Package index
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cdb_build_cdb()
- Create a CompadreDB object from user-specified data
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cdb_fetch()
- Fetch the COM(P)ADRE database from compadre-db.org or a local file
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cdb_metadata()
- Extract metadata from a COM(P)ADRE database
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cdb_check_species()
- Check whether a COM(P)ADRE database contains one or more species of interest
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cdb_collapse()
- Collapse a COM(P)ADRE database by averaging matrices over levels of one or more grouping variables
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cdb_compare()
- Compare two versions or subsets of a COM(P)ADRE database
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cdb_flag()
- Flag potential issues in matrices of a COM(P)ADRE database
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mpm_has_prop()
mpm_has_active()
mpm_has_dorm()
mpm_first_active()
- Extract stage-class information from CompadreMat or CompadreDB objects
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cdb_flatten()
- Convert a COM(P)ADRE database to a flat data frame with matrices and vectors stored in string representation
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cdb_id()
- Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of a given set of columns
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cdb_id_stages()
- Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of species and matrix stage class definitions
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cdb_id_studies()
- Create a vector of unique study identifiers from a COM(P)ADRE database
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cdb_mean_matF()
- Calculate a population-specific mean fecundity matrix for each set of matrices in a COM(P)ADRE database
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cdb_rbind()
- Merge two COM(P)ADRE databases via row-bind
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cdb_unflatten()
- Reconstitute a flattened COM(P)ADRE database (created by cdb_flatten) as a CompadreDB object
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cdb_unnest()
- Unnest a COM(P)ADRE database by spreading the components of CompadreMat into separate list-columns
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mat_elementwise_apply()
mpm_elementwise_apply()
- Apply a function element-wise to a list of matrices
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mat_mean()
mpm_mean()
- Calculate a mean over a list of matrices or CompadreMat objects
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mat_median()
mpm_median()
- Calculate a median over a list of matrices or CompadreMat objects
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mat_to_string()
vec_to_string()
string_to_mat()
string_to_vec()
- Convert vectors or square numeric matrices to and from string representation
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Compadre
Comadre
- Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples
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as.data.frame(<CompadreDB>)
as_tibble(<CompadreDB>)
head(<CompadreDB>)
tail(<CompadreDB>)
names(<CompadreDB>)
dim(<CompadreDB>)
merge(<CompadreDB>)
NumberAcceptedSpecies()
NumberStudies()
NumberMatrices()
- Methods for CompadreDB objects
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`[`(<CompadreDB>,<ANY>,<ANY>,<ANY>)
subset(<CompadreDB>)
- Subsetting CompadreDB objects
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fortify.CompadreDB()
filter.CompadreDB()
slice.CompadreDB()
arrange.CompadreDB()
mutate.CompadreDB()
group_by.CompadreDB()
ungroup.CompadreDB()
summarize.CompadreDB()
summarise.CompadreDB()
select.CompadreDB()
rename.CompadreDB()
left_join.CompadreDB()
right_join.CompadreDB()
inner_join.CompadreDB()
full_join.CompadreDB()
- Tidyverse methods for CompadreDB objects
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CompadreData()
`$`(<CompadreDB>)
`$<-`(<CompadreDB>)
`[[`(<CompadreDB>,<ANY>,<missing>)
`[[<-`(<CompadreDB>,<ANY>,<missing>)
VersionData()
Version()
DateCreated()
- CompadreDB Class
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CompadreLegacy
- Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examples
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matA()
matU()
matF()
matC()
matrixClass()
MatrixClassAuthor()
MatrixClassOrganized()
MatrixClassNumber()
- Methods for working with matrices in com(p)adre
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as_cdb()
- Convert legacy COM(P)ADRE database object to CompadreDB
-
cdb_build_cdb()
- Create a CompadreDB object from user-specified data
-
cdb_check_species()
- Check whether a COM(P)ADRE database contains one or more species of interest
-
cdb_collapse()
- Collapse a COM(P)ADRE database by averaging matrices over levels of one or more grouping variables
-
cdb_compare()
- Compare two versions or subsets of a COM(P)ADRE database
-
cdb_fetch()
- Fetch the COM(P)ADRE database from compadre-db.org or a local file
-
cdb_flag()
- Flag potential issues in matrices of a COM(P)ADRE database
-
cdb_flatten()
- Convert a COM(P)ADRE database to a flat data frame with matrices and vectors stored in string representation
-
cdb_id()
- Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of a given set of columns
-
cdb_id_stages()
- Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of species and matrix stage class definitions
-
cdb_id_studies()
- Create a vector of unique study identifiers from a COM(P)ADRE database
-
cdb_mean_matF()
- Calculate a population-specific mean fecundity matrix for each set of matrices in a COM(P)ADRE database
-
cdb_metadata()
- Extract metadata from a COM(P)ADRE database
-
cdb_rbind()
- Merge two COM(P)ADRE databases via row-bind
-
cdb_unflatten()
- Reconstitute a flattened COM(P)ADRE database (created by cdb_flatten) as a CompadreDB object
-
cdb_unnest()
- Unnest a COM(P)ADRE database by spreading the components of CompadreMat into separate list-columns
-
mat_elementwise_apply()
mpm_elementwise_apply()
- Apply a function element-wise to a list of matrices
-
mat_mean()
mpm_mean()
- Calculate a mean over a list of matrices or CompadreMat objects
-
mat_median()
mpm_median()
- Calculate a median over a list of matrices or CompadreMat objects
-
mpm_has_prop()
mpm_has_active()
mpm_has_dorm()
mpm_first_active()
- Extract stage-class information from CompadreMat or CompadreDB objects
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mat_to_string()
vec_to_string()
string_to_mat()
string_to_vec()
- Convert vectors or square numeric matrices to and from string representation