Al Jazeera used a mobile phone survey, satellite imagery, submitted photos and public data to try to confirm these reports and shed light on the scale of the conflict.
We called more than 35,000 numbers by random dialling on the Zain mobile network in South Sudan. The survey was distributed by a company called Viamo. Of those calls, more than 2,900 people listened to the introduction and selected a language, and 405 people completed the entire 14-question survey, which was designed in consultation with South Sudan land rights experts and statisticians.
We prerecorded questions in six languages: English, Arabic, Dinka, Nuer, Bari and Madi, and participants could respond to those multiple-choice questions by pressing number keys on their phones. In a few cases, open ended-questions allowed people to record an answer, which was later transcribed.
All the translations were verified by two different translators, to ensure accuracy, and the survey was tested several times before the collected results were considered useable. The survey included questions on demographics, displacement, destruction, and plans to return.
Read more about our methodology
When Logonda felt safe enough, after the soldiers had left, he rose from the burned patch of bushes and walked back to his house. He gathered a few items, including his bicycle, and began the 40km journey south to cross the Ugandan border.
But back in Mondikolok, known for its prominent red-roofed hexagonal church, six people were dead, according to Human Rights Watch (HRW) and several citizens interviewed by Al Jazeera.
A catechist was shot on his way to church to help lead the worship. A woman, shot and left for dead in burning grass. An elderly man, disabled, unable to run, shot where he was left by fleeing friends and family.
Just a few days earlier, Logonda had been up late at night. He had been disturbed by an unusual noise coming from the main road.
"I heard a fleet of vehicles, so I came out," he said. "As I came out, I saw those vehicles were the vehicles of soldiers. They were from Juba and they were going to the barracks. That gave me the sense that there was already a problem."
He decided to immediately send his wife and children to Uganda, to register as refugees and set up in the camp. He had a feeling problems were coming, but he never expected it to come so soon, just days after he sent them away.
What Logonda didn't know was that opposition soldiers were about to attack a government convoy a short distance from his village, according to a report by HRW.
In South Sudan, there is frequent fighting between the opposition soldiers, siding with former First Vice President Riek Machar and often controlling rural, forested areas, and the soldiers of the government army, who side with the country's President Kiir and have retained control in most cities and major towns. The tensions, often split by ethnic group, draw in citizens who happen to live in areas amid the fighting.
Opposition soldiers often fight from forested and overgrown areas, but single men found in villages in those regions can easily be accused of supporting them or even being one of their fighters.
Logonda said the soldiers were saying they were pursuing soldiers from the SPLA-IO (the opposition army).
"What I know is there are these soldiers in opposition," he said. "But not in Mondikolok; some kilometres away from Mondikolok."
He said none of those six killed by the soldiers was a member of the opposition troops.
"They were civilians, of course," he said. "The six were civilians. None of the soldiers were killed. They were all civilian."
They were civilians, of course," he said. "The six were civilians. None of the soldiers were killed. They were all civilian.Chaplain Logonda
The HRW report, based on interviews with more than 100 refugees and relying on multiple independent accounts of the same incident, said the soldiers "fired indiscriminately … in what seems to have been retaliation for hit-and-run attacks on their forces, failing to take any precautions to protect civilians."
It is a common counterinsurgency tactic used by the South Sudanese military, said Alan Boswell, now Crisis Group's Senior Analyst for South Sudan, based in neighbouring Kenya and who has researched South Sudan since before the country gained independence. He said the tactic often follows an ambush on government troops - or simply reports of opposition fighters starting to mobilise.
"And then there would be a punitive attack, usually by the government forces, usually on a civilian centre, usually a town, a village," says Boswell. "Sometimes, a couple of people are killed in that attack; other times, it's just looting and burning. What tends to happen is that the civilian population tends to flee."
The government has continually denied that its soldiers target civilians as a way to force them to relocate.
"The Army leadership does not condone intentional killing of civilians and deliberate destruction of their homes," said Major General Lul Ruai Koang, director for media and press and spokesperson for the South Sudanese army (SSPDF), in a WhatsApp response to questions from Al Jazeera.
"A few rogue soldiers, who had taken the law into their own hands, had been tried and sentenced for various crimes committed."
He cited the example of the sentencing last September in a Juba military court of 10 soldiers for crimes committed during an attack at the Terrain Hotel in July 2016. According to Amnesty International, the soldiers were found guilty of raping aid workers and murdering 32-year-old John Gatluak Nhial, a South Sudanese journalist who left behind his wife, three children, and another child born the day after he died.
Of the 405 people who answered Al Jazeera's mobile phone survey, more than 40 percent said they had been forced off their land or out of their home since December 2013. Nearly half of those people blamed government soldiers.
The survey question asked: "Who forced you off your land or out of your home?" A fifth of those who said they had been forced off their land since 2013, 39 people, blamed opposition soldiers, and another eight percent said it was due to both government and opposition soldiers.
David Deng, a human rights lawyer and land rights researcher who has been working on South Sudan since 2008 and is based in neighbouring Uganda, said before 2016, population displacement could often be attributed to many parties, but that changed after the breakdown of the peace agreement.
"From 2016 to 2017, I think the dynamic shifted and the government very much got the upper hand militarily, which they have retained to this day and, for the most part, they tend to be the ones who are military aggressors."
Logonda is now teaching at an overcrowded makeshift school in a crowded refugee settlement in Uganda.
Students pile onto crooked wooden tables and sit on the floor to study. He doubts many have hopes of graduating. He lives in a mud hut in an open field on a corner of the camp, where his daughter plays with pieces of rubbish she finds in the streets. He can barely afford to feed his family and the teacher, who prides himself on his education, had to pull two of his daughters out of school.
"When South Sudan attained independence, we were happy," he said. "We thought we were going to have everlasting peace. Now after five years' time, the reverse came true. People fled their homes … people were forced into exile."
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