Package 'vectorsurvR'

Calculate abundance

Description

Calculates abundance

Usage

getAbundance(
  collections,
  interval,
  species_list = NULL,
  trap_list = NULL,
  species_separate = FALSE
)

Arguments

collections	Collections data retrieved from getArthroCollections()
interval	Calculation interval for abundance, accepts “collection_date”,“Biweek”,“Week”, and “Month.
species_list	Species filter for calculating abundance. Species_display_name is the accepted notation.To see a list of species present in your data run unique(collections$species_display_name). If species is unspecified, the default NULL will return data for all species in data.
trap_list	Trap filter for calculating abundance. Trap_acronym is the is the accepted notation. Run unique(collections$trap_acronym) to see trap types present in your data. If trap_list is unspecified, the default NULL will return data for all trap types.
species_separate	Should the species in species_list have abundance calculated separately? Setting to FALSE calculates the combined abundance. The same result can be performed by calculating on one species at the time.

Value

A dataframe of abundance calculations

Examples

getAbundance(sample_collections,
             interval = 'Week',
             species_list = list('Cx pipiens'),
             trap_list = list('GRVD', 'CO2'),
             species_separate = FALSE)

---

Get Abundance Anomaly

Description

'getAbundanceAnomaly(...) 'requires at least five years prior to the target_year of arthro collections data to calculate for the specified parameters. The function uses the methods of the Gateway Abundance Anomaly calculator, and will not work if there is fewer than five years of data present.

Usage

getAbundanceAnomaly(
  collections,
  interval,
  target_year,
  species_list = NULL,
  trap_list = NULL,
  species_separate = FALSE
)

Arguments

collections	Collections data retrieved from 'getArthroCollections()'
interval	Calculation interval for abundance, accepts “collection_date”,“Biweek”,“Week”, and “Month
target_year	Year to calculate analysis on. Collections data must have a year range of at least (target_year - 5, target_year)
species_list	Species filter for calculating abundance. Species_display_name is the accepted notation.To see a list of species present in your data run 'unique(collections$species_display_name)'. If species is unspecified, the default NULL will return data for all species in data
trap_list	Trap filter for calculating abundance. Trap_acronym is the is the accepted notation. Run 'unique(collections$trap_acronym)' to see trap types present in your data. If trap_list is unspecified,the default NULL will return data for all trap types
species_separate	Should the species in species_list have abundance calculated separately? Setting to FALSE calculates the combined abundance. The same result can be performed by calculating on one species at the time description

Value

Abundance anomaly calculation

Examples

getAbundanceAnomaly(sample_collections,"Biweek",target_year=2020, species_list="Cx pipiens")

---

Get arthropod collections data

Description

'getArthroCollections()' obtains collections data on a year range [start_year, end_year] for authorized VectorSurv Gateway accounts.

Usage

getArthroCollections(token, start_year, end_year, arthropod, agency_ids = NULL)

Arguments

token	A valid access token returned from 'getToken()'
start_year	Start year of data
end_year	End year of data
arthropod	Specify arthropod type from: 'mosquito', 'tick'
agency_ids	Filter on agency id, default to NULL for all available agencies,otherwise provide a vector of agency ids

Value

A dataframe of collections

Examples

## Not run: 
token = getToken()
collections = getArthroCollections(token, 2021, 2022, 'mosquito',55, TRUE)
## End(Not run)

---

Calculate infection rate

Description

'getInfectionRate()' requires at least five years prior to the target_year of arthro collections data to calculate for the specified parameters. The function uses the methods of the Gateway Abundance Anomaly calculator, and will not work if there is fewer than five years of data present.

