calculate_ps: Estimation of the Main Parameters of the Pollen Season

Description Usage Arguments Details Value References See Also Examples

Description

Function to calculate the main parameters of the pollen season with regard to phenology and pollen intensity from a historical database of several pollen types. The function can use the most common methods in the definition of the pollen season.

Usage

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calculate_ps(data, method = "percentage", th.day = 100, perc = 95,
  def.season = "natural", reduction = FALSE, red.level = 0.9,
  derivative = 5, man = 11, th.ma = 5, n.clinical = 5,
  window.clinical = 7, window.grains = 5, th.pollen = 10,
  th.sum = 100, type = "none", interpolation = TRUE,
  int.method = "lineal", maxdays = 30, result = "table",
  plot = TRUE, export.plot = FALSE, export.result = FALSE)

Arguments

data

A data.frame object including the general database where calculation of the pollen season must be applied. This data.frame must include a first column in Date format and the rest of columns in numeric format belonging to each pollen type by column.

method

A character string specifying the method applied to calculate the pollen season and the main parameters. The implemented methods that can be used are: "percentage", "logistic", "moving", "clinical" or "grains". A more detailed information about the different methods for defining the pollen season may be consulted in Details.

th.day

A numeric value. The number of days whose pollen concentration is bigger than this threshold is calculated for each year and pollen type. This value will be obtained in the results of the function. The th.day argument will be 100 by default.

perc

A numeric value ranging 0_100. This argument is valid only for method = "percentage". This value represents the percentage of the total annual pollen included in the pollen season, removing (100_perc)/2% of the total pollen before and after of the pollen season. The perc argument will be 95 by default.

def.season

A character string specifying the method for selecting the best annual period to calculate the pollen season. The pollen seasons may occur within the natural year between two years. The implemented options that can be used are: "natural", "interannual" or "peak". The def.season argument will be "natural" by default. A more detailed information about the different methods for selecting the best annual period to calculate the pollen season may be consulted in Details.

reduction

A logical value. This argument is valid only for the "logistic" method. If FALSE the reduction of the pollen data is not applicable. If TRUE a reduction of the peaks above a certain level (red.level argument) will be carried out before the definition of the pollen season. The reduction argument will be FALSE by default. A more detailed information about the reduction process may be consulted in Details.

red.level

A numeric value ranging 0_1 specifying the percentile used as level to reduce the peaks of the pollen series before the definition of the pollen season. This argument is valid only for the "logistic" method. The red.level argument will be 0.90 by default, specifying the percentile 90.

derivative

A numeric (integer) value belonging to options of 4, 5 or 6 specifying the derivative that will be applied to calculate the asymptotes which determines the pollen season using the "logistic" method. This argument is valid only for the "logistic" method. The derivative argument will be 5 by default. More information may be consulted in Details.

man

A numeric (integer) value specifying the order of the moving average applied to calculate the pollen season using the "moving" method. This argument is valid only for the "moving" method. The man argument will be 11 by default.

th.ma

A numeric value specifying the threshold used for the "moving" method for defining the beginning and the end of the pollen season. This argument is valid only for the "moving" method. The th.ma argument will be 5 by default.

n.clinical

A numeric (integer) value specifying the number of days which must exceed a given threshold (th.pollen argument) for defining the beginning and the end of the pollen season. This argument is valid only for the "clinical" method. The n.clinical argument will be 5 by default.

window.clinical

A numeric (integer) value specifying the time window during which the conditions must be evaluated for defining the beginning and the end of the pollen season using the "clinical" method. This argument is valid only for the "clinical" method. The window.clinical argument will be 7 by default.

window.grains

A numeric (integer) value specifying the time window during which the conditions must be evaluated for defining the beginning and the end of the pollen season using the "grains" method. This argument is valid only for the "grains" method. The window.grains argument will be 5 by default.

th.pollen

A numeric value specifying the threshold that must be exceeded during a given number of days (n.clinical or window.grains arguments) for defining the beginning and the end of the pollen season using the "clinical" or "grains" methods. This argument is valid only for the "clinical" or "grains" methods. The th.pollen argument will be 10 by default.

th.sum

A numeric value specifying the pollen threshold that must be exceeded by the sum of daily pollen during a given number of days (n.clinical argument) exceeding a given daily threshold (th.pollen argument) for defining the beginning and the end of the pollen season using the "clinical" method. This argument is valid only for the "clinical" method. The th.sum argument will be 100 by default.

type

A character string specifying the parameters considered according to a specific pollen type for calculating the pollen season using the "clinical" method. The implemented pollen types that may be used are: "birch", "grasses", "cypress", "olive" or "ragweed". As result for selecting any of these pollen types the parameters n.clinical, window.clinical, th.pollen and th.sum will be automatically adjusted for the "clinical" method. If no pollen types are specified (type = "none"), these parameters will be considered by the user. This argument is valid only for the "clinical" method. The type argument will be "none" by default.

