vectorsurvR

VectorSurv

VectorSurv provides public health agencies the tools to manage, visualize and analyze the spread of vector-borne diseases and make informed decisions to protect public health.

The ‘vectorsurvR’ package is intended for users of VectorSurv, a public health vector borne disease surveillance system. The package contains functions tailored to data retrieved from the VectorSurv database. A valid VectorSurv username and password is required for data retrieval. Those without agency access can use sample datasets in place of real data. This documentation covers the functions in ‘vectorsurvR’ and introduces users to methods of R programming. The purpose of this documentation is to introduce and guide users with limited programming experience.

To install package from CRAN (recommended) run:

install.packages("vectorsurvR")

Or install the developing version from our github run:

devtools::install_github("UCD-DART/vectorsurvR")

Then load the package for use.

Data Retrieval

getToken()

Description

getToken() returns a token needed to run getArthroCollections() and getPools(). The function prompts users for their Gateway credentials. If credentials are accepted, the function returns a user token needed to obtain data and a list of agencies the user has access to.

Usage

getToken()

Arguments


token = getToken()

getArthroCollections(…)

Description

getArthroCollections(...) obtains collections data for a range of years. It prompts the user for their Gateway username and password before retrieving the associated data. You can only retrieve data from agencies linked to your Gateway account.

Usage

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

Arguments

#Example
collections = getArthroCollections(token, 2022,2023, 'mosquito',55)

getPools(…)

Description

getPools() similar to getArthroCollections() obtains pools on a year range (start_year, end_year) after supplying a valid token retrieved from getToken(). getPools() can retrieve data for both mosquito and tick pools.

Usage

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

#Example
pools = getPools(token, 2022,2023, 'mosquito')

Write Data to file

You can save retrieved data as a .csv file in your current directory using write.csv(). That same data can be retrieved using read.csv(). Writing data to a .csv can make the rendering process more efficient when generating reports in R. We recommend that you write the data pulled from our API into a csv and then load that data when generating reports.

#creates a file named "collections_18_23.csv" in your current directory
write.csv(x = collections, file = "collections_22_23.csv")

#loads collections data
collections = read.csv("collections_22_23.csv")

Sample Data

The ‘vectorsurvR’ package comes with two sample datasets which can be used in place of real collections and pools data. sample_collections and sample_pools will be used for example purposes in this document.

Data Processing

Data can be subset to contain columns of interest. Subsetting can also be used to reorder the columns in a data frame.Do not subset collections or pools data before inputting them into VectorSurv calculator functions to avoid losing essential columns. It is recommended to subset after calculations are complete and before inputting into a table generator. Remember, subsetting, filtering, grouping and summarising will not change the value of the data unless it is reassigned to the same variable name. We recommend creating a new variable for processed data.

Subsetting

#Subset using column names or index number

colnames(sample_collections) #displays column names and associated index
#>  [1] "agency_code"          "collection_id"        "collection_date"     
#>  [4] "surv_year"            "species_display_name" "sex_type"            
#>  [7] "trap_acronym"         "trap_problem_bit"     "num_trap"            
#> [10] "trap_nights"          "num_count"            "site_code"           
#> [13] "agency_id"            "county"               "collection_longitude"
#> [16] "collection_latitude"

#Subseting by name
head(sample_collections[c("collection_date", "species_display_name", "num_count")])
#> # A tibble: 6 × 3
#>   collection_date species_display_name num_count
#>   <date>          <chr>                    <int>
#> 1 2015-01-22      Cx pipiens                   1
#> 2 2015-01-10      Cx stigmatosoma              2
#> 3 2015-01-02      Cs inornata                  1
#> 4 2015-01-02      Cs inornata                 22
#> 5 2015-01-29      Cs inornata                 38
#> 6 2015-01-29      Cs incidens                  2

#by index
head(sample_collections[c(2, 4, 10)])
#> # A tibble: 6 × 3
#> # Groups:   surv_year [1]
#>   collection_id surv_year trap_nights
#>           <int>     <dbl>       <int>
#> 1       1374818      2015           6
#> 2       1368247      2015           8
#> 3       1366915      2015          15
#> 4       1366929      2015          15
#> 5       1377676      2015           7
#> 6       1377690      2015           7

#to save a subset
collections_subset = sample_collections[c(2, 4, 10)]

Filtering and subsetting in ‘dplyr’

‘dplyr’ is a powerful package for filtering and sub-setting data. It follows logic similar to SQL queries.

For more information on data manipulation using ‘dplyr’ Click Here

‘dplyr’ utilizes the pipe operator %>% to send data into functions. The head() function returns the first few rows of data, specifying head(1) tells the software to return only the first row for viewing purposes. Remove head() to see all the data or reassign the data to a new variable.

#NOTE: library was loaded above
library(dplyr)

#Subsetting columns with 'select()'
sample_collections %>%
  dplyr::select(collection_date, species_display_name, num_count) %>% head()
#> Adding missing grouping variables: `surv_year`
#> # A tibble: 6 × 4
#> # Groups:   surv_year [1]
#>   surv_year collection_date species_display_name num_count
#>       <dbl> <date>          <chr>                    <int>
#> 1      2015 2015-01-22      Cx pipiens                   1
#> 2      2015 2015-01-10      Cx stigmatosoma              2
#> 3      2015 2015-01-02      Cs inornata                  1
#> 4      2015 2015-01-02      Cs inornata                 22
#> 5      2015 2015-01-29      Cs inornata                 38
#> 6      2015 2015-01-29      Cs incidens                  2

Below are more examples for filtering data.


#filtering with dplyr 'filter'
collections_pip = sample_collections %>%
  filter(species_display_name == "Cx pipiens")

#filtering multiple arguments using '%in%'
collections_pip_tar = sample_collections %>%
  filter(species_display_name %in% c("Cx pipiens", "Cx tarsalis"))

Grouping and Summarising

In addition to filtering and sub-setting, data can be group by variables and summarized.

