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Commit b89452c7 authored by patrick.lambert's avatar patrick.lambert
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with right package for home-made observers

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data/input/northeastamerica/RIO_obs_NEA.xml
View file @ b89452c7
......@@ -66,12 +66,12 @@
</yAxisLabel>
<variableName>getFemaleSpawnerEffective</variableName>
</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
<miscellaneous.TemporalRangeSerieChart>
<observer.TemporalRangeSerieChart>
<title>Range distribution</title>
<xAxisLabel>Time (season)</xAxisLabel>
<yAxisLabel>latitude</yAxisLabel>
<variableName>getRangeDistributionWithLat</variableName>
</miscellaneous.TemporalRangeSerieChart>
</observer.TemporalRangeSerieChart>
<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
<graphType>LINE</graphType>
<title>Mean age at first reproduction for female</title>
......@@ -127,7 +127,7 @@
<java-class>environment.RiverBasin</java-class>
<fr.cemagref.observation.kernel.ObservablesHandler>
<observers>
<miscellaneous.TemporalSerieChartForBasin>
<observer.TemporalSerieChartForBasin>
<graphType>LINE</graphType>
<title>Number of juveniles</title>
<xAxisLabel>Time
......@@ -135,14 +135,14 @@
</xAxisLabel>
<yAxisLabel>number of juveniles</yAxisLabel>
<variableName>getJuvenileNumber</variableName>
</miscellaneous.TemporalSerieChartForBasin>
<miscellaneous.TemporalSerieChartForBasin>
</observer.TemporalSerieChartForBasin>
<observer.TemporalSerieChartForBasin>
<graphType>LINE</graphType>
<title>% Autochtone</title>
<xAxisLabel>Time (season)</xAxisLabel>
<yAxisLabel>% Autochtone</yAxisLabel>
<variableName>getLastPercentageOfAutochtone</variableName>
</miscellaneous.TemporalSerieChartForBasin>
</observer.TemporalSerieChartForBasin>
</observers>
</fr.cemagref.observation.kernel.ObservablesHandler>
</entry>
......
exploration/GR3D_Rdescription/deathBasinW.Rmd
View file @ b89452c7
......@@ -12,7 +12,7 @@ output:
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(echo = TRUE, include = FALSE)
```
```{r include = FALSE}
......@@ -24,15 +24,29 @@ library(flextable)
```
```{r load data, include = FALSE}
distance <- as.matrix(read.csv("../../data/input/northeastamerica/distanceGridNEA.csv", row.names = 1, stringsAsFactors = FALSE))
distance <- distance %>%
distanceNEA <- as.matrix(read.csv("../../data/input/northeastamerica/distanceGridNEA.csv", row.names = 1, stringsAsFactors = FALSE))
distanceNEA <- distanceNEA %>%
replace(., col(.) == row(.), NA) %>%
as.data.frame() %>% mutate(destination = row.names(.)) %>%
pivot_longer(cols = -destination, names_to = 'departure', values_to = 'distance') %>%
dplyr::select(departure, destination, distance) %>%
arrange(departure, distance)
riverBasins = read.csv("../../data/input/northeastamerica/nea_riverbasins.csv")
riverBasinsNEA = read.csv("../../data/input/northeastamerica/nea_riverbasins.csv")
distanceAA <- as.matrix(read.csv("../../data/input/atlanticarea/distanceGridAA.csv", row.names = 1, stringsAsFactors = FALSE))
distanceAA <- distanceAA %>%
replace(., col(.) == row(.), NA) %>%
as.data.frame() %>% mutate(destination = row.names(.)) %>%
pivot_longer(cols = -destination, names_to = 'departure', values_to = 'distance') %>%
dplyr::select(departure, destination, distance) %>%
arrange(departure, distance)
riverBasinsAA = read.csv("../../data/input/atlanticarea/aa_basins.csv")
riverAARougier2015 = read.csv("basinsRougieretal2015.csv", stringsAsFactors = FALSE) %>% rename(basin_id = id, basin_name = nomBV) %>%
mutate(basin_name =replace(basin_name, basin_name == "Sevre_Niortaise", "Sevre Niortaise"))
```
......@@ -41,16 +55,23 @@ source("GR3Dfunction.R")
```
From the distance grid file used by GR3D for the US application, the data, after reshaping, look like
# *Computation of the death basin weight*
```{r distance, echo=FALSE, include = FALSE}
#paged.print=TRUE
