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LimaRAF committed Jan 11, 2024
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42 changes: 21 additions & 21 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ section 'Details on step 3').

Species occurrence records should be submitted to a data cleaning and validation
process to make sure that only the data with a minimum quality will be used in
the assessments. The `plantR` package (Lima et al. 2022) provides different
the assessments. The `plantR` package (Lima et al. 2023) provides different
tools to standardize the notation associated with species records and to
validate the locality, geographical coordinates, taxonomic nomenclature and
species identifications. It also includes tools for the retrieval and removal of
Expand All @@ -132,12 +132,12 @@ specimen duplicates across biological collections.

Different population metrics are necessary for applying the IUCN criteria A, B,
C and D (criterion E is currently not considered in this workflow). A new
version 2.0 of the `ConR` package (Dauby et al. 2017, Dauby & Lima 2022) was
version 2.0 of the `ConR` package (Dauby et al. 2017, Dauby & Lima 2023) was
developed to include new functions to calculate most of these metrics.

For criterion A, the `ConR` package provides a function for fitting
statistical models to the population size vector to obtain the reductions at
a specific point in time (`ConR::pop.decline.fit()`), based on linear,
a specific point in time (`ConR::pop.decline()`), based on linear,
exponential, quadratic, logistic and other trends of population decline
through time. This is important because the time interval of population decline
needed for the assessments of criterion A or C (10 years or one-, two- or
Expand Down Expand Up @@ -165,7 +165,7 @@ This step corresponds to the assignment of one of the IUCN Red List Categories
obtained in the previous step against the IUCN quantitative thresholds and
conditions. As mentioned above, specific functions were developed to assess the
IUCN criteria A, B, C and D, which are freely available in the new version 2.0
of the `ConR` R package (Dauby et al. 2017, Dauby & Lima 2022 - see functions
of the `ConR` R package (Dauby et al. 2017, Dauby & Lima 2023 - see functions
`ConR::criterion_A()`, `ConR::criterion_B()`, `ConR::criterion_C()` and
`ConR::criterion_D()`). A specific function was also developed to tell apart NT
from LC categories (see function `ConR::near.threatened()`).
Expand Down Expand Up @@ -270,16 +270,16 @@ species-specific proxies of DD. But the pertinence of this solution may vary
according to the group of organism being assessed (e.g. sessile vs. mobile
organisms).

Still related to criterion B, the quality of the geographical coordinates
and the confidence in the species identifications can both impact the estimates
of EOO and AOO. In THREAT, we only used geographically validated records for
estimating these metrics, which is the standard procedure adopted by CNCFlora,
Still related to criterion B, the quality of the geographical coordinates and
the confidence in the species identifications can both impact the estimates of
EOO and AOO. In THREAT, we only used geographically validated records for
estimating these metrics, which is the standard procedure adopted by CNCFlora,
the local Red List Authority. Concerning the confidence in the species
identifications, we preferably conducted assessments based only on
identifications vetted by plant taxonomists. However, for species with fewer
records (< 75), we added extra records with lower taxonomic confidence levels
based on their position with respect to the EOO of the species. We preferably added
records inside or close to the species EOO.
records (< 75), we added extra records with lower taxonomic confidence levels
based on their position with respect to the EOO of the species. We preferably
added records inside or close to the species EOO.