#groups by species and collection date and sums the number counted

sample_collections %>%
  group_by(collection_date, species_display_name) %>%
  summarise(sum_count = sum(num_count, na.rm = T)) %>%
  head()
#> `summarise()` has grouped output by 'collection_date'. You can override using
#> the `.groups` argument.
#> # A tibble: 6 × 3
#> # Groups:   collection_date [2]
#>   collection_date species_display_name sum_count
#>   <date>          <chr>                    <int>
#> 1 2015-01-02      Cs incidens                 15
#> 2 2015-01-02      Cs inornata                 88
#> 3 2015-01-02      Cx pipiens                  46
#> 4 2015-01-02      Cx tarsalis                  3
#> 5 2015-01-10      An freeborni                 4
#> 6 2015-01-10      Cs incidens                  1


#groups by species and collection date and takes the average the number counted

sample_collections %>%
  group_by(collection_date, species_display_name) %>%
  summarise(avg_count = mean(num_count, na.rm = T)) %>%
  head()
#> `summarise()` has grouped output by 'collection_date'. You can override using
#> the `.groups` argument.
#> # A tibble: 6 × 3
#> # Groups:   collection_date [2]
#>   collection_date species_display_name avg_count
#>   <date>          <chr>                    <dbl>
#> 1 2015-01-02      Cs incidens                5  
#> 2 2015-01-02      Cs inornata                8  
#> 3 2015-01-02      Cx pipiens                11.5
#> 4 2015-01-02      Cx tarsalis                1.5
#> 5 2015-01-10      An freeborni               4  
#> 6 2015-01-10      Cs incidens                1

Pivoting

Data can be manipulated into long and wide (spreadsheet) forms using pivot_wider() and pivot_longer() from the ‘tidyr’ package. By default data from the API is in long form. Here we pivot on species and sex condition names using num_count as values. The end result is data with num_count values in the columns named species_sex. For more on pivoting see ??pivot_longer() and ??pivot_wider().

library(tidyr)

collections_wide = pivot_wider(
  sample_collections,
  names_from = c("species_display_name","sex_type"),
  values_from = "num_count"
)
#> Warning: Values from `num_count` are not uniquely identified; output will contain
#> list-cols.
#> • Use `values_fn = list` to suppress this warning.
#> • Use `values_fn = {summary_fun}` to summarise duplicates.
#> • Use the following dplyr code to identify duplicates.
#>   {data} |>
#>   dplyr::summarise(n = dplyr::n(), .by = c(agency_code, collection_id,
#>   collection_date, surv_year, trap_acronym, trap_problem_bit, num_trap,
#>   trap_nights, site_code, agency_id, county, collection_longitude,
#>   collection_latitude, species_display_name, sex_type)) |>
#>   dplyr::filter(n > 1L)

Calculations

Abundance

getAbundance(…)

Description

getAbundance() uses any amount of mosquito collections data to calculate the abundance for the specified parameters. The function calculates using the methods of the Gateway Abundance calculator.

Usage

getAbundance(collections,interval, species = NULL, trap = NULL, separate_by = NULL)