Usage

getInfectionRate(
  pools,
  interval,
  target_disease,
  pt_estimate,
  scale = 1000,
  species_list = NULL,
  trap_list = NULL
)

Arguments

pools	Pools data retrieved from 'getPools()'
interval	Calculation interval for infection rate, accepts “collection_date”,“Biweek”,“Week”, and “Month
target_disease	The disease to calculate infection rate for–i.e. “WNV”. Disease acronyms are the accepted input. To see a list of disease acronyms, run 'unique(pools$target_acronym)'
pt_estimate	The estimation type for infection rate. Options include: “mle”,“bc-mle”, “mir”
scale	Constant to multiply infection rate by
species_list	Species filter for calculating infection rate species_display_name is the accepted notation. To see a list of species present in your data run 'unique(pools$species_display_name)'. If species is unspecified, the default 'NULL' will return data for all species in data.
trap_list	Trap filter for calculating infection rate. Trap_acronym is the is the accepted notation. Run 'unique(pools$trap_acronym)' to see trap types present in your data. If trap_list is unspecified, the default 'NULL' will return data for all trap types.

Value

Dataframe of infection rate calculation

Examples

getInfectionRate(sample_pools,
                 interval = "Biweek",
                 target_disease = "WNV",
                 pt_estimate = "mle",
                 scale = 1000,
                 species_list = list("Cx pipiens"),
                 trap_list = list("CO2"))

---

Get Pools data

Description

Retrieves VectorSurv pools data for desired year range

Usage

getPools(token, start_year, end_year, arthropod, agency_ids = NULL)

Arguments

token	access token retrived from 'getToken()'
start_year	Beginning of year range
end_year	End of year range
arthropod	Specify arthropod type from: 'mosquito', 'tick', 'nontick'
agency_ids	Filter on agency id, default to NULL for all available agencies,otherwise provide a vector of agency ids

Value

Dataframe of pools data

Examples

## Not run: 
token = getToken()
getPools(token, start_year = 2020, end_year = 2021, arthropod = 'tick', 55)
## End(Not run)

---

Get Pools Frequency Table

Description

'getPoolsComparisionTable()' produces a frequency table for positive, negative, and pending pools counts by year and species. The more years present in the data, the larger the table.

Usage

getPoolsComparisionTable(
  pools,
  interval,
  target_disease,
  species_separate = FALSE
)

Arguments

pools	Pools data retrieved from 'getPools()'
interval	Calculation interval for comparison table, accepts “collection_date”,“Biweek”,“Week”, and “Month
target_disease	The disease to calculate infection rate for–i.e. “WNV”. Disease acronyms are the accepted input. To see a list of disease acronyms, run 'unique(pools$target_acronym)'
species_separate	Should the pools comparison be split by species of each pool. Default is FALSE

Value

Frequency table of for pools data

Examples

getPoolsComparisionTable(sample_pools,
                         interval = "Biweek",
                         target_disease = "WNV",
                          species_separate = TRUE)

---

Get region data

Description

'getSites()' obtains site data for authorized VectorSurv Gateway accounts.

Usage

getRegions(token)

Arguments

token

A valid access token returned from 'getToken()'

Value

A dataframe of region data, used internally to merge spatial information to collections

---

Get sites data

Description

'getSites()' obtains site data for authorized VectorSurv Gateway accounts.

Usage

getSites(token)

Arguments

token

A valid access token returned from 'getToken()'

Value

A dataframe of site data

Examples

## Not run: 
token = getToken()
sites = getSites(token)
## End(Not run)

---

Get authentication token

Description

getToken() returns a token needed to run getArthroCollections() and getPools(). Prints agencies associated with account credentials. The function prompts users for a VectorSurv account credentials.

Usage

getToken()

Value

User token

Examples

## Not run: token = getToken()

---

Calculate vector index

Description

'getVectorIndex()'requires at least five years prior to the target_year of arthro collections data to calculate for the specified parameters. The function uses the methods of the Gateway Abundance Anomaly calculator, and will not work if there is fewer than five years of data present.