The final information needed to apply criterion B is the spatial extent (i.e.
scale) of the impacts of threat events that can impact all individuals of
Expand Down Expand Up @@ -311,13 +311,13 @@ in this workflow, but currently, we decided not to apply the subcriterion D2.
tabl <- "
|Data Limitations/Uncertainties |Criteria |Metric impacted |Solution |
|:----------------|:--------|:---------------|:--------|
| Generation Length | A and C | Pop. size decline | Group-specific imputation |
| Proportion of Mature Individuals | C and D | Pop. size | Group-specific Imputation |
| Impact of harvest trends | A and C | Pop. size decline | Group-specific imputation |
| Impact of habitat quality changes | A and C | Pop. size decline | Group-specific imputation |
| Generation Length | A & C | Pop. size decline | Group-specific imputation |
| Proportion of Mature Individuals | C & D | Pop. size | Group-specific Imputation |
| Impact of harvest trends | A & C | Pop. size decline | Group-specific imputation |
| Impact of habitat quality changes | A & C | Pop. size decline | Group-specific imputation |
| Average Dispersal Distance | B1/B2 | Subpops./Fragmentation | Estimation from data |
| Geographical coordinates of records | B1/B2 | EOO and AOO | Use only valid records |
| Species identification of records | B1/B2 | EOO and AOO | Add extra records, if needed |
| Geographical coordinates of records | B1/B2 | EOO & AOO | Use only valid records |
| Species identification of records | B1/B2 | EOO & AOO | Add extra records, if needed |
| Scale of threat events | B1/B2 | Number of locations | Set a fixed value |
| Subpopulation limits | C2a(i)| Size of subpopulations | Subcriteria applied in few cases|
| Future threats | D2 | - | Subcriteria not applied |
Expand Down Expand Up @@ -369,9 +369,9 @@ Please cite this repository as:

> **Renato A. F. de Lima, Gilles Dauby, André L. de Gasper, Eduardo P.
Fernandez, Alexander C. Vibrans, Alexandre A. de Oliveira, Paulo I. Prado,
Vinícius C. Souza, Marinez F. de Siqueira & Hans ter Steege. (2023).
Comprehensive conservation assessments reveal high extinction risks across
Atlantic Forest trees. Manuscript under review**
Vinícius C. Souza, Marinez F. de Siqueira & Hans ter Steege. (2024).
[Comprehensive conservation assessments reveal high extinction risks across
Atlantic Forest trees](https://doi.org/10.1126/science.abq5099). Science. DOI: 10.1126/science.abq5099.**

### Funding

Expand Down Expand Up @@ -402,7 +402,7 @@ conservation assessments using distribution data. Ecol. Evol. 7, 11292–11303
(2017).

> G. Dauby, R. A. F. de Lima, ConR: Computation of Parameters Used in
Preliminary Assessment of Conservation Status (R package version 2.0.0) (2022).
Preliminary Assessment of Species Conservation Status (R package version 2.1) (2023).

> IUCN, Guidelines for application of IUCN Red List criteria at regional and
national levels Version 4.0. (IUCN Species Survival Commission, 2012).
Expand Down
42 changes: 22 additions & 20 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ assessments using criteria A and C (see section ‘Details on step 3’).
Species occurrence records should be submitted to a data cleaning and
validation process to make sure that only the data with a minimum
quality will be used in the assessments. The `plantR` package (Lima et
al. 2022) provides different tools to standardize the notation
al. 2023) provides different tools to standardize the notation
associated with species records and to validate the locality,
geographical coordinates, taxonomic nomenclature and species
identifications. It also includes tools for the retrieval and removal of
Expand All @@ -133,18 +133,18 @@ specimen duplicates across biological collections.
Different population metrics are necessary for applying the IUCN
criteria A, B, C and D (criterion E is currently not considered in this
workflow). A new version 2.0 of the `ConR` package (Dauby et al. 2017,
Dauby & Lima 2022) was developed to include new functions to calculate
Dauby & Lima 2023) was developed to include new functions to calculate
most of these metrics.

For criterion A, the `ConR` package provides a function for fitting
statistical models to the population size vector to obtain the
reductions at a specific point in time (`ConR::pop.decline.fit()`),
based on linear, exponential, quadratic, logistic and other trends of
population decline through time. This is important because the time
interval of population decline needed for the assessments of criterion A
or C (10 years or one-, two- or three-generation lengths - see IUCN
2019) often does not correspond exactly to the observed population sizes
for most species.
reductions at a specific point in time (`ConR::pop.decline()`), based on
linear, exponential, quadratic, logistic and other trends of population
decline through time. This is important because the time interval of
population decline needed for the assessments of criterion A or C (10
years or one-, two- or three-generation lengths - see IUCN 2019) often
does not correspond exactly to the observed population sizes for most
species.