Arguments

getAbundance(
  sample_collections,
  interval = "Biweek",
  species = c("Cx tarsalis", "Cx pipiens"),
  trap = "CO2",
  separate_by = NULL
)
#>    Agency Year Biweek   County                 Species Count TrapEvents Trap
#> 1  AGENCY 2021      4 County 1              Cx pipiens    10          3  CO2
#> 2  AGENCY 2021      7 County 1              Cx pipiens     4          3  CO2
#> 3  AGENCY 2021      8 County 1 Cx pipiens, Cx tarsalis    23         10  CO2
#> 4  AGENCY 2021     10 County 1              Cx pipiens     9          5  CO2
#> 5  AGENCY 2021     11 County 1 Cx pipiens, Cx tarsalis    17         13  CO2
#> 6  AGENCY 2021     12 County 1 Cx pipiens, Cx tarsalis   474         10  CO2
#> 7  AGENCY 2021     13 County 1              Cx pipiens   338         12  CO2
#> 8  AGENCY 2021     14 County 1 Cx pipiens, Cx tarsalis    79          9  CO2
#> 9  AGENCY 2021     15 County 1 Cx pipiens, Cx tarsalis  3137         10  CO2
#> 10 AGENCY 2021     16 County 1 Cx pipiens, Cx tarsalis  2265         12  CO2
#> 11 AGENCY 2021     17 County 1 Cx pipiens, Cx tarsalis    23          8  CO2
#> 12 AGENCY 2021     18 County 1             Cx tarsalis    49          6  CO2
#> 13 AGENCY 2021     19 County 1             Cx tarsalis    35         10  CO2
#> 14 AGENCY 2021     20 County 1             Cx tarsalis    39         10  CO2
#> 15 AGENCY 2021     21 County 1 Cx pipiens, Cx tarsalis    16          6  CO2
#> 16 AGENCY 2020      9 County 1             Cx tarsalis    56          4  CO2
#> 17 AGENCY 2020     10 County 1 Cx pipiens, Cx tarsalis    24          6  CO2
#> 18 AGENCY 2020     11 County 1 Cx pipiens, Cx tarsalis   204         15  CO2
#> 19 AGENCY 2020     12 County 1 Cx pipiens, Cx tarsalis   251         10  CO2
#> 20 AGENCY 2020     13 County 1 Cx pipiens, Cx tarsalis   208         14  CO2
#> 21 AGENCY 2020     14 County 1 Cx pipiens, Cx tarsalis  2584         12  CO2
#> 22 AGENCY 2020     15 County 1 Cx pipiens, Cx tarsalis    38          8  CO2
#> 23 AGENCY 2020     16 County 1 Cx pipiens, Cx tarsalis   345          8  CO2
#> 24 AGENCY 2020     17 County 1 Cx pipiens, Cx tarsalis  1670         10  CO2
#> 25 AGENCY 2020     18 County 1             Cx tarsalis    79          7  CO2
#> 26 AGENCY 2020     19 County 1 Cx pipiens, Cx tarsalis   187         13  CO2
#> 27 AGENCY 2020     20 County 1             Cx tarsalis    43         12  CO2
#> 28 AGENCY 2020     21 County 1 Cx pipiens, Cx tarsalis    61         13  CO2
#> 29 AGENCY 2020     22 County 1 Cx pipiens, Cx tarsalis    12         11  CO2
#> 30 AGENCY 2020     23 County 1 Cx pipiens, Cx tarsalis     9          8  CO2
#> 31 AGENCY 2020     24 County 1              Cx pipiens     3          4  CO2
#> 32 AGENCY 2019      4 County 1              Cx pipiens     3          1  CO2
#> 33 AGENCY 2019      9 County 1 Cx pipiens, Cx tarsalis    18          9  CO2
#> 34 AGENCY 2019     10 County 1 Cx pipiens, Cx tarsalis    22          7  CO2
#> 35 AGENCY 2019     11 County 1 Cx pipiens, Cx tarsalis   564         16  CO2
#> 36 AGENCY 2019     12 County 1              Cx pipiens    51          4  CO2
#> 37 AGENCY 2019     13 County 1 Cx pipiens, Cx tarsalis   881         13  CO2
#> 38 AGENCY 2019     14 County 1 Cx pipiens, Cx tarsalis   266          6  CO2
#> 39 AGENCY 2019     15 County 1 Cx pipiens, Cx tarsalis  4239         16  CO2
#> 40 AGENCY 2019     16 County 1 Cx pipiens, Cx tarsalis    68         14  CO2
#> 41 AGENCY 2019     17 County 1 Cx pipiens, Cx tarsalis    77          7  CO2
#> 42 AGENCY 2019     18 County 1 Cx pipiens, Cx tarsalis   262          6  CO2
#> 43 AGENCY 2019     19 County 1 Cx pipiens, Cx tarsalis    54          9  CO2
#> 44 AGENCY 2019     20 County 1 Cx pipiens, Cx tarsalis   214         12  CO2
#> 45 AGENCY 2019     21 County 1             Cx tarsalis    37          9  CO2
#> 46 AGENCY 2018     10 County 1 Cx pipiens, Cx tarsalis   304         16  CO2
#> 47 AGENCY 2018     11 County 1 Cx pipiens, Cx tarsalis    96         16  CO2
#> 48 AGENCY 2018     12 County 1 Cx pipiens, Cx tarsalis    90         16  CO2
#> 49 AGENCY 2018     13 County 1 Cx pipiens, Cx tarsalis  4016         13  CO2
#> 50 AGENCY 2018     14 County 1 Cx pipiens, Cx tarsalis   486          9  CO2
#> 51 AGENCY 2018     15 County 1 Cx pipiens, Cx tarsalis   147         11  CO2
#> 52 AGENCY 2018     16 County 1 Cx pipiens, Cx tarsalis  1611         14  CO2
#> 53 AGENCY 2018     17 County 1 Cx pipiens, Cx tarsalis    41         13  CO2
#> 54 AGENCY 2018     18 County 1 Cx pipiens, Cx tarsalis   211         13  CO2
#> 55 AGENCY 2018     19 County 1              Cx pipiens   125         10  CO2
#> 56 AGENCY 2018     20 County 1 Cx pipiens, Cx tarsalis    47         10  CO2
#> 57 AGENCY 2018     21 County 1             Cx tarsalis    11          9  CO2
#> 58 AGENCY 2017      8 County 1              Cx pipiens    10          4  CO2
#> 59 AGENCY 2017      9 County 1 Cx pipiens, Cx tarsalis    18          8  CO2
#> 60 AGENCY 2017     10 County 1 Cx pipiens, Cx tarsalis   149         16  CO2
#> 61 AGENCY 2017     11 County 1 Cx pipiens, Cx tarsalis   351         13  CO2
#> 62 AGENCY 2017     12 County 1 Cx pipiens, Cx tarsalis    65         17  CO2
#> 63 AGENCY 2017     13 County 1 Cx pipiens, Cx tarsalis   209         19  CO2
#> 64 AGENCY 2017     14 County 1 Cx pipiens, Cx tarsalis   410         23  CO2
#> 65 AGENCY 2017     15 County 1 Cx pipiens, Cx tarsalis   669         10  CO2
#> 66 AGENCY 2017     16 County 1 Cx pipiens, Cx tarsalis  2574         13  CO2
#> 67 AGENCY 2017     17 County 1 Cx pipiens, Cx tarsalis  4535         22  CO2
#> 68 AGENCY 2017     18 County 1 Cx pipiens, Cx tarsalis   462         17  CO2
#> 69 AGENCY 2017     19 County 1 Cx pipiens, Cx tarsalis   144         10  CO2
#> 70 AGENCY 2017     20 County 1 Cx pipiens, Cx tarsalis    49         22  CO2
#> 71 AGENCY 2017     21 County 1             Cx tarsalis   138         16  CO2
#> 72 AGENCY 2016      8 County 1             Cx tarsalis    68         12  CO2
#> 73 AGENCY 2016      9 County 1 Cx pipiens, Cx tarsalis    13         11  CO2
#> 74 AGENCY 2016     10 County 1 Cx pipiens, Cx tarsalis   323          9  CO2
#> 75 AGENCY 2016     11 County 1 Cx pipiens, Cx tarsalis    52         15  CO2
#> 76 AGENCY 2016     12 County 1 Cx pipiens, Cx tarsalis   559         26  CO2
#> 77 AGENCY 2016     13 County 1 Cx pipiens, Cx tarsalis  1189         21  CO2
#> 78 AGENCY 2016     14 County 1 Cx pipiens, Cx tarsalis    94         10  CO2
#> 79 AGENCY 2016     15 County 1 Cx pipiens, Cx tarsalis  2198         18  CO2
#> 80 AGENCY 2016     16 County 1 Cx pipiens, Cx tarsalis  1128         10  CO2
#> 81 AGENCY 2016     17 County 1 Cx pipiens, Cx tarsalis  1107         18  CO2
#> 82 AGENCY 2016     18 County 1 Cx pipiens, Cx tarsalis   330         16  CO2
#> 83 AGENCY 2016     19 County 1 Cx pipiens, Cx tarsalis   160         17  CO2
#> 84 AGENCY 2016     20 County 1 Cx pipiens, Cx tarsalis    38         16  CO2
#> 85 AGENCY 2016     21 County 1 Cx pipiens, Cx tarsalis     8          9  CO2
#> 86 AGENCY 2015      8 County 1              Cx pipiens     8          6  CO2
#> 87 AGENCY 2015      9 County 1 Cx pipiens, Cx tarsalis    12         10  CO2
#> 88 AGENCY 2015     10 County 1 Cx pipiens, Cx tarsalis   612         27  CO2
#> 89 AGENCY 2015     11 County 1 Cx pipiens, Cx tarsalis   318         19  CO2
#> 90 AGENCY 2015     12 County 1 Cx pipiens, Cx tarsalis   737         16  CO2
#> 91 AGENCY 2015     13 County 1 Cx pipiens, Cx tarsalis   405         17  CO2
#> 92 AGENCY 2015     14 County 1 Cx pipiens, Cx tarsalis   531         15  CO2
#> 93 AGENCY 2015     15 County 1 Cx pipiens, Cx tarsalis   780         10  CO2
#> 94 AGENCY 2015     16 County 1 Cx pipiens, Cx tarsalis   805         18  CO2
#> 95 AGENCY 2015     17 County 1 Cx pipiens, Cx tarsalis  2433         15  CO2
#> 96 AGENCY 2015     18 County 1 Cx pipiens, Cx tarsalis  2056         20  CO2
#> 97 AGENCY 2015     19 County 1 Cx pipiens, Cx tarsalis   164         17  CO2
#> 98 AGENCY 2015     20 County 1 Cx pipiens, Cx tarsalis   569         22  CO2
#> 99 AGENCY 2015     21 County 1              Cx pipiens    45          5  CO2
#>    Abundance
#> 1       3.33
#> 2       1.33
#> 3       2.30
#> 4       1.80
#> 5       1.31
#> 6      47.40
#> 7      28.17
#> 8       8.78
#> 9     313.70
#> 10    188.75
#> 11      2.88
#> 12      8.17
#> 13      3.50
#> 14      3.90
#> 15      2.67
#> 16     14.00
#> 17      4.00
#> 18     13.60
#> 19     25.10
#> 20     14.86
#> 21    215.33
#> 22      4.75
#> 23     43.12
#> 24    167.00
#> 25     11.29
#> 26     14.38
#> 27      3.58
#> 28      4.69
#> 29      1.09
#> 30      1.12
#> 31      0.75
#> 32      3.00
#> 33      2.00
#> 34      3.14
#> 35     35.25
#> 36     12.75
#> 37     67.77
#> 38     44.33
#> 39    264.94
#> 40      4.86
#> 41     11.00
#> 42     43.67
#> 43      6.00
#> 44     17.83
#> 45      4.11
#> 46     19.00
#> 47      6.00
#> 48      5.62
#> 49    308.92
#> 50     54.00
#> 51     13.36
#> 52    115.07
#> 53      3.15
#> 54     16.23
#> 55     12.50
#> 56      4.70
#> 57      1.22
#> 58      2.50
#> 59      2.25
#> 60      9.31
#> 61     27.00
#> 62      3.82
#> 63     11.00
#> 64     17.83
#> 65     66.90
#> 66    198.00
#> 67    206.14
#> 68     27.18
#> 69     14.40
#> 70      2.23
#> 71      8.62
#> 72      5.67
#> 73      1.18
#> 74     35.89
#> 75      3.47
#> 76     21.50
#> 77     56.62
#> 78      9.40
#> 79    122.11
#> 80    112.80
#> 81     61.50
#> 82     20.62
#> 83      9.41
#> 84      2.38
#> 85      0.89
#> 86      1.33
#> 87      1.20
#> 88     22.67
#> 89     16.74
#> 90     46.06
#> 91     23.82
#> 92     35.40
#> 93     78.00
#> 94     44.72
#> 95    162.20
#> 96    102.80
#> 97      9.65
#> 98     25.86
#> 99      9.00