ft <- head(distance,15) %>% flextable() %>% set_formatter_type(fmt_double = "%.02f") %>% autofit()
set_caption(ft, 'Examples of distance (in km) between departure and destination basins')
#
```
## *Baseline*
The parameters for the kernel function based on accessibility from @rougier2015CombinedUseEmpirical are:
*The weight for destination basin* $j_2$ *from basin* $j_1$ *is:*
$$w_{j_1\rightarrow j_2} = \frac {1} {1 + e ^{\alpha_0 + \alpha_1 \cdot {\frac {( D_{j_1\rightarrow j_2} - \mu_D)} {\sigma_D} } } }$$
*The sum of weights for the departure basin* $j_1$ *is:* $$w_{j_1} = \sum_{j_2 \neq j_1} {w_{j_1\rightarrow j_2}}$$
*The mean weight across all basins is then:* $$\overline{w} = \sum_{j_1 =1}^{n_B} {w_{j_1}}$$
*It is advised to use this mean value for the death basin weight. Notice that the* $\mu_D$ *and* $\sigma_D$ *depend on the basins list considered.*
## *Atlantic area application*
*The parameters for the kernel function based on accessibility for Atlantic Area application defined in @rougier2015CombinedUseEmpirical are:*
```{r}
alpha0 = -2.9
......@@ -60,35 +81,56 @@ standardDeviationInterDistance = 978
```
```{r include = FALSE}
meanInterDistance <- mean(distance$distance, na.rm = TRUE )
standardDeviationInterDistance <- sd(distance$distance, na.rm = TRUE)
*and the resulting death basin weight is*
```{r}
wDeathBasin = .4
```
Notice that the $\mu_D$ and $\sigma_D$ depend on the basins list considered. The true values for $\mu_D$ and $\sigma_D$ are respectively `r meanInterDistance` and `r standardDeviationInterDistance`. So there is a problem in the AA application <!--# calculte rhe value for Rougier 2015 --> since the number of basins was increased in comparison with @rougier2015CombinedUseEmpirical.
```{r echo =TRUE, include = FALSE}
distanceAA <- distanceAA %>% mutate(W = logitKernel(distance, alpha0, alpha1, meanInterDistance, standardDeviationInterDistance))
```
```{r}
riverAARougier2015 %>% select(basin_name) %>% setdiff(riverBasinsAA %>% select(basin_name))
distanceAA %>% inner_join(riverAARougier2015, by =c('departure' = 'basin_id')) %>%
inner_join(riverAARougier2015, by =c('destination' = 'nomBV')) %>%
group_by(departure) %>%
summarise(sumW = sum(W, na.rm = TRUE), .groups = 'drop') %>%
summarise(mean(sumW)) %>% unlist()
```{r kernel function, echo = TRUE}
range = round(range(distance$distance, na.rm = TRUE))
dist = range[1]:range[2]
dataKernel = data.frame(dist = dist, w = logitKernel(dist, alpha0, alpha1, meanInterDistance, standardDeviationInterDistance))
dataKernel %>% ggplot(aes(x=dist, y=w)) + geom_line() + labs(x='distance between departure and destination basins (km)')
```
The weight for destination basin $j_2$ from basin $j_1$ is:
##
$$w_{j_1\rightarrow j_2} = \frac {1} {1 + e ^{\alpha_0 + \alpha_1 \cdot {\frac {( D_{j_1\rightarrow j_2} - \mu_D)} {\sigma_D} } } }$$
## *North East America application*
```{r echo =TRUE, include = FALSE}
distance <- distance %>% mutate(W = logitKernel(distance, alpha0, alpha1, meanInterDistance, standardDeviationInterDistance))
*From the distance grid file used by GR3D for the US application, the data, after reshaping, look like*
```{r distance, echo=FALSE, include = FALSE}
#paged.print=TRUE
ft <- head(distanceNEA,15) %>% flextable() %>% set_formatter_type(fmt_double = "%.02f") %>% autofit()
set_caption(ft, 'Examples of distance (in km) between departure and destination basins')
#
```
The sum of weights for the departure basin $j_1$ is: $$w_{j_1} = \sum_{j_2 \neq j_1} {w_{j_1\rightarrow j_2}}$$
```{r include = FALSE}
meanInterDistance <- mean(distance$distance, na.rm = TRUE )
standardDeviationInterDistance <- sd(distance$distance, na.rm = TRUE)
```
The mean weight across all basins is then: $$\overline{w} = \sum_{j_1 =1}^{n_B} {w_{j_1}}$$
$\mu_D$ *and* $\sigma_D$ *values for this application are respectively `r meanInterDistance` and `r standardDeviationInterDistance`.*
It is advised to use this value for the death basin weight.
