IN fig-regional-level-enc-forest caption, add note that indicator values are not final, and serve only as prrof of concept for the indicator workflow
|
|
||
| These results suggest that, at least for semi-natural ecosystems, using polygons with an overall good condition score will still give reference heights that are suitable for calculating the gjengroing index. | ||
| str(rasksuksIndexPoly) |
|
|
||
| ```{r validation-enc-index, fig.cap="Scatter plot displaying reference heights for good condition according to NiN field-mapping ecological condition overall score and sub-score for Rask suksesjon in semi-natural ecosystems"} | ||
| rasksuksIndexPoly %>% |
There was a problem hiding this comment.
set warning: false
| ``` | ||
|
|
||
| ## 12. Export file | ||
| fig-validation-enc shows that encroachment indicator has higher values (good condition) with the better condition scores for Rask suksesjon (1=good) and that the condition does indeed get poorer when Rask suksesjon has a poorer condition score (3 and 4). However, all Rask suksesjon values have relatively high encroachment indicator scores (mean \> 0.8), suggesting that the encroachment indicator is giving better condition scores than what is actually measured in the field. A reason for this can be that the scaling function does not fit well with the data or that the indicator also needs a threshold value for when the condition is good or not (X~60~). |
There was a problem hiding this comment.
Add @ at the start to fix cross ref
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.