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Regarding the methodology, from the link:

Tone is judged from the perspective of the actor. Negative stories include stories where the actor is criticized directly. An example is a headline story where Senate minority leader Chuck Schumer criticized Trump when the Labor Department’s April economic report showed that fewer jobs were created than had been predicted. Schumer was quoted as saying, in part: “Eleven weeks into his administration, we have seen nothing from President Trump on infrastructure, on trade, or on any other serious job-creating initiative.”[8] Negative stories also consist of stories where an event, trend, or development reflects unfavorably on the actor. Examples are the stories that appeared under the headlines “President Trump’s approval rating hits a new low”[9] and “GOP withdraws embattled health care bill, handing major setback to Trump, Ryan.”[10]

Negative things happening to or because of somebody isn't indicative of bias in the reporting.