Abundance Anomaly (comparison to 5 year average)

getAbundanceAnomaly()

Description

getAbundanceAnomaly(...) requires at least five years prior to the target_year of mosquito 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 = NULL, trap = NULL, separate_by = NULL)

Arguments


getAbundanceAnomaly(sample_collections,
                    interval = "Biweek",
                    target_year = 2020,
                    species = c("Cx tarsalis", "Cx pipiens"),
                    trap = "CO2",
                    separate_by  = "species") 
#> Warning in getAbundanceAnomaly(sample_collections, interval = "Biweek", : There
#> are years greater than the target year in the data. These years will not be
#> included in the anomaly calculation.
#>    Biweek     Species Agency Year   County Count TrapEvents Trap Abundance
#> 1      10  Cx pipiens AGENCY 2020 County 1     1          6  CO2      0.17
#> 2      10 Cx tarsalis AGENCY 2020 County 1    23          6  CO2      3.83
#> 3      11  Cx pipiens AGENCY 2020 County 1    24         15  CO2      1.60
#> 4      11 Cx tarsalis AGENCY 2020 County 1   180         15  CO2     12.00
#> 5      12  Cx pipiens AGENCY 2020 County 1     5         10  CO2      0.50
#> 6      12 Cx tarsalis AGENCY 2020 County 1   246         10  CO2     24.60
#> 7      13  Cx pipiens AGENCY 2020 County 1    93         14  CO2      6.64
#> 8      13 Cx tarsalis AGENCY 2020 County 1   115         14  CO2      8.21
#> 9      14  Cx pipiens AGENCY 2020 County 1   287         12  CO2     23.92
#> 10     14 Cx tarsalis AGENCY 2020 County 1  2297         12  CO2    191.42
#> 11     15  Cx pipiens AGENCY 2020 County 1    29          8  CO2      3.62
#> 12     15 Cx tarsalis AGENCY 2020 County 1     9          8  CO2      1.12
#> 13     16  Cx pipiens AGENCY 2020 County 1    87          8  CO2     10.88
#> 14     16 Cx tarsalis AGENCY 2020 County 1   258          8  CO2     32.25
#> 15     17  Cx pipiens AGENCY 2020 County 1    13         10  CO2      1.30
#> 16     17 Cx tarsalis AGENCY 2020 County 1  1657         10  CO2    165.70
#> 17     18 Cx tarsalis AGENCY 2020 County 1    79          7  CO2     11.29
#> 18     19  Cx pipiens AGENCY 2020 County 1    44         13  CO2      3.38
#> 19     19 Cx tarsalis AGENCY 2020 County 1   143         13  CO2     11.00
#> 20     20 Cx tarsalis AGENCY 2020 County 1    43         12  CO2      3.58
#> 21     21  Cx pipiens AGENCY 2020 County 1    31         13  CO2      2.38
#> 22     21 Cx tarsalis AGENCY 2020 County 1    30         13  CO2      2.31
#> 23      9 Cx tarsalis AGENCY 2020 County 1    56          4  CO2     14.00
#>    FiveYearAvg           YearsInAverage   Delta
#> 1       1.8820 2015,2016,2017,2018,2019  -90.97
#> 2      16.1200 2015,2016,2017,2018,2019  -76.24
#> 3       2.3260 2015,2016,2017,2018,2019  -31.21
#> 4      15.3640 2015,2016,2017,2018,2019  -21.90
#> 5       5.3240 2015,2016,2017,2018,2019  -90.61
#> 6      15.7850      2015,2016,2017,2018   55.84
#> 7       5.8140 2015,2016,2017,2018,2019   14.21
#> 8      87.8140 2015,2016,2017,2018,2019  -90.65
#> 9       4.8300 2015,2016,2017,2018,2019  395.24
#> 10     27.3620 2015,2016,2017,2018,2019  599.58
#> 11     22.2620 2015,2016,2017,2018,2019  -83.74
#> 12     86.8040 2015,2016,2017,2018,2019  -98.71
#> 13     26.9020 2015,2016,2017,2018,2019  -59.56
#> 14     68.1900 2015,2016,2017,2018,2019  -52.71
#> 15      8.8460 2015,2016,2017,2018,2019  -85.30
#> 16     79.9520 2015,2016,2017,2018,2019  107.25
#> 17     28.9700 2015,2016,2017,2018,2019  -61.03
#> 18      7.6160 2015,2016,2017,2018,2019  -55.62
#> 19      3.4675      2015,2016,2017,2019  217.23
#> 20      3.8240 2015,2016,2017,2018,2019   -6.38
#> 21      4.5550                2015,2016  -47.75
#> 22      3.6825      2016,2017,2018,2019  -37.27
#> 23      0.7375      2015,2016,2017,2019 1798.31

Infection Rate

getInfectionRate()

Description

getInfectionRate(...) estimates the arbovirus infection rate based on testing pools of mosquitoes.

