analyse_trend {AeRobiology}

Calculating and Plotting Trends of Pollen Data (summary plot).

Description

Function to calculate the main seasonal indexes of the pollen season (Start Date, Peak Date, End Date and Pollen Integral). Trends analysis of the parameters over the seasons. Summary dot plot showing the distribution of the main seasonal indexes over the years.

Usage

analyse_trend(data, interpolation = TRUE, int.method = "lineal",
  export.plot = TRUE, export.format = "pdf", export.result = TRUE,
  method = "percentage", quantil = 0.75, significant = 0.05,
  split = TRUE, result = "table", ...)

Arguments

data

A data.frame object. This data.frame should include a first column in format Date and the rest of columns in format numeric belonging to each pollen type by column.

interpolation

A logical value specifying if the visualization shows the gaps in the inputs data (interpolation = FALSE) or if an interpolation method is used for filling the gaps (interpolation = TRUE). By default, interpolation = TRUE.

int.method

A character string with the name of the interpolation method to be used. The implemented methods that may be used are: "lineal", "movingmean", "tseries" or "spline". By default, int.method = "lineal".

export.plot

A logical value specifying if a plot will be exported or not. If FALSE graphical results will only be displayed in the active graphics window. If TRUE graphical results will be displayed in the active graphics window and also one pdf/png file will be saved within the plot_AeRobiology directory automatically created in the working directory. By default, export.plot = TRUE.

export.format

A character string specifying the format selected to save the plot. The implemented formats that may be used are: "pdf" or "png". By default, export.format = "pdf".

export.result

A logical value. If export.result = TRUE, a table is exported with the extension .xlsx, in the directory table_AeRobiology. This table has the information about the slope "beta coefficient of a lineal model using as predictor the year and as dependent variable one of the main pollen season indexes". The information is referred to the main pollen season indexes: Start Date, Peak Date, End Date and Pollen Integral.

method

A character string specifying the method applied to calculate the pollen season and the main seasonal parameters. The implemented methods that can be used are: "percentage", "logistic", "moving", "clinical" or "grains". By default, method = "percentage" (perc = 95%). A more detailed information about the different methods for defining the pollen season may be consulted in the function calculate_ps.

quantil

A numeric value (between 0 and 1) indicating the quantile of data to be displayed in the graphical output of the function. quantil = 1 would show all the values, however a lower quantile will exclude the most extreme values of the sample. To split the parameters using a different sampling units (e.g. dates and pollen concentrations) can be used low vs high values of quantil argument (e.g. 0.5 vs 1). Also can be used an extra argument: split. By default, quantil = 0.75. quantil argument can only be applyed when split = FALSE.

significant

A numeric value indicating the significant level to be considered in the linear trends analysis. This p level is displayed in the graphical output of the function. By default, significant = 0.05.

split

A logical argument. If split = TRUE, the plot is separated in two according to the nature of the variables (i.e. dates or pollen concentrations). By default, split = TRUE.

result

A character object with the definition of the object to be produced by the function. If result == "plot", the function returns a list of objects of class ggplot2; if result == "table", the function returns a data.frame. By default, result = "table".

...

Additional arguments for the function calculate_ps are also accepted.

Details

This function allows to study time series trends of the pollen season. Even though the package was originally designed to treat aeropalynological data, it can be used to study many other atmospheric components (e.g., bacteria in the air, fungi, insects ...) (Buters et al., 2018; Oteros et al., 2019). The study of trends in pollen time series is a common approach to study the impact of climate change or other environmental factors on vegetation (Galan et al., 2016; Garcia_Mozo et al., 2016; Recio et al., 2018). This tool can also be useful for studying trends in other fields (Oteros et al., 2015).

Value

If result == "plot", the function returns a list of objects of class ggplot2; if result == "table", the function returns a data.frame with the hourly patterns. The plot is of the class ggplot2 or a list of plots of the class ggplot2 (depending on the argument split). This is a combined dot plot showing the trends (slope and p value) of the main seasonal features.
The object of the class data.frame has the information about the slope (beta coefficient of a lineal model using as predictor the year and as dependent variable one of the main pollen season indexes). The information is referred to the main pollen season indexes: Start Date, Peak Date, End Date and Pollen Integral.

References

Buters, J. T. M., Antunes, C., Galveias, A., Bergmann, K. C., Thibaudon, M., Galan, C., ... & Oteros, J. (2018). Pollen and spore monitoring in the world. Clinical and translational allergy, 8(1), 9.

Galan, C., Alcazar, P., Oteros, J., Garcia_Mozo, H., Aira, M. J., Belmonte, J., ... & Perez_Badia, R. (2016). Airborne pollen trends in the Iberian Peninsula. Science of the Total Environment, 550, 53_59.

Garcia_Mozo, H., Oteros, J. A., & Galan, C. (2016). Impact of land cover changes and climate on the main airborne pollen types in Southern Spain. Science of the Total Environment, 548, 221_228.

Oteros, J., Garcia_Mozo, H., Botey, R., Mestre, A., & Galan, C. (2015). Variations in cereal crop phenology in Spain over the last twenty_six years (1986_2012). Climatic Change, 130(4), 545_558.

Oteros, J., Bartusel, E., Alessandrini, F., Nunez, A., Moreno, D. A., Behrendt, H., ... & Buters, J. (2019). Artemisia pollen is the main vector for airborne endotoxin. Journal of Allergy and Clinical Immunology.

Recio, M., Picornell, A., Trigo, M. M., Gharbi, D., Garcia_Sanchez, J., & Cabezudo, B. (2018). Intensity and temporality of airborne Quercus pollen in the southwest Mediterranean area: Correlation with meteorological and phenoclimatic variables, trends and possible adaptation to climate change. Agricultural and Forest Meteorology, 250, 308_318.

See Also

calculate_ps; plot_trend

Examples

data("munich_pollen")
analyse_trend(munich_pollen, interpolation = FALSE, export.result = FALSE, export.plot = FALSE)