```{r kernel function, echo = TRUE, include = FALSE}
range = round(range(distance$distance, na.rm = TRUE))
dist = range[1]:range[2]
dataKernel = data.frame(dist = dist, w = logitKernel(dist, alpha0, alpha1, meanInterDistance, standardDeviationInterDistance))
dataKernel %>% ggplot(aes(x=dist, y=w)) + geom_line() + labs(x='distance between departure and destination basins (km)')
```
The histogram of weights sum in NorthEast America application is given by
*The histogram of weights sum in North East America application is given by*
```{r histogram, echo=FALSE, message=FALSE, warning=FALSE, fig.cap="Distribution of weight sums for departure basins"}
distance %>% group_by(departure) %>% summarise(sumW = sum(W, na.rm = TRUE)) %>%
......@@ -104,7 +146,7 @@ deathBasinWeight <- distance %>%
summarise(mean(sumW)) %>% unlist()
```
The dashed blue line corresponds to the mean weight ($w_{j_1}$ =`r round(deathBasinWeight, 4)` that is advised to be used as death basin weight. For a departure basin with a $w_{j_1}$ below this value, the strayers mortality is higher than 50 %. For these departure basins, most destination basins are far from the departure basin, the sum of destination basins weights is low and the death basin is attractive.
*The dashed blue line corresponds to the mean weight (*$w_{j_1}$ *=`r round(deathBasinWeight, 4)` that is advised to be used as death basin weight. For a departure basin with a* $w_{j_1}$ *below this value, the strayers mortality is higher than 50 %. For these departure basins, most destination basins are far from the departure basin, the sum of destination basins weights is low and the death basin is attractive.*
```{r, echo =FALSE, warning = FALSE, include = FALSE, mortalyRateLatitude, fig.cap ="Evolution of mortality rate in the death basin according to departure basin latitude"}
distance %>% group_by(departure) %>% summarise(sumW = sum(W, na.rm = TRUE), .groups = 'drop') %>%
......@@ -114,6 +156,10 @@ distance %>% group_by(departure) %>% summarise(sumW = sum(W, na.rm = TRUE), .gro
```
## Virtual linear network of basin
## full universe
```{r fake list of basin, echo false, include = TRUE}
nbBasin = 100
distBetweenBasin = 10
......@@ -159,6 +205,8 @@ drawMortalityVslatitude(data=basinDistance)
```
##Sampled universe
```{r irregular sampling of fake universe, echo FALSE}
sampledBasin <- basin %>% sample_n(25) %>% arrange(latitude)
......@@ -178,7 +226,7 @@ drawMortalityVslatitude(sampledBasinDistance)
The strayer mortality increases at the edge of the distribution.
The selection of basins impacts the strayers mortality. It is probably safer to considered a constant rate rather a death basin.
The selection of basins impacts the strayers mortality. It is probably safer to considered a constant rate rather a death basin. It ais a priority to improve the coverage of the area by increasing the number of basins considered.
The logit function to compute the basin weights introduces a plateau for the short distance that leads to random destination in the the departure vicinity
......
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