Usage

getVectorIndex(
  collections,
  pools,
  interval,
  target_disease,
  pt_estimate,
  scale = 1000,
  species_list = NULL,
  trap_list = NULL
)

Arguments

collections	Collections data retrieved from 'getArthroCollections()'
pools	Pools data retrieved from 'getPools()'
interval	Calculation interval for vector index, accepts “collection_date”,“Biweek”,“Week”, and “Month
target_disease	The disease to calculate infection rate for–i.e. “WNV”. Disease acronyms are the accepted input. To see a list of disease acronyms, run 'unique(pools$target_acronym)'
pt_estimate	The estimation type for infection rate. Options include: “mle”,“bc-”mle”, “mir”
scale	Constant to multiply infection rate, default is 1000
species_list	Species filter for calculating abundance. Species_display_name is the accepted notation. To see a list of species present in your data run 'unique(pools$species_display_name)'. If species is unspecified, the default 'NULL' will return data for all species in data.
trap_list	Trap filter for calculating abundance. Trap_acronym is the is the accepted notation. Run 'unique(pools$trap_acronym)' to see trap types present in your data. If trap_list is unspecified, the default 'NULL' will return data for all trap types.

Value

Dataframe containing the vector index calculation

Examples

getVectorIndex(sample_collections, sample_pools, "Month", "WNV", "mle" )

---

Plot infection rate

Description

plotInfectionRate() plots the output returned from 'getInfectionRate()' with confidence intervals using ggplot

Usage

plotInfectionRate(InfRtOutput, year)

Arguments

InfRtOutput	Output from returned 'getInfectionRate()'
year	Year to plot infection rate on

Value

ggplot object

Examples

IR = getInfectionRate(sample_pools,
                      interval = "Week",
                      target_disease = "WNV",
                      pt_estimate = "mle", species_list = c("Cx pipiens"),
                      trap_list = c("CO2","GRVD") )
plotInfectionRate(InfRtOutput = IR, year = 2017)

---

Process abundance anomaly

Description

‘processAbunAnom()' processes the output returned from 'getAbundanceAnomaly()' into a long form suitable for plotting using ’ggplot'

Usage

processAbunAnom(AbAnomOutput)

Arguments

AbAnomOutput

output from 'getAbunAnom()'

Value

Abundance anomaly output processed into long form

Examples

AbAnOut = getAbundanceAnomaly(sample_collections,
                             interval = "Biweek",
                             target_year = 2020,
                             species_list = c("Cx tarsalis", "Cx pipiens"),
                             species_separate = TRUE)
AbAnOut_L = processAbunAnom(AbAnOut)

---

Sample Mosquito Collections Data

Description

Sample Mosquito Collections data imitates the essential components of real mosquito collections data

Usage

sample_collections

Format

A data frame with 2500 rows and 13 variables:

collection_id

double Collection identification number

collection_date

character The date the trap was picked up for collection

num_trap

integer The number of unique traps in operation at one site

site_code

integer Identifying code of site

surv_year

double Surveillance year of collection

trap_nights

integer The number of nights a trap was in the field

trap_problem_bit

logical If these was an issue with the trap

num_count

integer Number of arthropods present in collection

sex_type

character Sex of collected arthropods

species_display_name

character Species name of collected arthropods

trap_acronym

character The acronym of the trap placed in the field

Source

https://vectorsurv.org/

---

Sample Pools Data

Description

Sample Pools data imitates the essential components of real mosquito pools data needed for calculations

Usage

sample_pools

Format

A data frame with 2500 rows and 10 variables:

pool_id

integer Pool identification number

surv_year

integer Surveillance year of pool

site_code

integer Identifying code of site

collection_date

character The date the trap was picked up for collection

sex_type

integer Sex type of collected arthropods

num_count

integer Number of arthropods present in collection

target_acronym

character The disease being tested for in the pool

method_name

character Method used to test pool for disease

status_name

character Status of the tested disease, confirmed or negative

trap_acronym

character The acronym of the trap placed in the field

species_display_name

character Species name of collected arthropods

Source

https://vectorsurv.org/

---