Usage

getInfectionRate(pools,interval, target_year, target_disease,pt_estimate, scale = 1000, species = c(NULL), trap = c(NULL))

Arguments

getInfectionRate(sample_pools, 
                      interval = "Week",
                      target_disease = "WNV",
                      pt_estimate = "mle", 
                      scale = 1000,
                      species = c("Cx pipiens", "Cx tarsalis"),
                      trap = c("CO2"),
                      separate_by="species", wide = FALSE )
#> # A tibble: 275 × 9
#> # Groups:   Year, Week [160]
#>     Year  Week Agency Species     Trap  Disease InfectionRate LowerCI UpperCI
#>    <dbl> <dbl> <chr>  <chr>       <chr> <chr>           <dbl>   <dbl>   <dbl>
#>  1  2015    18 AGENCY Cx pipiens  CO2   WNV                 0       0       0
#>  2  2015    18 AGENCY Cx tarsalis CO2   WNV                 0       0       0
#>  3  2015    19 AGENCY Cx pipiens  CO2   WNV                 0       0       0
#>  4  2015    20 AGENCY Cx tarsalis CO2   WNV                 0       0       0
#>  5  2015    21 AGENCY Cx pipiens  CO2   WNV                 0       0       0
#>  6  2015    21 AGENCY Cx tarsalis CO2   WNV                 0       0       0
#>  7  2015    22 AGENCY Cx pipiens  CO2   WNV                 0       0       0
#>  8  2015    22 AGENCY Cx tarsalis CO2   WNV                 0       0       0
#>  9  2015    23 AGENCY Cx pipiens  CO2   WNV                 0       0       0
#> 10  2015    23 AGENCY Cx tarsalis CO2   WNV                 0       0       0
#> # ℹ 265 more rows

Vector Index

getVectorIndex()

Description

getVectorIndex(...) The vector index is the relative abundance of infected mosquitoes and is a way to quickly estimate the risk of arbovirus transmission in an area. Vector index is the product of the abundance and infection rate for a given time interval: \(Vector Index = Infection Rate * Abundance\)

Usage

getVectorIndex(collections, pools, interval, , target_disease, pt_estimate,species=NULL, trap = NULL,)

Arguments - collections: collections data retrieved from getArthroCollections(...) - pools: Pools data retrieved from getPools(...)

Note: Years from pools and collections data must overlap

getVectorIndex(sample_collections, 
               sample_pools,
               interval = "Biweek",
               target_disease = "WNV",
               pt_estimate = "bc-mle", 
              
               separate_by = c("agency","species"),
               wide = FALSE) 
#> # A tibble: 1,233 × 13
#>     Year Biweek Agency Species         Count Trap   TrapEvents Abundance Disease
#>    <dbl>  <dbl> <chr>  <chr>           <int> <chr>       <int>     <dbl> <chr>  
#>  1  2015      1 AGENCY An freeborni        4 " MMT…        186      0.02 <NA>   
#>  2  2015      1 AGENCY Cs incidens         5 " MMT…        186      0.03 <NA>   
#>  3  2015      1 AGENCY Cs inornata       125 " MMT…        186      0.67 <NA>   
#>  4  2015      1 AGENCY Cx pipiens         41 " MMT…        186      0.22 <NA>   
#>  5  2015      1 AGENCY Cx stigmatosoma     2 " MMT…        186      0.01 <NA>   
#>  6  2015      1 AGENCY Cx tarsalis         4 " MMT…        186      0.02 <NA>   
#>  7  2015      2 AGENCY Cs incidens        10 " MMT…        137      0.07 <NA>   
#>  8  2015      2 AGENCY Cs inornata       147 " MMT…        137      1.07 <NA>   
#>  9  2015      2 AGENCY Cx pipiens         12 " MMT…        137      0.09 <NA>   
#> 10  2015      2 AGENCY Cx stigmatosoma     1 " MMT…        137      0.01 <NA>   
#> # ℹ 1,223 more rows
#> # ℹ 4 more variables: InfectionRate <dbl>, LowerCI <dbl>, UpperCI <dbl>,
#> #   VectorIndex <dbl>
sample_collections%>%filter(species_display_name=="Cx tarsalis", trap_acronym=="CO2")
#> # A tibble: 342 × 16
#> # Groups:   surv_year [7]
#>    agency_code collection_id collection_date surv_year species_display_name
#>    <chr>               <int> <date>              <dbl> <chr>               
#>  1 AGENCY            1392822 2015-04-26           2015 Cx tarsalis         
#>  2 AGENCY            1411490 2015-05-17           2015 Cx tarsalis         
#>  3 AGENCY            1412519 2015-05-22           2015 Cx tarsalis         
#>  4 AGENCY            1415729 2015-05-25           2015 Cx tarsalis         
#>  5 AGENCY            1399581 2015-05-04           2015 Cx tarsalis         
#>  6 AGENCY            1413728 2015-05-22           2015 Cx tarsalis         
#>  7 AGENCY            1408922 2015-05-15           2015 Cx tarsalis         
#>  8 AGENCY            1400736 2015-05-08           2015 Cx tarsalis         
#>  9 AGENCY            1402308 2015-05-11           2015 Cx tarsalis         
#> 10 AGENCY            1412359 2015-05-22           2015 Cx tarsalis         
#> # ℹ 332 more rows
#> # ℹ 11 more variables: sex_type <chr>, trap_acronym <chr>,
#> #   trap_problem_bit <lgl>, num_trap <int>, trap_nights <int>, num_count <int>,
#> #   site_code <dbl>, agency_id <dbl>, county <chr>, collection_longitude <dbl>,
#> #   collection_latitude <dbl>

Tables

getPoolsComparisionTable()

Description

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

Usage

getPoolsComparisionTable(pools,target_disease, species_separate=F)