interpolation

A logical value. If FALSE the interpolation of the pollen data is not applicable. If TRUE an interpolation of the pollen series will be applied to complete the gaps with no data before the calculation of the pollen season. The interpolation argument will be TRUE by default. A more detailed information about the interpolation method may be consulted in Details.

int.method

A character string specifying the method selected to apply the interpolation method in order to complete the pollen series. The implemented methods that may be used are: "lineal", "movingmean", "spline" or "tseries". The int.method argument will be "lineal" by default.

maxdays

A numeric (integer value) specifying the maximum number of consecutive days with missing data that the algorithm is going to interpolate. If the gap is bigger than the argument value, the gap will not be interpolated. Not valid with int.method = "tseries". The maxdays argument will be 30 by default.

result

A character string specifying the output for the function. The implemented outputs that may be obtained are: "table" and "list". The argument result will be "table" by default.

plot

A logical value specifying if a set of plots based on the definition of the pollen season will be shown in the plot history or not. If FALSE graphical results will not be shown. If TRUE a set of plots will be shown in the plot history. The plot argument will be TRUE by default.

export.plot

A logical value specifying if a set of plots based on the definition of the pollen season will be saved in the workspace. If TRUE a pdf file for each pollen type showing graphically the definition of the pollen season for each studied year will be saved within the plot_AeRobiology directory created in the working directory. The plot argument will be FALSE by default.

export.result

A logical value specifying if a excel file including all parameters for the definition of the pollen season saved in the working directoty will be required or not. If FALSE the results will not exported. If TRUE the results will be exported as xlsx file including all parameters calculated from the definition of the pollen season within the table_AeRobiology directory created in the working directory. The export.result argument will be FALSE by default.

Details

This function allows to calculate the pollen season using five different methods which are described below. After calculating the start_date, end_date and peak_date for the pollen season all rest of parameters have been calculated as detailed in Value section.

The pollen season of the species may occur during the natural year (Calendar year: from 1. January to 31. December) or the start_date and the end_date of the pollen season may happen in two different natural years (or calendar years). This consideration has been taken into account and in this package different method for defining the period for calculating the pollen season have been implemented. In this sense, the def.season argument has been incorporated in three options:

Pollen time series frequently have different gaps with no data and this fact could be a problem for the calculation of specific methods for defining the pollen season even providing incorrect results. In this sense by default a linear interpolation will be carried out to complete these gaps before to define the pollen season (interpolation = TRUE). Additionally, the users may select other interpolation methods using the int.method argument, as "lineal", "movingmean", "spline" or "tseries". For more information to see the interpollen function.

Value

This function returns different results:
data.frame when result = "table" including the main parameters of the pollen season with regard to phenology and pollen intensity as:

list when result = "list" including the main parameters of the pollen season, one pollen type by element plots when plot = TRUE showing graphically the definition of the pollen season for each studied year in the plot history. If export.result = TRUE this data.frame will also be exported as xlsx file within the table_AeRobiology directory created in the working directory. If export.result = FALSE the results will also be showed as list object named list.ps.
If export.plot = TRUE a pdf file for each pollen type showing graphically the definition of the pollen season for each studied year will be saved within the plot_AeRobiology directory created in the working directory.

References

Andersen, T.B., 1991. A model to predict the beginning of the pollen season. Grana, 30(1), pp.269_275.

Cunha, M., Ribeiro, H., Costa, P. and Abreu, I., 2015. A comparative study of vineyard phenology and pollen metrics extracted from airborne pollen time series. Aerobiologia, 31(1), pp.45_56.

Galan, C., Garcia_Mozo, H., Carinanos, P., Alcazar, P. and Dominguez_Vilches, E., 2001. The role of temperature in the onset of the Olea europaea L. pollen season in southwestern Spain. International Journal of Biometeorology, 45(1), pp.8_12.

Nilsson, S. and Persson, S., 1981. Tree pollen spectra in the Stockholm region (Sweden), 1973_1980. Grana, 20(3), pp.179_182.

Pfaar, O., Bastl, K., Berger, U., Buters, J., Calderon, M.A., Clot, B., Darsow, U., Demoly, P., Durham, S.R., Galan, C., Gehrig, R., Gerth van Wijk, R., Jacobsen, L., Klimek, L., Sofiev, M., Thibaudon, M. and Bergmann, K.C., 2017. Defining pollen exposure times for clinical trials of allergen immunotherapy for pollen_induced rhinoconjunctivitis_an EAACI position paper. Allergy, 72(5), pp.713_722.

Ribeiro, H., Cunha, M. and Abreu, I., 2007. Definition of main pollen season using logistic model. Annals of Agricultural and Environmental Medicine, 14(2), pp.259_264.

See Also

interpollen, plot_ps

Examples

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data("munich_pollen")
calculate_ps(munich_pollen, plot = TRUE, result = "table")

AeRobiology documentation built on June 3, 2019, 9:03 a.m.