ISSS608 2017-18 T3 Assign Chan En Ying Grace

“Mine dear rose pipits, whence did do thou vanish?”

Background

Methodology

Did Rose Pipit kicketh the bucket?

Which song belongs to thee?

Conclusion

Overview (Mini-Challenge 1)

In 2017, it was suggested that the Kasios Furniture manufacturing company may have been a primary contributor to the apparent reduction of the number of nesting pairs of the Rose-Crested Blue Pipit. Kasios supposedly used the banned substance Methylosmolene in their manufacturing process. However, process waste in the northeast region of the Preserve and Methylosmolene was detected in their smokestack emissions.

Kasios now claims that the analysis was flawed. To combat these conclusions, Kasios has launched their own “investigation” into the Pipit situation, and they are now reporting that there are plenty of Rose-crested Blue Pipits happily living and nesting in the Preserve. To back up this claim, they have provided a set of Pipit bird calls, recently recorded across the Preserve, with locations of where they were recorded. Clearly, they claim, the Pipits are a thriving population, and Kasios will provide even more supporting evidence as their investigation proceeds.

The Pangera Ornithology Conservation Society is at their wit’s end at what to do about this turn of events. The townsfolk and Preserve rangers seem satisfied that the recordings back up Kasios’ claims. Mistford College does not have another Pipit expert they can call upon for help. But, they do have a collection of bird calls from the Preserve that has been vetted by various ornithology groups as having accurate identifications. They have heard that new techniques from machine learning and visual analytics can be applied, where these calls could be classified and analyzed using these technologies.

Research Questions

Using R programming, techniques from visual and geospatial analytics will be applied to answer the following research questions:

1.	What are the patterns, trends and anomalies across the bird species in the Preserve over the time of collection?
2.	What happened to the state of the Rose Pipits? Are Pipits actually thriving across the Preserve?
3.	Does the set of bird calls supplied by Kasios support the claim of Pipits being found across the Preserve?

Data Sources

The following lists the data attributes used for the analysis. The data is obtained from http://vacommunity.org/VAST+Challenge+2018+MC1.

No.	Name	Attributes	Format	No. of Records
1.	The Lekagul Roadway Map	Class : RasterLayer Dimensions : 200, 200, 40000 (nrow, ncol, ncell) Resolution : 1, 1 (x, y) Extent : 0, 200, 0, 200 (xmin, xmax, ymin, ymax) Coord. ref. : NA Names : Lekagul_Roadways_2018 Values : 0, 255 (min, max)	BMP	Single Layer
2.	Metadata of Bird Call Collection	File ID English_name Vocalization_type Quality Time Date X,Y Coordinates	CSV	2081 Birds; 19 Species
3.	Test Birds from Kasios	Bird ID X,Y Coordinates	CSV	15 Birds
4.	Audio of Bird Call Collection	Name of Audio File (containing species & bird ID) MP3 Audio of Bird Call/Song Acoustic Parameters, extracted using analyzeFolder() include: duration voiced ampl_mean, ampl_median, ampl_sd amplVoiced_mean, amplVoiced_median, amplVoiced_sd dom_mean, dom_median, dom_sd entropy_mean, entropy_median, entropy_sd f1_freq_mean, f1_freq_median, f1_freq_sd f1_width_mean, f1_width_median, f1_width_sd f2_freq_mean, f2_freq_median, f2_freq_sd f2_width_mean, f2_width_median, f2_width_sd f3_freq_mean, f3_freq_median, f3_freq_sd f3_width_mean, f3_width_median, f3_width_sd harmonics_mean, harmonics_median, harmonics_sd HNR_mean, HNR_median, HNR_sd meanFreq_mean, meanFreq_median, meanFreq_sd peakFreq_mean, peakFreq_median, peakFreq_sd pitch_mean, pitch_median, pitch_sd pitchAutocor_mean, pitchAutocor_median, pitchAutocor_sd pitchSpec_mean, pitchSpec_median, pitchSpec_sd quartile25_mean, quartile25_median, quartile25_sd quartile50_mean, quartile50_median, quartile50_sd quartile75_mean, quartile75_median, quartile75_sd specSlope_mean, specSlope_median, specSlope_sd	MP3	2081 Recording
5.	Audio of Test Birds from Kasios	Name of Audio File (with Bird ID) MP3 Audio of Bird Call/Song Acoustic Parameters, extracted using analyzeFolder() include: duration voiced ampl_mean, ampl_median, ampl_sd amplVoiced_mean, amplVoiced_median, amplVoiced_sd dom_mean, dom_median, dom_sd entropy_mean, entropy_median, entropy_sd f1_freq_mean, f1_freq_median, f1_freq_sd f1_width_mean, f1_width_median, f1_width_sd f2_freq_mean, f2_freq_median, f2_freq_sd f2_width_mean, f2_width_median, f2_width_sd f3_freq_mean, f3_freq_median, f3_freq_sd f3_width_mean, f3_width_median, f3_width_sd harmonics_mean, harmonics_median, harmonics_sd HNR_mean, HNR_median, HNR_sd meanFreq_mean, meanFreq_median, meanFreq_sd peakFreq_mean, peakFreq_median, peakFreq_sd pitch_mean, pitch_median, pitch_sd pitchAutocor_mean, pitchAutocor_median, pitchAutocor_sd pitchSpec_mean, pitchSpec_median, pitchSpec_sd quartile25_mean, quartile25_median, quartile25_sd quartile50_mean, quartile50_median, quartile50_sd quartile75_mean, quartile75_median, quartile75_sd specSlope_mean, specSlope_median, specSlope_sd	MP3	15 Recording