Arguments

getPoolsComparisionTable(
  sample_pools,
  interval = "Week",
  target_disease = "WNV"
)
#> # A tibble: 169 × 6
#> # Groups:   Year, Week [169]
#>     Year  Week Negative Confirmed Total `Percent Positive`
#>    <dbl> <dbl>    <int>     <int> <int>              <dbl>
#>  1  2015    18        3         0     3                  0
#>  2  2015    19        1         0     1                  0
#>  3  2015    20        3         0     3                  0
#>  4  2015    21        9         0     9                  0
#>  5  2015    22        9         0     9                  0
#>  6  2015    23        5         0     5                  0
#>  7  2015    24        6         0     6                  0
#>  8  2015    25        8         0     8                  0
#>  9  2015    26        5         0     5                  0
#> 10  2015    27        9         1    10                 10
#> # ℹ 159 more rows

Styling Dataframes with ‘kable’

Professional looking tables can be produced using the ‘kable’ and ‘kableExtra’ packages.



library(kableExtra)
#> 
#> Attaching package: 'kableExtra'
#> The following object is masked from 'package:dplyr':
#> 
#>     group_rows

AbAnOutput = getAbundance(
  sample_collections,
  interval = "Biweek",
  
  species = c("Cx tarsalis", "Cx pipiens"),
  trap = "CO2",
  separate_by = "species")

head(AbAnOutput)
#>   Agency Year Biweek   County     Species Count TrapEvents Trap Abundance
#> 1 AGENCY 2021      4 County 1  Cx pipiens    10          3  CO2      3.33
#> 2 AGENCY 2021      7 County 1  Cx pipiens     4          3  CO2      1.33
#> 3 AGENCY 2021      8 County 1  Cx pipiens    10         10  CO2      1.00
#> 4 AGENCY 2021      8 County 1 Cx tarsalis    13         10  CO2      1.30
#> 5 AGENCY 2021     10 County 1  Cx pipiens     9          5  CO2      1.80
#> 6 AGENCY 2021     11 County 1  Cx pipiens     5         13  CO2      0.38

#kable table where column names, font_size, style and much more can be customized