For criterion B, the `ConR` package provides functions for calculating
the Extent of Occurrence (EOO - `ConR::EOO.computing()`), Area of
Expand All @@ -170,7 +170,7 @@ population metrics obtained in the previous step against the IUCN
quantitative thresholds and conditions. As mentioned above, specific
functions were developed to assess the IUCN criteria A, B, C and D,
which are freely available in the new version 2.0 of the `ConR` R
package (Dauby et al. 2017, Dauby & Lima 2022 - see functions
package (Dauby et al. 2017, Dauby & Lima 2023 - see functions
`ConR::criterion_A()`, `ConR::criterion_B()`, `ConR::criterion_C()` and
`ConR::criterion_D()`). A specific function was also developed to tell
apart NT from LC categories (see function `ConR::near.threatened()`).
Expand Down Expand Up @@ -327,13 +327,13 @@ THREAT workflow.

| Data Limitations/Uncertainties | Criteria | Metric impacted | Solution |
|:------------------------------------|:---------|:-----------------------|:---------------------------------|
| Generation Length | A and C | Pop. size decline | Group-specific imputation |
| Proportion of Mature Individuals | C and D | Pop. size | Group-specific Imputation |
| Impact of harvest trends | A and C | Pop. size decline | Group-specific imputation |
| Impact of habitat quality changes | A and C | Pop. size decline | Group-specific imputation |
| Generation Length | A & C | Pop. size decline | Group-specific imputation |
| Proportion of Mature Individuals | C & D | Pop. size | Group-specific Imputation |
| Impact of harvest trends | A & C | Pop. size decline | Group-specific imputation |
| Impact of habitat quality changes | A & C | Pop. size decline | Group-specific imputation |
| Average Dispersal Distance | B1/B2 | Subpops./Fragmentation | Estimation from data |
| Geographical coordinates of records | B1/B2 | EOO and AOO | Use only valid records |
| Species identification of records | B1/B2 | EOO and AOO | Add extra records, if needed |
| Geographical coordinates of records | B1/B2 | EOO & AOO | Use only valid records |
| Species identification of records | B1/B2 | EOO & AOO | Add extra records, if needed |
| Scale of threat events | B1/B2 | Number of locations | Set a fixed value |
| Subpopulation limits | C2a(i) | Size of subpopulations | Subcriteria applied in few cases |
| Future threats | D2 | \- | Subcriteria not applied |
Expand Down Expand Up @@ -384,8 +384,10 @@ Please cite this repository as:
> **Renato A. F. de Lima, Gilles Dauby, André L. de Gasper, Eduardo P.
> Fernandez, Alexander C. Vibrans, Alexandre A. de Oliveira, Paulo I.
> Prado, Vinícius C. Souza, Marinez F. de Siqueira & Hans ter Steege.
> (2023). Comprehensive conservation assessments reveal high extinction
> risks across Atlantic Forest trees. Manuscript under review**
> (2024). [Comprehensive conservation assessments reveal high extinction
> risks across Atlantic Forest
> trees](https://doi.org/10.1126/science.abq5099). Science. DOI:
> 10.1126/science.abq5099.**
### Funding

Expand Down Expand Up @@ -419,8 +421,8 @@ repository.
> data. Ecol. Evol. 7, 11292–11303 (2017).
> G. Dauby, R. A. F. de Lima, ConR: Computation of Parameters Used in
> Preliminary Assessment of Conservation Status (R package version
> 2.0.0) (2022).
> Preliminary Assessment of Species Conservation Status (R package
> version 2.1) (2023).
> IUCN, Guidelines for application of IUCN Red List criteria at regional
> and national levels Version 4.0. (IUCN Species Survival Commission,
Expand Down

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