AbAnOutput %>%
  kbl() %>%
  kable_styling(
    bootstrap_options = "striped",
    font_size = 14,
    latex_options = "scale_down"
  ) %>%
  footnote(general = "Table X: Combined biweekly Abundance Calculation for Cx. tarsalis, pipiens in CO2 traps", general_title = "")
Agency Year Biweek County Species Count TrapEvents Trap Abundance
AGENCY 2021 4 County 1 Cx pipiens 10 3 CO2 3.33
AGENCY 2021 7 County 1 Cx pipiens 4 3 CO2 1.33
AGENCY 2021 8 County 1 Cx pipiens 10 10 CO2 1.00
AGENCY 2021 8 County 1 Cx tarsalis 13 10 CO2 1.30
AGENCY 2021 10 County 1 Cx pipiens 9 5 CO2 1.80
AGENCY 2021 11 County 1 Cx pipiens 5 13 CO2 0.38
AGENCY 2021 11 County 1 Cx tarsalis 12 13 CO2 0.92
AGENCY 2021 12 County 1 Cx pipiens 45 10 CO2 4.50
AGENCY 2021 12 County 1 Cx tarsalis 429 10 CO2 42.90
AGENCY 2021 13 County 1 Cx pipiens 338 12 CO2 28.17
AGENCY 2021 14 County 1 Cx pipiens 40 9 CO2 4.44
AGENCY 2021 14 County 1 Cx tarsalis 39 9 CO2 4.33
AGENCY 2021 15 County 1 Cx pipiens 23 10 CO2 2.30
AGENCY 2021 15 County 1 Cx tarsalis 3114 10 CO2 311.40
AGENCY 2021 16 County 1 Cx pipiens 71 12 CO2 5.92
AGENCY 2021 16 County 1 Cx tarsalis 2194 12 CO2 182.83
AGENCY 2021 17 County 1 Cx pipiens 18 8 CO2 2.25
AGENCY 2021 17 County 1 Cx tarsalis 5 8 CO2 0.62
AGENCY 2021 18 County 1 Cx tarsalis 49 6 CO2 8.17
AGENCY 2021 19 County 1 Cx tarsalis 35 10 CO2 3.50
AGENCY 2021 20 County 1 Cx tarsalis 39 10 CO2 3.90
AGENCY 2021 21 County 1 Cx pipiens 1 6 CO2 0.17
AGENCY 2021 21 County 1 Cx tarsalis 15 6 CO2 2.50
AGENCY 2020 9 County 1 Cx tarsalis 56 4 CO2 14.00
AGENCY 2020 10 County 1 Cx pipiens 1 6 CO2 0.17
AGENCY 2020 10 County 1 Cx tarsalis 23 6 CO2 3.83
AGENCY 2020 11 County 1 Cx pipiens 24 15 CO2 1.60
AGENCY 2020 11 County 1 Cx tarsalis 180 15 CO2 12.00
AGENCY 2020 12 County 1 Cx pipiens 5 10 CO2 0.50
AGENCY 2020 12 County 1 Cx tarsalis 246 10 CO2 24.60
AGENCY 2020 13 County 1 Cx pipiens 93 14 CO2 6.64
AGENCY 2020 13 County 1 Cx tarsalis 115 14 CO2 8.21
AGENCY 2020 14 County 1 Cx pipiens 287 12 CO2 23.92
AGENCY 2020 14 County 1 Cx tarsalis 2297 12 CO2 191.42
AGENCY 2020 15 County 1 Cx pipiens 29 8 CO2 3.62
AGENCY 2020 15 County 1 Cx tarsalis 9 8 CO2 1.12
AGENCY 2020 16 County 1 Cx pipiens 87 8 CO2 10.88
AGENCY 2020 16 County 1 Cx tarsalis 258 8 CO2 32.25
AGENCY 2020 17 County 1 Cx pipiens 13 10 CO2 1.30
AGENCY 2020 17 County 1 Cx tarsalis 1657 10 CO2 165.70
AGENCY 2020 18 County 1 Cx tarsalis 79 7 CO2 11.29
AGENCY 2020 19 County 1 Cx pipiens 44 13 CO2 3.38
AGENCY 2020 19 County 1 Cx tarsalis 143 13 CO2 11.00
AGENCY 2020 20 County 1 Cx tarsalis 43 12 CO2 3.58
AGENCY 2020 21 County 1 Cx pipiens 31 13 CO2 2.38
AGENCY 2020 21 County 1 Cx tarsalis 30 13 CO2 2.31
AGENCY 2020 22 County 1 Cx pipiens 2 11 CO2 0.18
AGENCY 2020 22 County 1 Cx tarsalis 10 11 CO2 0.91
AGENCY 2020 23 County 1 Cx pipiens 8 8 CO2 1.00
AGENCY 2020 23 County 1 Cx tarsalis 1 8 CO2 0.12
AGENCY 2020 24 County 1 Cx pipiens 3 4 CO2 0.75
AGENCY 2019 4 County 1 Cx pipiens 3 1 CO2 3.00
AGENCY 2019 9 County 1 Cx pipiens 15 9 CO2 1.67
AGENCY 2019 9 County 1 Cx tarsalis 3 9 CO2 0.33
AGENCY 2019 10 County 1 Cx pipiens 8 7 CO2 1.14
AGENCY 2019 10 County 1 Cx tarsalis 14 7 CO2 2.00
AGENCY 2019 11 County 1 Cx pipiens 25 16 CO2 1.56
AGENCY 2019 11 County 1 Cx tarsalis 539 16 CO2 33.69
AGENCY 2019 12 County 1 Cx pipiens 51 4 CO2 12.75
AGENCY 2019 13 County 1 Cx pipiens 36 13 CO2 2.77
AGENCY 2019 13 County 1 Cx tarsalis 845 13 CO2 65.00
AGENCY 2019 14 County 1 Cx pipiens 14 6 CO2 2.33
AGENCY 2019 14 County 1 Cx tarsalis 252 6 CO2 42.00
AGENCY 2019 15 County 1 Cx pipiens 160 16 CO2 10.00
AGENCY 2019 15 County 1 Cx tarsalis 4079 16 CO2 254.94
AGENCY 2019 16 County 1 Cx pipiens 14 14 CO2 1.00
AGENCY 2019 16 County 1 Cx tarsalis 54 14 CO2 3.86
AGENCY 2019 17 County 1 Cx pipiens 3 7 CO2 0.43
AGENCY 2019 17 County 1 Cx tarsalis 74 7 CO2 10.57
AGENCY 2019 18 County 1 Cx pipiens 175 6 CO2 29.17
AGENCY 2019 18 County 1 Cx tarsalis 87 6 CO2 14.50
AGENCY 2019 19 County 1 Cx pipiens 42 9 CO2 4.67
AGENCY 2019 19 County 1 Cx tarsalis 12 9 CO2 1.33
AGENCY 2019 20 County 1 Cx pipiens 134 12 CO2 11.17
AGENCY 2019 20 County 1 Cx tarsalis 80 12 CO2 6.67
AGENCY 2019 21 County 1 Cx tarsalis 37 9 CO2 4.11
AGENCY 2018 10 County 1 Cx pipiens 8 16 CO2 0.50
AGENCY 2018 10 County 1 Cx tarsalis 296 16 CO2 18.50
AGENCY 2018 11 County 1 Cx pipiens 80 16 CO2 5.00
AGENCY 2018 11 County 1 Cx tarsalis 16 16 CO2 1.00
AGENCY 2018 12 County 1 Cx pipiens 27 16 CO2 1.69
AGENCY 2018 12 County 1 Cx tarsalis 63 16 CO2 3.94
AGENCY 2018 13 County 1 Cx pipiens 132 13 CO2 10.15
AGENCY 2018 13 County 1 Cx tarsalis 3884 13 CO2 298.77
AGENCY 2018 14 County 1 Cx pipiens 34 9 CO2 3.78
AGENCY 2018 14 County 1 Cx tarsalis 452 9 CO2 50.22
AGENCY 2018 15 County 1 Cx pipiens 105 11 CO2 9.55
AGENCY 2018 15 County 1 Cx tarsalis 42 11 CO2 3.82
AGENCY 2018 16 County 1 Cx pipiens 782 14 CO2 55.86
AGENCY 2018 16 County 1 Cx tarsalis 829 14 CO2 59.21
AGENCY 2018 17 County 1 Cx pipiens 6 13 CO2 0.46
AGENCY 2018 17 County 1 Cx tarsalis 35 13 CO2 2.69
AGENCY 2018 18 County 1 Cx pipiens 200 13 CO2 15.38
AGENCY 2018 18 County 1 Cx tarsalis 11 13 CO2 0.85
AGENCY 2018 19 County 1 Cx pipiens 125 10 CO2 12.50
AGENCY 2018 20 County 1 Cx pipiens 31 10 CO2 3.10
AGENCY 2018 20 County 1 Cx tarsalis 16 10 CO2 1.60
AGENCY 2018 21 County 1 Cx tarsalis 11 9 CO2 1.22
AGENCY 2017 8 County 1 Cx pipiens 10 4 CO2 2.50
AGENCY 2017 9 County 1 Cx pipiens 11 8 CO2 1.38
AGENCY 2017 9 County 1 Cx tarsalis 7 8 CO2 0.88
AGENCY 2017 10 County 1 Cx pipiens 11 16 CO2 0.69
AGENCY 2017 10 County 1 Cx tarsalis 138 16 CO2 8.62
AGENCY 2017 11 County 1 Cx pipiens 33 13 CO2 2.54
AGENCY 2017 11 County 1 Cx tarsalis 318 13 CO2 24.46
AGENCY 2017 12 County 1 Cx pipiens 43 17 CO2 2.53
AGENCY 2017 12 County 1 Cx tarsalis 22 17 CO2 1.29
AGENCY 2017 13 County 1 Cx pipiens 135 19 CO2 7.11
AGENCY 2017 13 County 1 Cx tarsalis 74 19 CO2 3.89
AGENCY 2017 14 County 1 Cx pipiens 86 23 CO2 3.74
AGENCY 2017 14 County 1 Cx tarsalis 324 23 CO2 14.09
AGENCY 2017 15 County 1 Cx pipiens 230 10 CO2 23.00
AGENCY 2017 15 County 1 Cx tarsalis 439 10 CO2 43.90
AGENCY 2017 16 County 1 Cx pipiens 295 13 CO2 22.69
AGENCY 2017 16 County 1 Cx tarsalis 2279 13 CO2 175.31
AGENCY 2017 17 County 1 Cx pipiens 286 22 CO2 13.00
AGENCY 2017 17 County 1 Cx tarsalis 4249 22 CO2 193.14
AGENCY 2017 18 County 1 Cx pipiens 31 17 CO2 1.82
AGENCY 2017 18 County 1 Cx tarsalis 431 17 CO2 25.35
AGENCY 2017 19 County 1 Cx pipiens 138 10 CO2 13.80
AGENCY 2017 19 County 1 Cx tarsalis 6 10 CO2 0.60
AGENCY 2017 20 County 1 Cx pipiens 42 22 CO2 1.91
AGENCY 2017 20 County 1 Cx tarsalis 7 22 CO2 0.32
AGENCY 2017 21 County 1 Cx tarsalis 138 16 CO2 8.62
AGENCY 2016 8 County 1 Cx tarsalis 68 12 CO2 5.67
AGENCY 2016 9 County 1 Cx pipiens 6 11 CO2 0.55
AGENCY 2016 9 County 1 Cx tarsalis 7 11 CO2 0.64
AGENCY 2016 10 County 1 Cx pipiens 59 9 CO2 6.56
AGENCY 2016 10 County 1 Cx tarsalis 264 9 CO2 29.33
AGENCY 2016 11 County 1 Cx pipiens 8 15 CO2 0.53
AGENCY 2016 11 County 1 Cx tarsalis 44 15 CO2 2.93
AGENCY 2016 12 County 1 Cx pipiens 17 26 CO2 0.65
AGENCY 2016 12 County 1 Cx tarsalis 542 26 CO2 20.85
AGENCY 2016 13 County 1 Cx pipiens 91 21 CO2 4.33
AGENCY 2016 13 County 1 Cx tarsalis 1098 21 CO2 52.29
AGENCY 2016 14 County 1 Cx pipiens 7 10 CO2 0.70
AGENCY 2016 14 County 1 Cx tarsalis 87 10 CO2 8.70
AGENCY 2016 15 County 1 Cx pipiens 208 18 CO2 11.56
AGENCY 2016 15 County 1 Cx tarsalis 1990 18 CO2 110.56
AGENCY 2016 16 County 1 Cx pipiens 454 10 CO2 45.40
AGENCY 2016 16 County 1 Cx tarsalis 674 10 CO2 67.40
AGENCY 2016 17 County 1 Cx pipiens 395 18 CO2 21.94
AGENCY 2016 17 County 1 Cx tarsalis 712 18 CO2 39.56
AGENCY 2016 18 County 1 Cx pipiens 78 16 CO2 4.88
AGENCY 2016 18 County 1 Cx tarsalis 252 16 CO2 15.75
AGENCY 2016 19 County 1 Cx pipiens 23 17 CO2 1.35
AGENCY 2016 19 County 1 Cx tarsalis 137 17 CO2 8.06
AGENCY 2016 20 County 1 Cx pipiens 28 16 CO2 1.75
AGENCY 2016 20 County 1 Cx tarsalis 10 16 CO2 0.62
AGENCY 2016 21 County 1 Cx pipiens 1 9 CO2 0.11
AGENCY 2016 21 County 1 Cx tarsalis 7 9 CO2 0.78
AGENCY 2015 8 County 1 Cx pipiens 8 6 CO2 1.33
AGENCY 2015 9 County 1 Cx pipiens 1 10 CO2 0.10
AGENCY 2015 9 County 1 Cx tarsalis 11 10 CO2 1.10
AGENCY 2015 10 County 1 Cx pipiens 14 27 CO2 0.52
AGENCY 2015 10 County 1 Cx tarsalis 598 27 CO2 22.15
AGENCY 2015 11 County 1 Cx pipiens 38 19 CO2 2.00
AGENCY 2015 11 County 1 Cx tarsalis 280 19 CO2 14.74
AGENCY 2015 12 County 1 Cx pipiens 144 16 CO2 9.00
AGENCY 2015 12 County 1 Cx tarsalis 593 16 CO2 37.06
AGENCY 2015 13 County 1 Cx pipiens 80 17 CO2 4.71
AGENCY 2015 13 County 1 Cx tarsalis 325 17 CO2 19.12
AGENCY 2015 14 County 1 Cx pipiens 204 15 CO2 13.60
AGENCY 2015 14 County 1 Cx tarsalis 327 15 CO2 21.80
AGENCY 2015 15 County 1 Cx pipiens 572 10 CO2 57.20
AGENCY 2015 15 County 1 Cx tarsalis 208 10 CO2 20.80
AGENCY 2015 16 County 1 Cx pipiens 172 18 CO2 9.56
AGENCY 2015 16 County 1 Cx tarsalis 633 18 CO2 35.17
AGENCY 2015 17 County 1 Cx pipiens 126 15 CO2 8.40
AGENCY 2015 17 County 1 Cx tarsalis 2307 15 CO2 153.80
AGENCY 2015 18 County 1 Cx pipiens 288 20 CO2 14.40
AGENCY 2015 18 County 1 Cx tarsalis 1768 20 CO2 88.40
AGENCY 2015 19 County 1 Cx pipiens 98 17 CO2 5.76
AGENCY 2015 19 County 1 Cx tarsalis 66 17 CO2 3.88
AGENCY 2015 20 County 1 Cx pipiens 351 22 CO2 15.95
AGENCY 2015 20 County 1 Cx tarsalis 218 22 CO2 9.91
AGENCY 2015 21 County 1 Cx pipiens 45 5 CO2 9.00
Table X: Combined biweekly Abundance Calculation for Cx. tarsalis, pipiens in CO2 traps

Data using ‘datatables’

Interactive html only tables can be produced using the ‘DT’ package. ‘DT’ tables allow for sorting and filtering with in a webpage. These are ideal for viewing data but are not compatible with pdf or word formats.

library(DT)

AbAnOutput %>%
  datatable(colnames =  c("Disease Year", "Biweek", "Count", "Species","Trap Type","Trap Events", "Abundance"))

table(vectorsurvR:::testing_collections$trap_acronym, vectorsurvR:::testing_collections$surv_year) %>%
  kbl(align = "c") %>%
  kable_paper(
    full_width = F,
    html_font = "arial",
    lightable_options = "striped",
  ) %>%
  add_header_above(c("Trap Type", "Years" = 6)) %>%
  footnote(general = "Table 3: Traps deployed by year", general_title = "") %>%
  row_spec(c(3, 9, 10), background = "yellow") %>%
  column_spec(c(4), background = "orange")
Trap Type
Years
2019 2020 2021 2022 2023 2024
BACKPACK 0 0 26 33 11 5
BGSENT 2318 90 11158 14163 13535 18943
BTLJC 30 33 63 0 0 0
CDCAGO 20 0 0 0 0 0
CO2 12201 11622 10901 9719 12364 13475
FLANNEL 3 3 9 14 11 6
GRVD 9560 10184 9221 8611 9069 8910
LCKR 1434 3119 3707 3693 3559 3831
NJLT 3062 844 0 0 0 0
OTHER 0 0 10 11 37 517
OVI 4 0 0 294 0 0
WRKR 0 0 77 0 0 0
Table 3: Traps deployed by year